James L. Zehnder, M.D.
Professor of Pathology (Research) and of Medicine (Hematology)
Bio
Dr. Jim Zehnder is board-certified in Internal Medicine and Hematology. He completed Internal Medicine residency, was Chief Resident in Medicine, completed Hematology and Oncology fellowships and a K08 sponsored research postdoctoral fellowship - all at Stanford. He is the founding director of the Stanford Molecular Pathology Laboratory (in 1995). His current roles are Director of Clinical Pathology, Director of the Molecular Pathology Fellowship, Director of the Coagulation Laboratory, attending pathologist on the molecular pathology service and the attending physician on the clinical hematology service. His main research interests include molecular pathogenesis of acquired cytopenias, genetic testing for inherited non-malignant hematologic disorders, next-generation sequencing approaches to T and B cell clonality testing, somatic mutations in cancer and assessment of minimal residual disease in cancer patients. His clinical interests include diagnosis and treatment of disorders of thrombosis and hemostasis.
Clinical Focus
- Cancer > Hematology
- Hematology
- Pathology and Laboratory Medicine
- Anatomic and Clinical Pathology
Academic Appointments
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Professor - University Medical Line, Pathology
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Professor - University Medical Line, Medicine - Hematology
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Member, Bio-X
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Member, Cardiovascular Institute
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Member, Stanford Cancer Institute
Administrative Appointments
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Director, Clinical Pathology, Department of Pathology, Stanford University School of Medicine (2016 - Present)
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Director, Coagulation and Molecular Pathology Laboratories, Stanford Hospital (1995 - Present)
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Attending Physician, Hematology Service, Stanford Hospital (1995 - Present)
Professional Education
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Medical Education: Tufts Medical Center (1984) MA
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Fellowship: Stanford University Hematology and Oncology Fellowship (1993) CA
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Residency: Stanford University Internal Medicine Residency (1988) CA
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Board Certification: American Board of Internal Medicine, Hematology (2016)
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Board Certification, American Board of Internal Medicine, Hematology (2016)
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Board Certification: American Board of Internal Medicine, Internal Medicine (1987)
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MD, Tufts Univ. School of Medicine, Medicine (1984)
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BA, UC Santa Cruz, Chemistry (1979)
Current Research and Scholarly Interests
Dr. James Zehnder is board-certified in Internal Medicine and Hematology. He completed Internal Medicine residency, was Chief Resident in Medicine, completed Hematology and Oncology fellowships and a K08 sponsored research postdoctoral fellowship - all at Stanford. He is the founding director of the Stanford Molecular Pathology Laboratory (in 1995). His current roles are Director of Clinical Pathology, Director of the Molecular Pathology Fellowship, Director of the Coagulation Laboratory, attending pathologist on the molecular pathology service and the attending physician on the clinical hematology service. His main research and clinical interests include molecular pathogenesis of acquired cytopenias, genetic testing for inherited non-malignant hematologic disorders, next-generation sequencing approaches to T and B cell clonality testing, somatic mutations in cancer and assessment of minimal residual disease in cancer patients.
Clinical Trials
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A Longitudinal Study of Plasma EBV DNA in Nasopharyngeal Carcinoma From Both Endemic and Non-Endemic Patient Populations
Not Recruiting
1. To determine the prognostic implication of plasma Epstein-Bar Virus (EBV) DNA concentrations, as measured by quantitative polymerase chain reaction (PCR) in patients with nasopharyngeal carcinoma (NPC). 2. To relate pretreatment plasma EBV DNA concentration to WHO classification of these tumors both in endemic and non-endemic areas. 3. To determine whether pretreatment plasma EBV DNA can serve as a prognostic factor for both endemic and non-endemic patient populations.
Stanford is currently not accepting patients for this trial. For more information, please contact Quynh-Thu Le, 650-498-6184.
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A Study to Test the Safety of the Investigational Drug Selitrectinib in Children and Adults That May Treat Cancer
Not Recruiting
This research study is done to test the safety of the new drug selitrectinib in children and adults with cancer having a change in a particular gene (NTRK1, NTRK2 or NTRK3). The drug may treat cancer by interfering with the effect of the NTRK genes on cancer growth. The study also investigates how the drug is absorbed and processed in the human body, and how well and for how long the cancer responds to the drug. This is the first study to test selitrectinib in humans with cancer, for whom no other effective therapy exists.
Stanford is currently not accepting patients for this trial. For more information, please contact Cancer Clinical Trials Office (CCTO), 650-498-7061.
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Bone Marrow Grafting for Leukemia and Lymphoma
Not Recruiting
The purpose of this study is to obtain tissue samples for ongoing studies regarding transplant outcomes and complications.
Stanford is currently not accepting patients for this trial. For more information, please contact Physician Referrals, 650-723-0822.
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Evaluation of Pathwork Tissue of Origin (TOO) Test for Human Malignancies
Not Recruiting
The pathworks tissue of origin test is a microarray-based test with the goal of identifying the tissue of origin in patients with metastatic tumors of unknown primary site.
Stanford is currently not accepting patients for this trial. For more information, please contact James Zehnder, (650) 723 - 9232.
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Genome-Wide Gene Expression Profiling of Patients With ITP Receiving Thrombopoietin Mimetics
Not Recruiting
Introduction: Ineffective platelet production has been proven to play a role in the etiology of Immune Thrombocytopenia (ITP) in addition to increased platelet destruction. The second-generation thrombopoietin (TPO) mimetics have shown good efficacy in boosting platelet counts in the great majority of patients with chronic ITP in several clinical trials.1, 2 Nevertheless, about 20% of patients with ITP fail to respond to the TPO mimetic treatment. Those treatment-resistant patients are un-characterized and the reasons for the lack of response have not been studied. The identification of predictive blood biomarkers of patients' response to treatment will be useful in reducing both cost and potential side effects; and it will be of equal importance and interest to investigate the molecular mechanisms underlying the patients' heterogeneous responses to TPO mimetic treatment. Specific Aims: 1. To identify blood classifier genes which correlate with patients' response to TPO mimetic treatment. 2. To compare the blood gene expression changes in responders and non-responders after TPO mimetic treatment and explore the possible molecular mechanisms accounting for the non-responsiveness to the treatment.
Stanford is currently not accepting patients for this trial. For more information, please contact James L Zehnder, MD, 650-723-9232.
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Integrated Whole-Genome Analysis of Hematologic Disorders
Not Recruiting
We will use new technologies to look at the DNA, RNA, proteins, and metabolites in the disease-containing blood, bone marrow, or tissue and normal cells from the skin. Our goal is to analyze all of the genes in the diseased and normal skin sample. By comparing the results of the diseased sample and normal skin cells and the results of the two types of genetic information (DNA and RNA), we should be able to identify genetic changes that are important for the initiation, progression, or treatment response of that particular disorder.
Stanford is currently not accepting patients for this trial. For more information, please contact Jason D Merker, 650-922-1885.
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Phase 2 Fludarabine, Cytoxan and FCCAM <Alemtuzumab> in Untreated B-Cell Chronic Lymphocytic Leukemia
Not Recruiting
The primary objective of this study was to evaluate the safety and efficacy of the combination of fludarabine and cyclophosphamide in previously untreated CLL patients. Participants will receive fludarabine and cyclophosphamide on days 1, 2, and 3 of six 28-day cycles.
Stanford is currently not accepting patients for this trial. For more information, please contact Nini Estevez, (650) 725 - 4041.
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Phase 2 Study of Temozolomide to Treat Poor Risk / Refractory Acute Myeloid Leukemia
Not Recruiting
Open-label, non-randomized, parallel assignment, phase 2 trial assessing the safety and efficacy of distinct temozolomide treatment regimens for patients with AML and poor prognosis
Stanford is currently not accepting patients for this trial. For more information, please contact Richa Rajwanshi, (650) 736 - 4031.
2024-25 Courses
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Independent Studies (10)
- Directed Reading in Medicine
MED 299 (Aut, Win, Spr, Sum) - Directed Reading in Pathology
PATH 299 (Aut, Win, Spr, Sum) - Early Clinical Experience in Medicine
MED 280 (Aut, Win, Spr, Sum) - Early Clinical Experience in Pathology
PATH 280 (Aut, Win, Spr, Sum) - Graduate Research
MED 399 (Aut, Win, Spr, Sum) - Graduate Research
PATH 399 (Aut, Win, Spr, Sum) - Medical Scholars Research
MED 370 (Aut, Win, Spr, Sum) - Medical Scholars Research
PATH 370 (Aut, Win, Spr, Sum) - Undergraduate Research
MED 199 (Aut, Win, Spr, Sum) - Undergraduate Research
PATH 199 (Aut, Win, Spr, Sum)
- Directed Reading in Medicine
All Publications
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p53 immunohistochemistry as an ancillary tool for rapid assessment of residual disease in TP53-mutated acute myeloid leukemia and myelodysplastic syndromes.
American journal of clinical pathology
2024
Abstract
Measurable residual disease flow cytometry (MRD-FC) and molecular studies are the most sensitive methods for detecting residual malignant populations after therapy for TP53-mutated acute myeloid leukemia and myelodysplastic neoplasms (TP53+ AML/MDS). However, their sensitivity is limited in suboptimal aspirates or when the immunophenotype of the neoplastic blasts overlaps with erythroids or normal maturing myeloid cells. In this study, we set out to determine if p53 immunohistochemistry (IHC) correlates with MRD-FC and next-generation sequencing (NGS) in the posttherapy setting and to determine the utility of p53 IHC to detect residual disease in the setting of negative or equivocal MRD-FC.We retrospectively identified 28 pre- and posttherapy bone marrow biopsy specimens from 9 patients with TP53+ AML/MDS and a p53 overexpressor phenotype by IHC (strong 3+ staining at initial diagnosis). Next-generation sequencing and/or MRD-FC results were collected for each specimen.Using a threshold of more than ten 2-3+ cells in any one 400× field, p53 IHC detected residual disease with a sensitivity of 94% and a specificity of 89%. The threshold used in this study showed a high degree of concordance among 6 blinded pathologists (Fleiss κ = 0.97).Our study suggests that p53 IHC can be used as a rapid tool (within 24 hours) to aid in the detection of residual disease that may complement MRD-FC or NGS in cases in which the flow cytometry immunophenotype is equivocal and/or the bone marrow aspirate is suboptimal.
View details for DOI 10.1093/ajcp/aqae034
View details for PubMedID 38643353
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Impact of C-reactive Protein on Anticoagulation Monitoring in Extracorporeal Membrane Oxygenation.
Journal of cardiothoracic and vascular anesthesia
2024
Abstract
To evaluate the impact of inflammation on anticoagulation monitoring for patients supported with extracorporeal membrane oxygenation (ECMO).Prospective single-center cohort study.University-affiliated tertiary care academic medical center.Adult venovenous and venoarterial ECMO patients anticoagulated with heparin/ MEASUREMENTS AND MAIN RESULTS: C-Reactive protein (CRP) was used as a surrogate for overall inflammation. The relationship between CRP and the partial thromboplastin time (PTT, seconds) was evaluated using a CRP-insensitive PTT assay (PTT-CRP) in addition to measurement using a routine PTT assay. Data from 30 patients anticoagulated with heparin over 371 ECMO days was included. CRP levels (mg/dL) were significantly elevated (median, 17.2; interquartile range [IQR], 9.2-26.1) and 93% of patients had a CRP of ≥5. The median PTT (median 58.9; IQR, 46.9-73.3) was prolonged by 11.3 seconds compared with simultaneously measured PTT-CRP (median, 47.6; IQR, 40.1-55.5; p < 0.001). The difference between PTT and PTT-CRP generally increased with CRP elevation from 2.7 for a CRP of <5.0 to 13.0 for a CRP between 5 and 10, 17.7 for a CRP between 10 and 15, and 15.1 for a CRP of >15 (p < 0.001). In a subgroup of patients, heparin was transitioned to argatroban, and a similar effect was observed (median PTT, 62.1 seconds [IQR, 53.0-78.5 seconds] vs median PTT-CRP, 47.6 seconds [IQR, 41.3-57.7 seconds]; p < 0.001).Elevations in CRP are common during ECMO and can falsely prolong PTT measured by commonly used assays. The discrepancy due to CRP-interference is important clinically given narrow PTT targets and may contribute to hematological complications.
View details for DOI 10.1053/j.jvca.2024.04.006
View details for PubMedID 38960805
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The highs and lows of cyclic thrombocytopenia.
British journal of haematology
2023
Abstract
Cyclic thrombocytopenia (CTP) is characterized by periodic platelet oscillation with substantial amplitude. Most CTP cases have a thrombocytopenic background and are often misdiagnosed as immune thrombocytopenia with erratically effective treatment choices. CTP also occurs during hydroxyurea treatment in patients with myeloproliferative diseases. While the aetiology of CTP remains uncertain, here we evaluate historical, theoretical and clinical findings to provide a framework for understanding CTP pathophysiology. CTP retains the intrinsic oscillatory factors defined by the homeostatic regulation of platelet count, presenting as reciprocal platelet/thrombopoietin oscillations and stable oscillation periodicity. Moreover, CTP patients possess pathogenic factors destabilizing the platelet homeostatic system thereby creating opportunities for external perturbations to initiate and sustain the exaggerated platelet oscillations. Beyond humoral and cell-mediated autoimmunity, we propose recently uncovered germline and somatic genetic variants, such as those of MPL, STAT3 or DNMT3A, as pathogenic factors in thrombocytopenia-related CTP. Likewise, the JAK2 V617F or BCR::ABL1 translocation that drives underlying myeloproliferative diseases may also play a pathogenic role in hydroxyurea-induced CTP, where hydroxyurea treatment can serve as both a trigger and a pathogenic factor of platelet oscillation. Elucidating the pathogenic landscape of CTP provides an opportunity for targeted therapeutic approaches in the future.
View details for DOI 10.1111/bjh.19239
View details for PubMedID 38083878
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Diagnostic impact of RNA-based next-generation sequencing fusion panel for solid tumors: A single-institution experience.
American journal of clinical pathology
2023
Abstract
Gene rearrangements frequently act as oncogenic driver mutations and determine the onset and progression of cancer. RNA-based next-generation sequencing (NGS) is being used with increasing frequency for solid tumors. The purpose of our study is to investigate the feasibility and utility of an RNA-based NGS fusion panel for solid tumors.We conducted a retrospective, single-institution review of fusion panels requested between May 2022 and March 2023. Demographic, clinical, pathologic, and molecular findings of the patients were reviewed. The utility of the RNA-based NGS fusion panel for the pathologic diagnosis of solid tumors was assessed.Our study included 345 cases, and a fusion event was identified in 24.3% (78/321) of cases. Among the 110 cases submitted for diagnostic purposes, a fusion event was detected in 42.7% (47/110) of cases. The results led to refinement or clarification of the initial diagnosis in 31.9% (15/47) of cases and agreement or support for the initial diagnosis in 59.6% (28/47) of cases. Furthermore, our study indicated that the overall cellularity (tumor and normal tissue) of the tested specimen influences the success of the testing process.In summary, this study demonstrated the feasibility and utility of an RNA-based NGS fusion panel for a wide variety of solid tumors in the appropriate clinicopathologic context. These findings warrant further validation in larger studies involving multiple institutional patient cohorts.
View details for DOI 10.1093/ajcp/aqad148
View details for PubMedID 38001052
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Molecular Diagnosis and Treatment Guidance of <i>EGFR-</i>Positive Metastatic Non-Small-Cell Lung Adenocarcinoma from Pleural Effusion Cell-Free DNA Targeted Sequencing
ELSEVIER SCIENCE INC. 2023: S133
View details for Web of Science ID 001145525900387
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The role of genetics in refractory immune thrombocytopenia.
British journal of haematology
2023; 203 (1): 62-64
Abstract
Patients with refractory immune thrombocytopenia (rITP) have increased morbidity and mortality. Currently, there is limited understanding of the cause of refractoriness and no markers to help direct novel treatment options. Understanding the reason(s) for refractoriness is crucial to determining novel treatment options. The pathogenesis underlying rITP has generally been thought to be an underlying genetic predisposition with an environmental trigger. Familial ITP remains rare, and there are few twin studies, suggesting that a simple genetic cause is unlikely. However, genetic mutations provide the background for several autoimmune diseases. In this review, we explore the evidence of either an inherited genetic cause of rITP or an acquired mutation, in particular one resulting in clonal expansion of cytotoxic T cells.
View details for DOI 10.1111/bjh.19110
View details for PubMedID 37735556
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Study of β1-transferrin and β2-transferrin using microprobe-capture in-emitter elution and high-resolution mass spectrometry.
Scientific reports
2023; 13 (1): 14974
Abstract
Cerebrospinal fluid (CSF) leak can be diagnosed in clinical laboratories by detecting a diagnostic marker β2-transferrin (β2-Tf) in secretion samples. β2-Tf and the typical transferrin (Tf) proteoform in serum, β1-transferrin (β1-Tf), are Tf glycoforms. An innovative affinity capture technique for sample preparation, called microprobe-capture in-emitter elution (MPIE), was incorporated with high-resolution mass spectrometry (HR-MS) to study the Tf glycoforms and the primary structures of β1-Tf and β2-Tf. To implement MPIE, an analyte is first captured on the surface of a microprobe, and subsequently eluted from the microprobe inside an electrospray emitter. The capture process is monitored in real-time via next-generation biolayer interferometry (BLI). When electrospray is established from the emitter to a mass spectrometer, the analyte is immediately ionized via electrospray ionization (ESI) for HR-MS analysis. Serum, CSF, and secretion samples were analyzed using MPIE-ESI-MS. Based on the MPIE-ESI-MS results, the primary structures of β1-Tf and β2-Tf were elucidated. As Tf glycoforms, β1-Tf and β2-Tf share the amino acid sequence but contain varying N-glycans: (1) β1-Tf, the major serum-type Tf, has two G2S2 N-glycans on Asn413 and Asn611; and (2) β2-Tf, the major brain-type Tf, has an M5 N-glycan on Asn413 and a G0FB N-glycan on Asn611. The resolving power of the innovative MPIE-ESI-MS method was demonstrated in the study of β2-Tf as well as β1-Tf. Knowing the N-glycan structures on β2-Tf allows for the design of more novel test methods for β2-Tf in the future.
View details for DOI 10.1038/s41598-023-42064-7
View details for PubMedID 37696850
View details for PubMedCentralID 345148
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HOW LOW IS LOW?-A RETROSPECTIVE CHART REVIEW TO EVALUATE THE CLINICAL RELEVANCE OF FACTOR FXIII DEFICIENCY
WILEY. 2023: 54
View details for Web of Science ID 001183805600073
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THE UTILIZATION OF A CHEMILUMINESCENCE-BASED IMMUNOASSAY [HEMOSIL HIT-AB<sub>( PF4-H)</sub>] IN DIAGNOSIS OF HEPARIN-INDUCED THROMBOCYTOPENIA
WILEY. 2023: 53
View details for Web of Science ID 001183805600072
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Genomic landscape of T-large granular lymphocyte leukemia and chronic lymphoproliferative disorder of NK cells: a single institution experience.
Leukemia & lymphoma
2023: 1-9
Abstract
LGLL is a rare and chronic lymphoproliferative disorder including T-LGLL and CLPD-NK. Here, we investigated the genomic profiles of LGLL with a focus on STAT3 and STAT5B mutations in a cohort of 49 patients (41 T-LGLL, 8 CLPD-NK). Our study indicated that STAT3 was identified in 38.8% (19/49) of all patients, while STAT5B occurred in only 8.2% (4/49) of patients. We found that STAT3 mutations were associated with lower ANC in T-LGLL patients. The average number of pathogenic/likely pathogenic mutations in STAT3/STAT5B-mutated patients was significantly higher than that in WT patients (1.78±1.17 vs 0.65±1.36, p=0.0032). Additionally, TET2-only mutated T-LGLL (n=5) had a significant reduction in platelet values compared with the WT (n=16) or STAT3-only mutated T-LGLL (n=12) (p<0.05). In conclusion, we compared the somatic mutational landscape between STAT3/STAT5B WT and mutated patients and correlate with their distinct clinical characteristics.
View details for DOI 10.1080/10428194.2023.2220450
View details for PubMedID 37330635
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Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens.
Blood advances
2023
Abstract
Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34+ cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin (ENKUR), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker, CDC20. Silencing of ENKUR by shRNA in CD34+ derived megakaryocytes further confirm this association with CDC20 at both RNA and protein levels; and indicate a likely role for the PI3K/Akt pathway. The inverse association of ENKUR and CDC20 expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.
View details for DOI 10.1182/bloodadvances.2022008939
View details for PubMedID 37315179
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Smoking status in acute myeloid leukemia is associated with worse overall survival and independent of prior non-hematopoietic malignancies, cytogenetic abnormalities, and WHO category.
Human pathology
2023
Abstract
Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy with several patient and disease associated variables known to impact prognosis. Tobacco smoking is an environmental factor associated with a greater incidence of AML, but there have been limited studies that evaluated smoking toward overall survival. We retrospectively searched for AML cases and collected clinical and diagnostic data for each case. We also used an independent next-generation sequencing (NGS) dataset to assess for a distinct mutational signature associated with smoking. When stratified by smoking status, there was a greater number of males, patients > 60 years of age, and patients with > 2 comorbidities within the smoking category (P < 0.05). Survival analysis demonstrated decreased survival probability in the smokers, male smokers, smokers with 1 other comorbidity, and smokers without a prior history of non-hematopoietic malignancy (P < 0.05) as compared to non-smokers. Smoking was associated with a decrease in survival within the WHO categories of AML NOS (P = 0.035) and AML RGA (P = 0.002). Multivariate analysis showed that patients who were smokers had a greater HR as compared to non-smokers after adjusting for the other covariates. Our findings demonstrated that smoking was independently associated with decreased overall survival after adjusting for other potentially confounding factors. In addition, our results suggest that a mutational signature can be recognized using NGS data in a subset of AML patients who smoke.
View details for DOI 10.1016/j.humpath.2023.03.005
View details for PubMedID 36921727
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Minimal/measurable residual disease (MRD) monitoring in patients with lymphoid neoplasms by high-throughput sequencing of the T-cell receptor.
The Journal of molecular diagnostics : JMD
2023
Abstract
High-throughput sequencing of the T-cell receptor beta (TRB) and gamma (TRG) loci is increasingly utilized due to its high sensitivity, specificity, and versatility in the diagnosis of various T-cell malignancies. Application of these technologies for tracking disease burden can be valuable in detecting recurrence, determining response to therapy, guiding future management of patients, and establishing endpoints for clinical trials. In this study, the performance of the commercially available LymphoTrack high-throughput sequencing assay was assessed for determining residual disease burden in patients with various T-cell malignancies seen at our institution. A custom bioinformatics pipeline and database was also developed to facilitate MRD analysis and clinical reporting. This assay demonstrated excellent test performance characteristics, achieving a sensitivity of 1 out of 100,000 T-cell equivalents for the DNA inputs evaluated and high concordance with orthogonal testing methods. This assay was further utilized to correlate disease burden in several patients, demonstrating its potential utility for monitoring patients with T-cell malignancies.
View details for DOI 10.1016/j.jmoldx.2023.02.002
View details for PubMedID 36870603
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Genomic Landscape of T-Large Granular Lymphocyte Leukemia and Chronic Lymphoproliferative Disorder of NK Cells: A Single Institution Experience
ELSEVIER SCIENCE INC. 2023: S1131-S1133
View details for Web of Science ID 000990969802252
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The role of CD8+ T cell clones in immune thrombocytopenia.
Blood
2023
Abstract
Immune thrombocytopenia (ITP) is traditionally considered an antibody-mediated disease. However, a number of features suggest alternative mechanisms of platelet destruction. In this study, we use a multi-dimensional approach to explore the role of cytotoxic CD8+ T cells in ITP. We characterised patients with ITP and compared them to age-matched controls using immunophenotyping, next-generation sequencing of T cell receptor (TCR) genes, single-cell RNA sequencing, and functional T cell and platelet assays. We found that adults with chronic ITP have increased polyfunctional, terminally differentiated effector memory CD8+ T cells (CD45RA+CD62L-) expressing intracellular interferon-g, tumour necrosis factor-a, and Granzyme B defining them as TEMRA cells. These TEMRA cells expand when the platelet count falls and show no evidence of physiological exhaustion. Deep sequencing of the T cell receptor showed expanded T cell clones in patients with ITP. T cell clones persisted over many years, were more prominent in patients with refractory disease, and expanded when the platelet count was low. Combined single-cell RNA and TCR sequencing of CD8+ T cells confirmed that the expanded clones are TEMRA cells. Using in vitro model systems, we show that CD8+ T cells from patients with ITP form aggregates with autologous platelets, release interferon-g and trigger platelet activation and apoptosis through TCR-mediated release of cytotoxic granules. These findings of clonally expanded CD8+ T cells causing platelet activation and apoptosis provide an antibody-independent mechanism of platelet destruction, indicating that targeting specific T-cell clones could be a novel therapeutic approach for patients with refractory ITP.
View details for DOI 10.1182/blood.2022018380
View details for PubMedID 36749920
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LIGHT-CHAIN PARAPROTEINS IN COAGULATION ASSAYS AND THEIR CLINICAL ASSOCIATIONS: A REPORT OF 6 CASES
WILEY. 2023: E51-E52
View details for Web of Science ID 000928179600093
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Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens.
bioRxiv : the preprint server for biology
2023
Abstract
Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34 + cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin ( ENKUR ), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker, CDC20 . Silencing of ENKUR by shRNA in CD34 + derived megakaryocytes further confirm this association with CDC20 at both RNA and protein levels; and indicate a likely role for the PI3K/Akt pathway. The inverse association of ENKUR and CDC20 expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.VISUAL ABSTRACT: Key Points: Enkurin, a calcium adaptor protein, is identified as a novel marker of pathogenesis in MPNs.MPN megakaryocyte and platelet expression of enkurin at RNA and protein levels is inversely associated with a cell differentiation cycle gene, CDC20.Likely role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.
View details for DOI 10.1101/2023.01.07.523111
View details for PubMedID 36712071
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IMPACT OF C-REACTIVE PROTEIN ON ANTICOAGULATION MONITORING IN EXTRACORPOREAL MEMBRANE OXYGENATION
LIPPINCOTT WILLIAMS & WILKINS. 2023: 54
View details for Web of Science ID 000921450900108
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3117- ENKURIN: A NOVEL MARKER FOR MYELOPROLIFERATIVE NEOPLASMS FROM VALIDATED PLATELET, MEGAKARYOCYTE, AND WHOLE BLOOD SPECIMENS (vol 111, pg S103, 2022)
EXPERIMENTAL HEMATOLOGY
2023; 117: 69
View details for DOI 10.1016/j.exphem.2022.10.006
View details for Web of Science ID 000921127900001
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Balancing the Qi in ITP.
Blood
2022; 140 (26): 2768-2770
View details for DOI 10.1182/blood.2022018373
View details for PubMedID 36580341
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Prevalence, mutational spectrum and clinical implications of clonal hematopoiesis of indeterminate potential in plasma cell dyscrasias.
Seminars in oncology
2022
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is common both in healthy individuals and patients with hematological cancers. Recent studies have showed worse prognosis for patients with multiple myeloma (MM) and non-Hodgkin lymphoma undergoing stem cell transplant, that have concomitant presence of CHIP. Data regarding the clinical and biological role of CHIP in plasma cell dyscrasias (PCDs) is rapidly increasing. However, the prevalence and prognostic implication of CHIP in patients with MM outside of the transplant setting, and in those with other more indolent PCDs remains elusive. Here we explored the prevalence and clinical implications of CHIP detected through next-generation sequencing in 209 patients with PCDs including MM, light chain (AL) amyloidosis (ALA), monoclonal gammopathy of undetermined significance (MGUS), and smoldering multiple myeloma (SMM). To avoid attributing the mutations to the plasma cell clone, CHIP was defined as the presence of DNMT3A, TET2, or ASXL1 mutations in the peripheral blood or bone marrow (DTA-CH). The prevalence of DTA-CH was 19% in patients with PCDs, with no difference between each PCD. TET2 (23%) and DNMT3A (22%), were the most frequently mutated genes. DTA-CH correlated with older age in MM (P = .001) and MGUS/SMM (P = 0.0007), as well as with coronary artery disease or congestive heart failure in MM (P = .03). DTA-CH did not predict worse OS or PFS in either MM or ALA, nor it predict higher risk of progression to MM in patients with MGUS/SMM. Our results overall further elucidate the prevalence and mutational spectrum of CHIP in PCDs, providing more information regarding the clinical relevance of CHIP in this patient population.
View details for DOI 10.1053/j.seminoncol.2022.11.001
View details for PubMedID 36503855
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Accurate Identification of Hemoglobin Variants By Top-Down Protein Analysis Using Capillary Electrophoresis-HighResolution Mass Spectrometry
AMER SOC HEMATOLOGY. 2022: 5384-5386
View details for DOI 10.1182/blood-2022-170457
View details for Web of Science ID 000893223205184
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Accurate Detection of Clinically Actionable Copy Number Variants in Diverse Hematological Neoplasms By Routine Targeted Sequencing: A Comparative Performance Study
AMER SOC HEMATOLOGY. 2022: 10712-10713
View details for DOI 10.1182/blood-2022-167900
View details for Web of Science ID 000893230303319
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CD8(+) TEMRA Clones Cause Platelet Lysis in Immune Thrombocytopenia
AMER SOC HEMATOLOGY. 2022: 2209-2210
View details for DOI 10.1182/blood-2022-166348
View details for Web of Science ID 000893223202090
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Neutral-Coating Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Top-Down Identification of Hemoglobin Variants.
Clinical chemistry
2022
Abstract
BACKGROUND: Identification of hemoglobin (Hb) variants is of significant value in the clinical diagnosis of hemoglobinopathy. However, conventional methods for identification of Hb variants in clinical laboratories can be inadequate due to the lack of structural characterization. We describe the use of neutral-coating capillary electrophoresis coupled with high-resolution mass spectrometry (CE-HR-MS) to achieve high-performance top-down identification of Hb variants.METHODS: An Orbitrap Q-Exactive Plus mass spectrometer was coupled with an ECE-001 capillary electrophoresis (Ce) unit through an EMASS-II ion source. A PS1 neutral-coating capillary was used for CE. Samples of red blood cells were lysed in water and diluted in 10 mM ammonium formate buffer for analysis. Deconvolution of raw mass spectrometry data was carried out to merge multiple charge states and isotopic peaks of an analyte to obtain its monoisotopic mass.RESULTS: The neutral-coating CE could baseline separate individual Hb subunits dissociated from intact Hb forms, and the HR-MS could achieve both intact-protein analysis and top-down analysis of analytes. A number of patient samples that contain Hb subunit variants were analyzed, and the variants were successfully identified using the CE-HR-MS method.CONCLUSIONS: The CE-HR-MS method has been demonstrated as a useful tool for top-down identification of Hb variants. With the ability to characterize the primary structures of Hb subunits, the CE-HR-MS method has significant advantages to complement or partially replace the conventional methods for the identification of Hb variants.
View details for DOI 10.1093/clinchem/hvac171
View details for PubMedID 36308334
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Rapid Detection of Pathogenic UBA1 Variants by MassARRAY in Patients with VEXAS Syndrome
ELSEVIER SCIENCE INC. 2022: S35
View details for Web of Science ID 000891281600100
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Multiplex Epstein-Barr virus BALF2 genotyping detects high-risk variants in plasma for population screening of nasopharyngeal carcinoma.
Molecular cancer
2022; 21 (1): 154
Abstract
Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) exhibits unusual geographic restriction despite ubiquitous lifelong infection. Screening programs can detect most NPC cases at an early stage, but existing EBV diagnostics are limited by false positives and low positive predictive value (PPV), leading to excess screening endoscopies, MRIs, and repeated testing. Recent EBV genome-wide association studies (GWAS) suggest that EBV BALF2 variants account for more than 80% of attributable NPC risk. We therefore hypothesized that high-risk BALF2 variants could be readily detected in plasma for once-lifetime screening triage.We designed and validated a multiplex genotyping assay to detect EBV BALF2 polymorphisms in human plasma. Targeted next-generation sequencing was used to validate this assay, conduct association studies with clinical phenotype, and longitudinally genotype plasma to assess within-host haplotype stability. We examined the association between NPC and BALF2 haplotypes in a large non-endemic population and three prior EBV GWAS. Finally, we estimated NPC mortality reduction, resource utilization, and cost-effectiveness of BALF2 variant-informed screening using a previously-validated cohort model.Following analytical validation, the BALF2 genotyping assay had 99.3% concordance with sequencing in a cohort of 24 NPC cases and 155 non-NPC controls. BALF2 haplotype was highly associated with NPC in this non-endemic population (I613V: odds ratio [OR] 7.9; V317M: OR 178.8). No other candidate BALF2 polymorphisms were significantly associated with NPC or hematologic disorders. Longitudinal genotyping revealed 97.8% within-host haplotype concordance, indicative of lifelong latent infection. In a meta-analysis of 755 NPC cases and 981 non-NPC controls, BALF2 I613V and V317M were significantly associated with NPC in both endemic and non-endemic populations. Modeled variant-informed screening strategies achieved a 46% relative increase in PPV with 7% decrease in effective screening sensitivity, thereby averting nearly half of screening endoscopies/MRIs among endemic populations in east/southeast Asia.EBV BALF2 haplotypes are temporally stable within hosts and can be readily detected in plasma via an inexpensive multiplex genotyping assay that offers near-perfect sequencing concordance. In endemic and non-endemic populations, I613V and V317M were highly associated with NPC and could be leveraged to develop variant-informed screening programs that mitigate false positives with small reductions in screening sensitivity.
View details for DOI 10.1186/s12943-022-01625-6
View details for PubMedID 35902864
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SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19.
Journal of neuropathology and experimental neurology
2022
Abstract
Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. RT-PCR screening of 16 regions from 20 COVID-19 autopsies found SARS-CoV-2 E gene viral sequences in 7 regions (2.5% of 320 samples), concentrated in 4/20 subjects (20%). Additional screening of olfactory bulb (OB), amygdala (AMY) and entorhinal area for E, N1, N2, RNA-dependent RNA polymerase, and S gene sequences detected one or more of these in OB in 8/21 subjects (38%). It is uncertain whether these RNA sequences represent viable virus. Significant histopathology was limited to 2/42 cases (4.8%), one with a large acute cerebral infarct and one with hemorrhagic encephalitis. Case-control RNAseq in OB and AMY found more than 5000 and 700 differentially expressed genes, respectively, unrelated to RT-PCR results; these involved immune response, neuronal constituents, and olfactory/taste receptor genes. Olfactory marker protein-1 reduction indicated COVID-19-related loss of OB olfactory mucosa afferents. Iba-1-immunoreactive microglia had reduced area fractions in cerebellar cortex and AMY, and cytokine arrays showed generalized downregulation in AMY and upregulation in blood serum in COVID-19 cases. Although OB is a major brain portal for SARS-CoV-2, COVID-19 brain changes are more likely due to blood-borne immune mediators and trans-synaptic gene expression changes arising from OB deafferentation.
View details for DOI 10.1093/jnen/nlac056
View details for PubMedID 35818336
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Management of antiplatelet therapy in patients with coronary stents undergoing noncardiac surgery.
The American journal of medicine
2022
View details for DOI 10.1016/j.amjmed.2022.05.014
View details for PubMedID 35636479
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Dysregulation of Brain inflammation in COVID-19: An autopsy series
OXFORD UNIV PRESS INC. 2022: 476
View details for Web of Science ID 000798368400137
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Acute Infarction, Hemorrhage and White Matter Beta-Amyloid Precursor Protein Immunostaining in COVID-19 and Control Subjects
OXFORD UNIV PRESS INC. 2022: 476
View details for Web of Science ID 000798368400135
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Diagnostic Impact of Next-Generation Sequencing Panels for Lymphoproliferative Neoplasms on Small-Volume Biopsies.
American journal of clinical pathology
2022
Abstract
We investigated the feasibility and utility of next-generation sequencing (NGS)-based targeted somatic mutation panels and IG/TR gene rearrangement assays in the diagnosis of lymphoproliferative disorders (LPDs) in small-volume biopsies.We performed a retrospective, single-institution review of all NGS assays requested over a 3-year period by hematopathologists for diagnostic purposes on small-volume biopsies.We identified 59 small-volume biopsies. The TR assay was most commonly requested (42 [71%]), followed by the somatic mutation panel (32 [54%]) and IG assay (26 [44%]). NGS studies were associated with a change in the diagnostic line in about half of cases (28 [47%]) and in a change in the likelihood of a diagnosis in a further 16 cases (27%); there was no diagnostic impact of NGS testing in 15 cases (25%).Implementation of NGS panel somatic mutation or IG/TR gene rearrangement assays on small-volume biopsies contributes to the diagnosis of LPDs in the majority of select cases for diagnostic purposes. The molecular diagnosis is considered in the context of the clinical, histologic, and immunophenotypic findings and does not by itself lead to a definitive diagnosis in small-volume biopsies.
View details for DOI 10.1093/ajcp/aqac045
View details for PubMedID 35552630
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Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification.
Journal of clinical microbiology
2022: e0017822
Abstract
The ability to distinguish between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of ongoing interest due to differences in transmissibility, responses to vaccination, clinical prognosis, and therapy. Although detailed genetic characterization requires whole-genome sequencing (WGS), targeted nucleic acid amplification tests can serve a complementary role in clinical settings, as they are more rapid and accessible than sequencing in most laboratories. We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2. This assay had 95 to 100% agreement with WGS for 502 upper respiratory tract swab samples collected between 26 April 2021 and 1 August 2021, consisting of 43 Alpha, 2 Beta, 20 Gamma, 378 Delta, and 59 non-VOC infections. Validation in a separate group of 230 WGS-confirmed Omicron variant samples collected in December 2021 and January 2022 demonstrated 100% agreement. This RT-qPCR-based approach can be implemented in clinical laboratories already performing SARS-CoV-2 nucleic acid amplification tests to assist in local epidemiological surveillance and clinical decision-making.
View details for DOI 10.1128/jcm.00178-22
View details for PubMedID 35465708
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Longitudinal study of 2 patients with cyclic thrombocytopenia, STAT3, and MPL mutations.
Blood advances
2022
Abstract
Cyclic thrombocytopenia (CTP) is a rare disease of periodic platelet count oscillations. The pathogenesis of CTP remains elusive. To study the underlying pathophysiology and genetic and cellular associations with CTP, we applied systems biology approaches to two patients with stable platelet cycling and reciprocal thrombopoietin (TPO) cycling at multiple time points through 2 cycles. Blood transcriptome analysis revealed cycling of platelet-specific genes, which are in parallel with and precede platelet count oscillation, indicating that cyclical platelet production leads platelet count cycling in both patients. Additionally, neutrophil and erythrocyte-specific genes also showed fluctuations correlating with platelet count changes, consistent with TPO effects on hematopoietic progenitors. Moreover, we found novel genetic associations with CTP. One patient had a novel germline heterozygous loss-of-function (LOF) thrombopoietin receptor (MPL) c.1210G>A mutation, and both had pathogenic somatic gain-of-function (GOF) variants in signal transducer and activator of transcription 3 (STAT3). In addition, both patients had clonal T-cell populations that remained stable throughout platelet count cycles. These mutations and clonal T cells may potentially involve in the pathogenic baseline in these patients rendering exaggerated persistent thrombopoiesis oscillations of their intrinsic rhythm upon homeostatic perturbations. This work provides new insights into the pathophysiology of CTP and possible therapies.
View details for DOI 10.1182/bloodadvances.2021006701
View details for PubMedID 35381066
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Smoking Status in Acute Myeloid Leukemia is Associated with Worse Overall Survival, Prior Non-Hematopoietic Malignancies, Cytogenetic Abnormalities, and WHO Category
SPRINGERNATURE. 2022: 970-972
View details for Web of Science ID 000770360202240
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Smoking Status in Acute Myeloid Leukemia is Associated with Worse Overall Survival, Prior Non-Hematopoietic Malignancies, Cytogenetic Abnormalities, and WHO Category
SPRINGERNATURE. 2022: 970-972
View details for Web of Science ID 000770361802240
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Diagnostic Impact of Next Generation Sequencing Panels for Lymphoproliferative Neoplasms on Small Volume Biopsies
SPRINGERNATURE. 2022: 948-949
View details for Web of Science ID 000770361802222
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Diagnostic Impact of Next Generation Sequencing Panels for Lymphoproliferative Neoplasms on Small Volume Biopsies
SPRINGERNATURE. 2022: 948-949
View details for Web of Science ID 000770360202222
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Potential pitfalls in multiplex PCR-based next-generation sequencing: a case-based report.
Journal of clinical pathology
2022
Abstract
Amplicon-based next-generation sequencing (NGS) assays employ highly sensitive, rapid, and cost-effective methods to detect clinically actionable mutations for the diagnosis, prognosis, and treatment of patients with cancer. However, recognition of certain limitations inherent to amplicon-based NGS assays is crucial for the correct interpretation and reporting of variants in the clinical setting. In this report, we illustrate three different potential pitfalls related to amplicon-based NGS assays based on our institutional experience and highlight how the risk of such events can be minimised.
View details for DOI 10.1136/jclinpath-2021-208105
View details for PubMedID 35145018
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ENKURIN: A NOVEL MARKER FOR MYELOPROLIFERATIVE NEOPLASMS FROM VALIDATED PLATELET, MEGAKARYOCYTE, AND WHOLE BLOOD SPECIMENS
ELSEVIER SCIENCE INC. 2022: S103
View details for Web of Science ID 000890643400166
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A Multiplex SNaPshot Assay is a Rapid and Cost-Effective Method for Detecting POLE Exonuclease Domain Mutations in Endometrial Carcinoma.
International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists
1800
Abstract
Determining the replicative DNA polymerase epsilon (POLE) mutation status in endometrial carcinomas (ECs) has important clinical implications given that the majority of "ultramutated" tumors harboring pathogenic exonuclease domain mutations in POLE (POLEmut) have a favorable prognosis, even among high-grade histotypes. Currently, there are no specific morphologic or immunophenotypic features that allow accurate detection of POLEmut tumors without molecular testing. Consequently, identifying POLEmut tumors has been challenging without employing costly and/or time-consuming DNA sequencing approaches. Here we developed a novel SNaPshot assay to facilitate routine and efficient POLE mutation testing in EC. The SNaPshot assay interrogates 15 nucleotide sites within exons 9, 11, 13, and 14 encoding the POLE exonuclease domain. The variant sites were selected based on recurrence, evidence of functional impact, association with high tumor mutation burden and/or detection in EC clinical outcome studies. Based on the pathogenic somatic variants reported in the literature, the assay is predicted to have a clinical sensitivity of 90% to 95% for ECs. Validation studies showed 100% specificity and sensitivity for the variants covered, with expected genotypic results for both the positive (n=11) and negative (n=20) patient controls on multiple repeat tests and dilution series. Analytic sensitivity was conservatively approximated at a 10% variant allele fraction (VAF), with documented detection as low as 5% VAF. As expected, the SNaPshot assay demonstrated greater sensitivity than Sanger sequencing for VAFs below 20%, an important characteristic for somatic mutation detection. Here we have developed and validated the first SNaPshot assay to detect hotspot POLE mutations. While next-generation sequencing and Sanger sequencing-based approaches have also been used to detect POLE mutations, a SNaPshot approach provides useful balance of analytical sensitivity, cost-effectiveness, and efficiency in a high-volume case load setting.
View details for DOI 10.1097/PGP.0000000000000841
View details for PubMedID 34907997
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MDS and MDS/MPN Genomic Subgroups Demonstrate Differential E x Vivo Drug Sensitivity
AMER SOC HEMATOLOGY. 2021
View details for DOI 10.1182/blood-2021-152103
View details for Web of Science ID 000835740102120
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Incidence and risk factors associated with bleeding and thrombosis following chimeric antigen receptor T-cell therapy
BLOOD ADVANCES
2021; 5 (21): 4465-4475
View details for DOI 10.1182/bloodadvances.2021004716.
View details for Web of Science ID 000718993700016
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Platelet transcriptome identifies progressive markers and potential therapeutic targets in chronic myeloproliferative neoplasms
CELL REPORTS MEDICINE
2021; 2 (10)
View details for DOI 10.1016/j.xcrm.2021.100425
View details for Web of Science ID 000709912800003
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Platelet transcriptome identifies progressive markers and potential therapeutic targets in chronic myeloproliferative neoplasms.
Cell reports. Medicine
2021; 2 (10): 100425
Abstract
Predicting disease progression remains a particularly challenging endeavor in chronic degenerative disorders and cancer, thus limiting early detection, risk stratification, and preventive interventions. Here, profiling the three chronic subtypes of myeloproliferative neoplasms (MPNs), we identify the blood platelet transcriptome as a proxy strategy for highly sensitive progression biomarkers that also enables prediction of advanced disease via machine-learning algorithms. The MPN platelet transcriptome reveals an incremental molecular reprogramming that is independent of patient driver mutation status or therapy. Subtype-specific markers offer mechanistic and therapeutic insights, and highlight impaired proteostasis and a persistent integrated stress response. Using a LASSO model with validation in two independent cohorts, we identify the advanced subtype MF at high accuracy and offer a robust progression signature toward clinical translation. Our platelet transcriptome snapshot of chronic MPNs demonstrates a proof-of-principle for disease risk stratification and progression beyond genetic data alone, with potential utility in other progressive disorders.
View details for DOI 10.1016/j.xcrm.2021.100425
View details for PubMedID 34755136
View details for PubMedCentralID PMC8561315
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SARS-CoV-2 Nucleocapsid Plasma Antigen for Diagnosis and Monitoring of COVID-19.
Clinical chemistry
2021
Abstract
BACKGROUND: Detection of SARS-CoV-2 nucleocapsid antigen in blood has been described, but the diagnostic and prognostic role of antigenemia is not well understood. This study aimed to determine the frequency, duration, and concentration of nucleocapsid antigen in plasma and its association with COVID-19 severity.METHODS: We utilized an ultrasensitive electrochemiluminescence immunoassay targeting SARS-CoV-2 nucleocapsid antigen to evaluate 777 plasma samples from 104 individuals with COVID-19. We compared plasma antigen to respiratory nucleic acid amplification testing (NAAT) in 74 individuals with COVID-19 from samples collected ± 1day of diagnostic respiratory NAAT, and in 52 SARS-CoV-2-negative individuals. We used Kruskal-Wallis tests, multivariable logistic regression, and mixed-effects modeling to evaluate whether plasma antigen concentration was associated with disease severity.RESULTS: Plasma antigen had 91.9% (95% CI 83.2-97.0%) clinical sensitivity and 94.2% (84.1-98.8%) clinical specificity. Antigen-negative plasma samples belonged to patients with later respiratory cycle thresholds (Ct) when compared with antigen-positive plasma samples. Median plasma antigen concentration (log10 fg/mL) was 5.4 (IQR 3.9-6.0) in outpatients, 6.0 (5.4-6.5) in inpatients, and 6.6 (6.1-7.2) in intensive care unit (ICU) patients. In models adjusted for age, sex, diabetes, and hypertension, plasma antigen concentration at diagnosis was associated with ICU admission (OR 2.8 [95% CI 1.2-6.2], P=.01), but not with non-ICU hospitalization. Rate of antigen decrease was not associated with disease severity.CONCLUSIONS: SARS-CoV-2 plasma nucleocapsid antigen exhibited comparable diagnostic performance to upper respiratory NAAT, especially among those with late respiratory Ct. In addition to currently available tools, antigenemia may facilitate patient triage to optimize intensive care utilization.
View details for DOI 10.1093/clinchem/hvab216
View details for PubMedID 34605900
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PLATELET TRANSCRIPTOME YIELDS PROGRESSIVE MARKERS IN CHRONIC MYELOPROLIFERATIVE NEOPLASMS AND IDENTIFIES PUTATIVE TARGETS OF THERAPY
ELSEVIER SCIENCE INC. 2021: S82
View details for Web of Science ID 000985360500124
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Mapping of SARS-CoV-2 Brain Invasion in COVID-19 Disease
OXFORD UNIV PRESS INC. 2021: 585
View details for Web of Science ID 000671021700115
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Brain Histopathology in Subjects with COVID-19 Disease
OXFORD UNIV PRESS INC. 2021: 585
View details for Web of Science ID 000671021700114
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Multiplex SARS-CoV-2 Genotyping RT-PCR for Population-Level Variant Screening and Epidemiologic Surveillance.
Journal of clinical microbiology
2021: JCM0085921
Abstract
Emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a nucleic acid amplification test (NAAT) to genotype mutations in the viral spike protein could facilitate high-throughput variant surveillance. We designed and analytically validated a one-step multiplex allele-specific reverse transcriptase polymerase chain reaction (RT-qPCR) to detect three non-synonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2 positive specimens from our San Francisco Bay Area population. Between December 1, 2020 and March 1, 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K+N501Y mutations. The assay had perfect (100%) concordance with whole-genome sequencing in a validation subset of 229 specimens, and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed rapid emergence of L452R in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021. We developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.
View details for DOI 10.1128/JCM.00859-21
View details for PubMedID 34037430
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Identification of a SARS-CoV-2 Variant with L452R and E484Q Neutralization Resistance Mutations.
Journal of clinical microbiology
2021
Abstract
The emergence of SARS-CoV-2 variants t 23 hat reduce antibody neutralization and vaccine efficacy is of significant global concern..
View details for DOI 10.1128/JCM.00741-21
View details for PubMedID 33952596
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Ultra-sensitive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antigen Detection for the Diagnosis of Coronavirus Disease 2019 (COVID-19) in Upper Respiratory Samples.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
2021
Abstract
An ultra-sensitive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen assay (S-PLEX, MesoScale Diagnostics) was evaluated in 250 retrospective and 200 prospective upper respiratory specimens. In samples with cycle threshold <35, there was 95%-98% positive and 93%-96% negative percent agreement with reverse transcription-polymerase chain reaction. S-PLEX may provide a high-throughput alternative to nucleic acid-based testing for coronavirus disease 2019 (COVID-19) diagnosis.
View details for DOI 10.1093/cid/ciab063
View details for PubMedID 33830203
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Mapping of SARS-CoV-2 Brain Invasion and Histopathology in COVID-19 Disease.
medRxiv : the preprint server for health sciences
2021
Abstract
The coronavirus SARS-CoV-2 (SCV2) causes acute respiratory distress, termed COVID-19 disease, with substantial morbidity and mortality. As SCV2 is related to previously-studied coronaviruses that have been shown to have the capability for brain invasion, it seems likely that SCV2 may be able to do so as well. To date, although there have been many clinical and autopsy-based reports that describe a broad range of SCV2-associated neurological conditions, it is unclear what fraction of these have been due to direct CNS invasion versus indirect effects caused by systemic reactions to critical illness. Still critically lacking is a comprehensive tissue-based survey of the CNS presence and specific neuropathology of SCV2 in humans. We conducted an extensive neuroanatomical survey of RT-PCR-detected SCV2 in 16 brain regions from 20 subjects who died of COVID-19 disease. Targeted areas were those with cranial nerve nuclei, including the olfactory bulb, medullary dorsal motor nucleus of the vagus nerve and the pontine trigeminal nerve nuclei, as well as areas possibly exposed to hematogenous entry, including the choroid plexus, leptomeninges, median eminence of the hypothalamus and area postrema of the medulla. Subjects ranged in age from 38 to 97 (mean 77) with 9 females and 11 males. Most subjects had typical age-related neuropathological findings. Two subjects had severe neuropathology, one with a large acute cerebral infarction and one with hemorrhagic encephalitis, that was unequivocally related to their COVID-19 disease while most of the 18 other subjects had non-specific histopathology including focal β-amyloid precursor protein white matter immunoreactivity and sparse perivascular mononuclear cell cuffing. Four subjects (20%) had SCV2 RNA in one or more brain regions including the olfactory bulb, amygdala, entorhinal area, temporal and frontal neocortex, dorsal medulla and leptomeninges. The subject with encephalitis was SCV2-positive in a histopathologically-affected area, the entorhinal cortex, while the subject with the large acute cerebral infarct was SCV2-negative in all brain regions. Like other human coronaviruses, SCV2 can inflict acute neuropathology in susceptible patients. Much remains to be understood, including what viral and host factors influence SCV2 brain invasion and whether it is cleared from the brain subsequent to the acute illness.
View details for DOI 10.1101/2021.02.15.21251511
View details for PubMedID 33619496
View details for PubMedCentralID PMC7899461
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DOAC-Stop in lupus anticoagulant testing: Direct oral anticoagulant interference removed in most samples.
Research and practice in thrombosis and haemostasis
2021; 5 (2): 314-325
Abstract
The use of direct oral anticoagulants (DOACs) is a convenient therapeutic option for patients at risk of thrombosis. DOACs interfere with clot-based testing for the identification of lupus anticoagulant antibodies (LACs) in patients with antiphospholipid syndrome (APS), a common cause of acquired thrombotic disease.To evaluate a commercially available reagent DOAC-Stop for the removal of DOAC interference encountered in LAC testing.We collected a cohort of 73 test samples from patients on DOAC therapy identified at a large institutional coagulation laboratory from March to December 2019, along with samples from 40 LAC positive and negative control patients not on therapy. Samples were treated with DOAC-Stop and tested for anti-Xa activity and thrombin time for the removal of apixaban, rivaroxaban, argatroban, and dabigatran activity from patient samples. Treated and untreated samples were tested using the activated partial thromboplastin time, silica clotting time, and dilute Russell's viper venom time to evaluate the reliability and utility of DOAC-Stop.DOAC-Stop markedly reduced DOAC interference from test samples (P < .05). DOAC-Stop had no effect on LAC testing in the absence of DOAC therapy, permitting the identification of all LAC positive and negative controls. DOAC-Stop removed false positives and false negatives resulting from DOAC interference and allows the identification of patients meeting criteria for the diagnosis of APS by LAC testing, as well as the detection of patients on rivaroxaban who are triple positive for APS.DOAC-Stop is an effective adjunct for the clinical laboratory faced with DOAC interference in LAC testing.
View details for DOI 10.1002/rth2.12472
View details for PubMedID 33733031
View details for PubMedCentralID PMC7938630
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Strand Specific Reverse Transcription PCR for Detection of Replicating SARS-CoV-2
EMERGING INFECTIOUS DISEASES
2021; 27 (2): 632–35
Abstract
We developed an assay that detects minus-strand RNA as a surrogate for actively replicating severe acute respiratory syndrome coronavirus 2. We detected minus-strand RNA in 41 persons with coronavirus disease up to 30 days after symptom onset. This assay might inform clinical decision-making about patient infectiousness.
View details for DOI 10.3201/eid2702.204168
View details for Web of Science ID 000631538500043
View details for PubMedID 33496233
View details for PubMedCentralID PMC7853532
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DOAC-Stop in lupus anticoagulant testing: Direct oral anticoagulant interference removed in most samples
RESEARCH AND PRACTICE IN THROMBOSIS AND HAEMOSTASIS
2021
View details for DOI 10.1002/rth2.12472
View details for Web of Science ID 000612110200001
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Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
2021; 72 (2): 323-326
Abstract
Using data for 20 912 patients from 2 large academic health systems, we analyzed the frequency of severe acute respiratory syndrome coronavirus 2 reverse-transcription polymerase chain reaction test discordance among individuals initially testing negative by nasopharyngeal swab who were retested on clinical grounds within 7 days. The frequency of subsequent positivity within this window was 3.5% and was similar across institutions.
View details for DOI 10.1093/cid/ciaa722
View details for PubMedID 33501957
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Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
2021; 72 (2): 323-326
Abstract
Using data for 20 912 patients from 2 large academic health systems, we analyzed the frequency of severe acute respiratory syndrome coronavirus 2 reverse-transcription polymerase chain reaction test discordance among individuals initially testing negative by nasopharyngeal swab who were retested on clinical grounds within 7 days. The frequency of subsequent positivity within this window was 3.5% and was similar across institutions.
View details for DOI 10.1093/cid/ciaa722
View details for PubMedID 33501950
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Case-Control Study of Individuals with Discrepant Nucleocapsid and Spike Protein SARS-CoV-2 IgG Results.
Clinical chemistry
2021
Abstract
Laboratory-based methods for SARS-CoV-2 antibody detection vary widely in performance. However, there are limited prospectively-collected data on assay performance, and minimal clinical information to guide interpretation of discrepant results.Over a two-week period, 1080 consecutive plasma samples submitted for clinical SARS-CoV-2 IgG testing were tested in parallel for anti-nucleocapsid IgG (anti-N, Abbott) and anti-spike IgG (anti-S1, EUROIMMUN). Chart review was conducted for samples testing positive or borderline on either assay, and for an age/sex-matched cohort of samples negative by both assays. CDC surveillance case definitions were used to determine clinical sensitivity/specificity and conduct receiver operating characteristics curve analysis.There were 52 samples positive by both methods, 2 positive for anti-N only, 34 positive for anti-S1 only, and 27 borderline for anti-S1. Of the 34 individuals positive for anti-S1 alone, 8 (24%) had confirmed COVID-19. No anti-S1 borderline cases were positive for anti-N or had confirmed/probable COVID-19. The anti-N assay was less sensitive (84.2% [95% CI 72.1-92.5%] versus 94.7% [95% CI 85.4-98.9%]) but more specific (99.2% [95% CI 95.5-100%] versus 86.9% [95% CI 79.6-92.3%]) than anti-S1. Abbott anti-N sensitivity could be improved to 96.5% with minimal effect on specificity if the index threshold was lowered from 1.4 to 0.6.Real-world concordance between different serologic assays may be lower than previously described in retrospective studies. These findings have implications for the interpretation of SARS-CoV-2 IgG results, especially with the advent of spike antigen-targeted vaccination, as a subset of patients with true infection are anti-N negative and anti-S1 positive.
View details for DOI 10.1093/clinchem/hvab045
View details for PubMedID 33720347
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Accurate detection and quantification of FLT3 internal tandem duplications in clinical hybrid capture next-generation sequencing data.
The Journal of molecular diagnostics : JMD
2021
Abstract
FLT3 internal tandem duplications (ITDs) are found in approximately one third of patients with acute myeloid leukemia (AML) and have important prognostic and therapeutic implications that have supported its assessment in routine clinical practice. Conventional methods for assessing FLT3-ITD status and allele burden have been primarily limited to PCR fragment size analysis due to the inherent difficulty in detecting large ITD variants by next-generation sequencing (NGS). In this study, we assess the performance of publicly available bioinformatic tools for the detection and quantification of FLT3-ITDs in clinical hybridization-capture NGS data. We found that FLT3_ITD_ext had the highest overall accuracy for detecting FLT3-ITDs and was able to accurately quantify allele burden. Although all other tools evaluated were able to detect FLT3-ITDs reasonably well, allele burden was consistently underestimated. We were able to significantly improve quantification of FLT3-ITD allelic burden independent of the detection method by utilizing soft-clipped reads and/or ITD junctional sequences. In addition, we show that identifying mutant reads by previously identified junctional sequences further improves the sensitivity of detecting FLT3-ITDs in post-treatment samples. Our results demonstrate that FLT3-ITDs can be reliably detected in clinical NGS data using available bioinformatic tools. We further describe how accurate quantification of FLT3-ITD allele burden can be added on to existing clinical NGS pipelines for routine assessment of FLT3-ITD status in patients with AML.
View details for DOI 10.1016/j.jmoldx.2021.07.012
View details for PubMedID 34363960
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Use of Outpatient-Derived COVID-19 Convalescent Plasma in COVID-19 Patients Before Seroconversion.
Frontiers in immunology
2021; 12: 739037
Abstract
Background: Transfusion of COVID-19 convalescent plasma (CCP) containing high titers of anti-SARS-CoV-2 antibodies serves as therapy for COVID-19 patients. Transfusions early during disease course was found to be beneficial. Lessons from the SARS-CoV-2 pandemic could inform early responses to future pandemics and may continue to be relevant in lower resource settings. We sought to identify factors correlating to high antibody titers in convalescent plasma donors and understand the magnitude and pharmacokinetic time course of both transfused antibody titers and the endogenous antibody titers in transfused recipients.Methods: Plasma samples were collected up to 174 days after convalescence from 93 CCP donors with mild disease, and from 16 COVID-19 patients before and after transfusion. Using ELISA, anti-SARS-CoV-2 Spike RBD, S1, and N-protein antibodies, as well as capacity of antibodies to block ACE2 from binding to RBD was measured in an in vitro assay. As an estimate for viral load, viral RNA and N-protein plasma levels were assessed in COVID-19 patients.Results: Anti-SARS-CoV-2 antibody levels and RBD-ACE2 blocking capacity were highest within the first 60 days after symptom resolution and markedly decreased after 120 days. Highest antibody titers were found in CCP donors that experienced fever. Effect of transfused CCP was detectable in COVID-19 patients who received high-titer CCP and had not seroconverted at the time of transfusion. Decrease in viral RNA was seen in two of these patients.Conclusion: Our results suggest that high titer CCP should be collected within 60 days after recovery from donors with past fever. The much lower titers conferred by transfused antibodies compared to endogenous production in the patient underscore the importance of providing CCP prior to endogenous seroconversion.
View details for DOI 10.3389/fimmu.2021.739037
View details for PubMedID 34594341
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Next generation sequencing confirms T-cell clonality in a subset of pediatric pityriasis lichenoides.
Journal of cutaneous pathology
2021
Abstract
Pityriasis lichenoides (PL) is a papulosquamous disease that affects both adults and children. Previous studies have shown a subset of this entity to have clonal T-cell populations via PCR based assays. In this study, we sought to implement next generation sequencing as a more sensitive and specific test to examine for T-cell clonality within the pediatric population.We identified 18 biopsy specimens from 12 pediatric patients with clinical and histopathologic findings compatible with PL. Patient demographics, clinical features, management, and histopathologic findings were reviewed. All specimens were analyzed for clonality with next generation sequencing of T-cell receptor beta (TRB) and gamma (TRG) genes.Of the 12 patients, 9 (75%) had complete resolution of lesions at the time of data collection (mean follow up 31 months). The remaining three patients significantly improved with methotrexate (with or without acitretin). Interestingly, 7 of 12 patients (58%) and 9 of 17 biopsy specimens (53%) showed evidence of T-cell clonality. Two patients showed matching TRB clones from different anatomic sites.T-cell clonality is a common finding in PL, likely representing a "reactive clonality" rather than a true lymphoproliferative disorder. Clonality alone cannot be used as a means to distinguish PL from lymphomatoid papulosis or cutaneous lymphoma. This article is protected by copyright. All rights reserved.
View details for DOI 10.1111/cup.14143
View details for PubMedID 34614220
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Machine Learning Predictability of Clinical Next Generation Sequencing for Hematologic Malignancies to Guide High-Value Precision Medicine.
AMIA ... Annual Symposium proceedings. AMIA Symposium
2021; 2021: 641-650
Abstract
Advancing diagnostic testing capabilities such as clinical next generation sequencing methods offer the potential to diagnose, risk stratify, and guide specialized treatment, but must be balanced against the escalating costs of healthcare to identify patient cases most likely to benefit from them. Heme-STAMP (Stanford Actionable Mutation Panel for Hematopoietic and Lymphoid Malignancies) is one such next generation sequencing test. Our objective is to assess how well Heme-STAMP pathological variants can be predicted given electronic health records data available at the time of test ordering. The model demonstrated AUROC 0.74 (95% CI: [0.72, 0.76]) with 99% negative predictive value at 6% specificity. A benchmark for comparison is the prevalence of positive results in the dataset at 58.7%. Identifying patients with very low or very high predicted probabilities of finding actionable mutations (positive result) could guide more precise high-value selection of patient cases to test.
View details for PubMedID 35308914
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A novel activating JAK1 mutation in chronic eosinophilic leukemia.
Blood advances
2021
Abstract
Hypereosinophilia (HE) has been arbitrarily defined as persistent eosinophilia >1.5 x109/L, and is broadly divided into primary (clonal or neoplastic; HEN), secondary/reactive (HER), or of undetermined significance (HEUS) when no cause is identified. The use of myeloid next generation sequencing panels has led to the detection of several mutations in patients previously diagnosed with HEUS, reassigning some patients to the category of HEN, specifically the World Health Organization category of chronic eosinophilic leukemia, not otherwise specified (CEL, NOS). Here we describe a novel somatic JAK1 pseudokinase domain mutation (R629_S632delinsSA) in a patient with HE that had been initially characterized as a variant of uncertain significance. We performed functional studies that demonstrate that this mutation results in growth factor independence of Ba/F3 cells in vitro and activation of the Janus Kinase-Signal Transducer and Activator of Transcription Proteins (JAK-STAT) pathway. These effects were abrogated by the JAK1/JAK2 inhibitor ruxolitinib. The R629_S632delinsSA is the first known somatic mutation in JAK1 linked to a clonal eosinophilic neoplasm, and highlights the importance of the JAK-STAT pathway in eosinophil survival.
View details for DOI 10.1182/bloodadvances.2021004237
View details for PubMedID 34496019
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Incidence and Risk Factors Associated with Bleeding and Thrombosis Following Chimeric Antigen Receptor T Cell Therapy.
Blood advances
2021
Abstract
Bleeding and thrombotic events are an emerging toxicity associated with chimeric antigen receptor (CAR) therapies. To determine their incidence, we retrospectively analyzed consecutive adult patients (n=127) with large B-cell lymphoma (LBCL) or B-cell acute lymphoblastic leukemia (B-ALL) treated between 2017-2020 with axicabtagene ciloleucel (axi-cel) (N=89) or a bispecific CD19/CD22 CAR (N=38). 12 (9.4%) and 8 (6.3%) patients developed bleeding and thrombosis within first 3 months, respectively. In the axi-cel subgroup, these occurred in 11.2% and 6.7%, respectively. Bleeding occurred between days 8-30 (median 17.5), and thrombosis between days 2-91 (median 29). Bleeding sites included genitourinary (N=6), soft tissue (N=2), intracranial (N=2), gastrointestinal (N=1), pulmonary (N=1), and were associated with features of consumptive coagulopathy. On univariate analysis, patients with bleeding were older (median 72 vs. 60 yrs, P<0.01), had lower baseline platelets (86 vs. 178 K/uL, P<0.01), lower platelet nadir after CAR-T (median 17.5 vs. 48 K/uL; P<0.01), lower fibrinogen nadir (median 122 vs. 340 ug/mL; P<0.01) and elevated LDH (P=0.01). ICANS grade ≥3 was associated with increased bleeding (50% vs. 15%; P=0.01), thrombosis (50% vs. 16%; P=0.04), PT prolongation, hypofibrinogenemia and elevated D-dimer. A paucity of events limited multivariate analysis, however low pre-treatment platelets were associated with bleeding in a multivariate logistic regression model. Patients with thrombocytopenia or severe ICANS are at increased risk of bleeding complications and should be closely monitored particularly within the first month after CAR therapy. Future studies in larger cohorts should assess risk factors for systemic coagulopathies in CAR-T therapy, including their association with neurotoxicity.
View details for DOI 10.1182/bloodadvances.2021004716
View details for PubMedID 34521106
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Combined SARS-CoV-2 nucleic acid amplification testing and respiratory virus panel RT-PCR on the Hologic Panther Fusion system.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
2021; 138: 104792
Abstract
Significant overlap exists between the symptoms of SARS-CoV-2 and other respiratory viruses. This poses a serious challenge to clinical diagnosis, laboratory testing, and infection control programs.To evaluate the performance of the Hologic Panther Fusion Respiratory Assays (RA) compared to the GenMark ePlex Respiratory Pathogen Panel (RPP) and to assess the ability of the Panther Fusion to perform parallel testing of SARS-CoV-2 and other respiratory viruses from a single sample.A diagnostic comparison study was carried out using 375 clinical nasopharyngeal specimens. Assay performance was assessed by overall, positive, and negative percent agreement and Cohen's kappa coefficient.Overall agreement between the Fusion RA and ePlex RPP was 97.3 % (95 % CI 96.3-98.0), positive percent agreement was 97.2 % (95 % CI 93.0-99.2), negative percent agreement was 97.3 % (95 % CI 96.3-98.0), and the kappa coefficient was 0.85 (95 % CI 0.81-0.89). Forty additional viruses in 30 specimens were detected by Fusion that were not detected by ePlex. The maximum specimen throughput for parallel testing of the Fusion Respiratory Assays with SARS-CoV-2 was 275 samples in 20.7 h for Fusion SARS-CoV-2 and 350 samples in 20.0 h for Aptima Transcription Mediated Amplification SARS-CoV-2.Fusion RA demonstrated substantial agreement compared to the ePlex RPP. However, the Fusion detected respiratory viruses not identified by ePlex, consistent with higher clinical sensitivity. Workflows for parallel testing of respiratory pathogens and SARS-CoV-2 demonstrate that the Panther Fusion instrument provides a flexible, moderate to high throughput testing option for pandemic and seasonal respiratory viruses.
View details for DOI 10.1016/j.jcv.2021.104792
View details for PubMedID 33770659
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Validation of a Next-Generation Sequencing-based T-Cell Receptor Gamma Gene Rearrangement Diagnostic Assay: Transitioning from Capillary Electrophoresis to Next-Generation Sequencing.
The Journal of molecular diagnostics : JMD
2021
Abstract
Assessment of T-cell receptor gamma (TRG) gene rearrangement is an important consideration in the diagnostic workup of lymphoproliferative diseases. Although fragment analysis by PCR and capillary electrophoresis (CE) is the current standard for such assessment in clinical molecular diagnostic laboratories, it does not provide sequence information and is only semi-quantitative. Next-generation sequencing (NGS)-based assays are an attractive alternative to the conventional fragment-size based methods since they generate results with specific clonotype sequence information and allow for more accurate quantitation. We therefore evaluated various test parameters and performance characteristics for a commercially available NGS-based TRG gene rearrangement assay by testing 101 clinical samples previously characterized by fragment analysis. The NGS TRG assay showed an overall accuracy of 83% and an analytical specificity of 100%, as compared to the CE-based assay. The concordance rate was 88∼95% for Vγ1-8, Vγ10 and Vγ11 gene families, but lower for the Vγ9 gene family. This difference was mostly attributed to the incomplete polyclonal symmetry resulting from the two-tube CE assay versus the one-tube design of the NGS assay. The NGS assay also demonstrated strengths in distinguishing different clonotypes with the same fragment size. Our clinical validation demonstrated robust performance of the NGS-based TRG assay and identified potential pitfalls associated with CE assay design that are important for understanding the observed discrepancies with the CE-based assay.
View details for DOI 10.1016/j.jmoldx.2021.03.008
View details for PubMedID 33892183
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Plasma as an alternative COVID-19 diagnostic specimen in a hospitalized patient negative for SARS-CoV-2 by nasopharyngeal swab.
Diagnostic microbiology and infectious disease
2021; 100 (3): 115365
Abstract
We present the case of an inpatient with pneumonia and repeatedly negative nasopharyngeal SARS-CoV-2 testing. In such challenging cases, alternative diagnostic options include lower respiratory tract and plasma SARS-CoV-2 RNA testing, of which the latter may be particularly useful where bronchoscopy is deferred due to clinical factors or transmission risk.
View details for DOI 10.1016/j.diagmicrobio.2021.115365
View details for PubMedID 33865070
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Evaluation of SARS-CoV-2 total antibody detection via a lateral flow nanoparticle fluorescence immunoassay.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
2021; 139: 104818
Abstract
The coronavirus disease 2019 (COVID-19) endgame may benefit from simple, accurate antibody testing to characterize seroprevalence and immunization coverage.To evaluate the performance of the lateral flow QIAreach anti-SARS-CoV-2 Total rapid nanoparticle fluorescence immunoassay compared to reference isotype-specific IgG, IgM, and IgA SARS-CoV-2 ELISA using S1 or receptor binding domain (RBD) as antigens.A diagnostic comparison study was carried out using 154 well-characterized heparin plasma samples. Agreement between assays was assessed by overall, positive, and negative percent agreement and Cohen's kappa coefficient.Overall agreement between the QIAreach anti-SARS-CoV-2 Total and any anti-spike domain (S1 or RBD) antibody isotype was 96.0 % (95 % CI 89.8-98.8), the positive percent agreement was 97.6 % (95 % CI 91.0-99.9), the negative percent agreement was 88.2 % (95 % CI 64.4-98.0). The kappa coefficient was 0.86 (95 % CI 0.72 to 0.99).The QIAreach anti-SARS-CoV-2 Total rapid antibody test provides comparable performance to high-complexity, laboratory-based ELISA.
View details for DOI 10.1016/j.jcv.2021.104818
View details for PubMedID 33932848
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Pembrolizumab in mycosis fungoides with PD-L1 structural variants.
Blood advances
2021; 5 (3): 771–74
View details for DOI 10.1182/bloodadvances.2020002371
View details for PubMedID 33560388
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Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
2021; 72 (2): 323–26
Abstract
Using data for 20 912 patients from 2 large academic health systems, we analyzed the frequency of severe acute respiratory syndrome coronavirus 2 reverse-transcription polymerase chain reaction test discordance among individuals initially testing negative by nasopharyngeal swab who were retested on clinical grounds within 7 days. The frequency of subsequent positivity within this window was 3.5% and was similar across institutions.
View details for DOI 10.1093/cid/ciaa722
View details for PubMedID 33543250
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Performance Characteristics of Mutational Signature Analysis in Targeted Panel Sequencing.
Archives of pathology & laboratory medicine
2021
Abstract
Mutational signatures have been described in the literature and a few centers have implemented pipelines for clinical reporting.To describe the performance of a mutational signature caller with clinical samples sequenced on a targeted next-generation sequencing panel with a small genomic footprint.One thousand six hundred eighty-two (n = 1682) clinical samples were analyzed for the presence of mutational signatures using deconstructSigs on variant calls with at least 20 variant reads.Signature 10 (associated with POLe mutation) achieved separation of cases and controls in hypermutated samples. Signatures 4 (associated with tobacco smoking) and 7 (associated with ultraviolet radiation) as an indicator of pulmonary or cutaneous primary sites showed moderate sensitivity and high specificity at optimal cutpoints. Mutational signatures in malignancies with unknown primaries were somewhat consistent with the clinically suspected primary site, with an apparent dose-response relationship between the number of variants analyzed and the ability of mutational signature analysis to correctly suggest a primary site.Mutational signatures represent an opportunity for orthogonal testing of primary site, which may be particularly useful in supporting cutaneous or pulmonary sites in poorly differentiated neoplasms. Tobacco smoking, ultraviolet radiation, and POLe mutational signatures are the most appropriate signatures for implementation. Even relatively small numbers of variants appear capable of supporting a clinically suspected primary.
View details for DOI 10.5858/arpa.2020-0536-OA
View details for PubMedID 33571361
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Performance of Nucleic Acid Amplification Tests for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Prospectively Pooled Specimens
EMERGING INFECTIOUS DISEASES
2021; 27 (1): 92–103
Abstract
Pooled nucleic acid amplification tests for severe acute respiratory syndrome coronavirus 2 could increase availability of testing at decreased cost. However, the effect of dilution on analytical sensitivity through sample pooling has not been well characterized. We tested 1,648 prospectively pooled specimens by using 3 nucleic acid amplification tests for severe acute respiratory syndrome coronavirus 2: a laboratory-developed real-time reverse transcription PCR targeting the envelope gene, and 2 commercially available Panther System assays targeting open reading frame 1ab. Positive percent agreement (PPA) of pooled versus individual testing ranged from 71.7% to 82.6% for pools of 8 and from 82.9% to 100.0% for pools of 4. We developed and validated an independent stochastic simulation model to estimate effects of dilution on PPA and efficiency of a 2-stage pooled real-time reverse transcription PCR testing algorithm. PPA was dependent on the proportion of tests with positive results, cycle threshold distribution, and assay limit of detection.
View details for DOI 10.3201/eid2701.203379
View details for Web of Science ID 000609135300011
View details for PubMedID 33183494
View details for PubMedCentralID PMC7774575
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Identification of a pathogenic TUBB1 variant in a Chinese family with congenital macrothrombocytopenia through whole genome sequencing.
Platelets
2021: 1–5
Abstract
Congenital macrothrombocytopenia is a genetically heterogeneous group of rare disorders. We herein report a large Chinese family presented with phenotypic variability involving thrombocytopenia and/or giant platelets. Whole genome sequencing (WGS) of the proband and one of his affected brothers identified a potentially pathogenic c.952 C > T heterozygous variant in the TUBB1 gene. This p.R318W β1-tubulin variant was also identified in three additional siblings and five members of the next generation. These findings were consistent with an autosomal dominant inheritance with incomplete penetrance. Moreover, impaired platelet agglutination in response to ristocetin was detected in the patient's brother. Half of the family members harboring the p.R318W mutation displayed significantly decreased external release of p-selectin by stimulated platelets. The p.R318W β1-tubulin mutation was identified for the first time in a Chinese family with congenital macrothrombocytopenia using WGS as an unbiased sequencing approach. Affected individuals within the family demonstrated impaired platelet aggregation and/or release functions.
View details for DOI 10.1080/09537104.2020.1869714
View details for PubMedID 33400601
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A Blueprint for Identifying Phenotypes and Drug Targets in Complex Disorders with Empirical Dynamics.
Patterns (New York, N.Y.)
2020; 1 (9): 100138
Abstract
A central challenge in medicine is translating from observational understanding to mechanistic understanding, where some observations are recognized as causes for the others. This can lead not only to new treatments and understanding, but also to recognition of novel phenotypes. Here, we apply a collection of mathematical techniques (empirical dynamics), which infer mechanistic networks in a model-free manner from longitudinal data, to hematopoiesis. Our study consists of three subjects with markers for cyclic thrombocytopenia, in which multiple cells and proteins undergo abnormal oscillations. One subject has atypical markers and may represent a rare phenotype. Our analyses support this contention, and also lend new evidence to a theory for the cause of this disorder. Simulations of an intervention yield encouraging results, even when applied to patient data outside our three subjects. These successes suggest that this blueprint has broader applicability in understanding and treating complex disorders.
View details for DOI 10.1016/j.patter.2020.100138
View details for PubMedID 33336196
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Database for Managing Results of High-Throughput Sequencing Clonality Assays in Clinical Laboratories
ELSEVIER SCIENCE INC. 2020: S54–S55
View details for Web of Science ID 000612939600168
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Accurate Detection and Quantification of FLT3 Internal Tandem Duplications in Clinical Hybrid Capture Next-Generation Sequencing Data
ELSEVIER SCIENCE INC. 2020: S50
View details for Web of Science ID 000612939600154
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Assessment of a High-Throughput Sequencing Assay for Measurable Residual Disease (MRD) Monitoring in Patients with T-Cell Malignancies
ELSEVIER SCIENCE INC. 2020: S16–S17
View details for Web of Science ID 000612939600050
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Comparison of Next-Generation Sequencing-Based TRG and TRB Assays for the Diagnostic Evaluation of T Cell Lymphoid Malignancies
ELSEVIER SCIENCE INC. 2020: S16
View details for Web of Science ID 000612939600048
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Retrospective Screening for SARS-CoV-2 RNA in California, USA, Late 2019
EMERGING INFECTIOUS DISEASES
2020; 26 (10): 2487–88
Abstract
To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. We found no evidence of earlier infection.
View details for DOI 10.3201/eid2610.202296
View details for Web of Science ID 000572522100035
View details for PubMedID 32620178
View details for PubMedCentralID PMC7510744
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Cutaneous T-cell lymphomas with pathogenic somatic mutations and absence of detectable clonal T-cell receptor gene rearrangement: two case reports.
Diagnostic pathology
2020; 15 (1): 122
Abstract
BACKGROUND: Cutaneous T-cell lymphomas (CTCL) are a heterogeneous group of extranodal non-Hodgkin lymphomas for which diagnosis can be challenging given the potential for overlap with inflammatory dermatoses. Current diagnostic criteria for CTCL incorporate clinical and histopathologic findings as well as results of T-cell receptor (TCR) gene sequencing. Molecular interrogation of TCR genes, TRG and TRB, has provento be a critical tool for confirming diagnoses of CTCL and for disease tracking after initiation of therapy or after stem cell transplant. Methods for confirming a diagnosis of lymphoma in the absence of TCR gene clonality are lacking. We present two patients with CTCL with pathogenic somatic mutations in the absence of TRG and TRB clonality.CASE PRESENTATIONS: Case 1: A 38-year-old male had a 19-year history of a diffuse skin rash with papulosquamous, granulomatous, and verrucous features and progressive ulcerated plaques and tumors demonstrating an atypical CD4+ T-cell infiltrate with expression of cytotoxic markers CD56, TIA-1, granzyme, and perforin on histopathology. No definitive evidence for T-cell clonality was detected by conventional PCR of 6 biopsies or by next-generation sequencing (NGS) of 14 biopsies. Somatic mutational profiling of a skin biopsy revealed pathogenic mutations in PIKC3D and TERT promoter hotspots, confirming the presence of a clonal process. Case 2: A 69-year-old male with a 13-year history of progressive, diffuse hypertrophic and eroded plaques showed an atypical CD4+ T-cell infiltrate with subset expression of TIA-1 and granzyme on histopathology. No TCR clonality was detected by TCR-NGS of 6 biopsies. Somatic mutational profiling of a skin biopsy detected a pathogenic mutation in TP53, confirming the presence of a clonal process.CONCLUSIONS: These cases highlight how detection of pathogenic somatic mutations can confirma diagnosis of lymphoma in a clinically and histopathologically suspicious cutaneous lymphoid proliferation without detectable TCR clonality.
View details for DOI 10.1186/s13000-020-01022-x
View details for PubMedID 32988392
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High Frequency of SARS-CoV-2 RNAemia and Association With Severe Disease.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
2020
Abstract
BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in blood, also known as RNAemia, has been reported, but its prognostic implications are poorly understood. This study aimed to determine the frequency of SARS-CoV-2 RNA in plasma and its association with coronavirus disease 2019 (COVID-19) clinical severity.METHODS: An analytical cross-sectional study was performed in a single-center tertiary care institution and included consecutive inpatients and outpatients with confirmed COVID-19. The prevalence of SARS CoV-2 RNAemia and the strength of its association with clinical severity variables were examined and included intensive care unit (ICU) admission, invasive mechanical ventilation, and 30-day all-cause mortality.RESULTS: Paired nasopharyngeal and plasma samples were included from 85 patients. The median age was 55 years, and individuals with RNAemia were older than those with undetectable SARS-CoV-2 RNA in plasma (63 vs 50 years; P = .04). Comorbidities were frequent including obesity (37.6%), hypertension (30.6%), and diabetes mellitus (22.4%). RNAemia was detected in 28/85 (32.9%) of patients, including 22/28 (78.6%) who required hospitalization. In models adjusted for age, RNAemia was detected more frequently in individuals who developed severe disease including ICU admission (32.1 vs 14.0%; P = .04) and invasive mechanical ventilation (21.4% vs 3.5%; P = .02). All 4 deaths occurred in individuals with detectable RNAemia. An additional 121 plasma samples from 28 individuals with RNAemia were assessed longitudinally, and RNA was detected for a maximum duration of 10 days.CONCLUSIONS: This study demonstrated a high proportion of SARS-CoV-2 RNAemia, and an association between RNAemia and clinical severity suggesting the potential utility of plasma viral testing as a prognostic indicator for COVID-19.
View details for DOI 10.1093/cid/ciaa1054
View details for PubMedID 32965474
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SARS-CoV-2 Antibody Responses Correlate with Resolution of RNAemia But Are Short-Lived in Patients with Mild Illness.
medRxiv : the preprint server for health sciences
2020
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, could offer protective immunity, and may affect clinical outcomes of COVID-19 patients. We analyzed 625 serial plasma samples from 40 hospitalized COVID-19 patients and 170 SARS-CoV-2-infected outpatients and asymptomatic individuals. Severely ill patients developed significantly higher SARS-CoV-2-specific antibody responses than outpatients and asymptomatic individuals. The development of plasma antibodies was correlated with decreases in viral RNAemia, consistent with potential humoral immune clearance of virus. Using a novel competition ELISA, we detected antibodies blocking RBD-ACE2 interactions in 68% of inpatients and 40% of outpatients tested. Cross-reactive antibodies recognizing SARS-CoV RBD were found almost exclusively in hospitalized patients. Outpatient and asymptomatic individuals' serological responses to SARS-CoV-2 decreased within 2 months, suggesting that humoral protection may be short-lived.
View details for DOI 10.1101/2020.08.15.20175794
View details for PubMedID 32839786
View details for PubMedCentralID PMC7444305
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Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
2020; 129: 104477
Abstract
BACKGROUND: Current guidelines for returning health care workers (HCW) to service after a positive SARS-CoV-2 RT-PCR test and ceasing of transmission precautions for patients is based on two general strategies. A test-based strategy that requires negative respiratory RT-PCR tests obtained after the resolution of symptoms. Alternatively, due to the limited availability of testing, many sites employ a symptom-based strategy that recommends excluding HCW from the workforce and keeping patients on contact precautions until a fixed period of time has elapsed from symptom recovery. The underlying assumption of the symptom-based strategy is that waiting for a fixed period of time is a surrogate for negative RT-PCR testing, which itself is a surrogate for the absence of shedding infectious virus.OBJECTIVES: To better understand the appropriate length of symptom based return to work and contact precaution strategies.STUDY DESIGN: We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center.RESULTS: We found that the average time to transition from RT-PCR positive to negative was 24 days after symptom onset and 10 % remained positive even 33 days after symptom onset. No difference was seen in HCW and patients.CONCLUSIONS: These findings suggest until definitive evidence of the length of infective viral shedding is obtained that the fixed length of time before returning to work or ceasing contract precautions be revised to over one-month.
View details for DOI 10.1016/j.jcv.2020.104477
View details for PubMedID 32505778
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Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients.
medRxiv : the preprint server for health sciences
2020
Abstract
BACKGROUND: SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) testing remains the cornerstone of laboratory-based identification of patients with COVID-19. As the availability and speed of SARS-CoV-2 testing platforms improve, results are increasingly relied upon to inform critical decisions related to therapy, use of personal protective equipment, and workforce readiness. However, early reports of RT-PCR test performance have left clinicians and the public with concerns regarding the reliability of this predominant testing modality and the interpretation of negative results. In this work, two independent research teams report the frequency of discordant SARS-CoV-2 test results among initially negative, repeatedly tested patients in regions of the United States with early community transmission and access to testing.METHODS: All patients at the University of Washington (UW) and Stanford Health Care undergoing initial testing by nasopharyngeal (NP) swab between March 2nd and April 7th, 2020 were included. SARS-CoV-2 RT-PCR was performed targeting the N, RdRp, S, and E genes and ORF1ab, using a combination of Emergency Use Authorization laboratory-developed tests and commercial assays. Results through April 14th were extracted to allow for a complete 7-day observation period and an additional day for reporting.RESULTS: A total of 23,126 SARS-CoV-2 RT-PCR tests (10,583 UW, 12,543 Stanford) were performed in 20,912 eligible patients (8,977 UW, 11,935 Stanford) undergoing initial testing by NP swab; 626 initially test-negative patients were re-tested within 7 days. Among this group, repeat testing within 7 days yielded a positive result in 3.5% (4.3% UW, 2.8% Stanford) of cases, suggesting an initial false negative RT-PCR result; the majority (96.5%) of patients with an initial negative result who warranted reevaluation for any reason remained negative on all subsequent tests performed within this window.CONCLUSIONS: Two independent research teams report the similar finding that, among initially negative patients subjected to repeat SARS-CoV-2 RT-PCR testing, the occurrence of a newly positive result within 7 days is uncommon. These observations suggest that false negative results at the time of initial presentation do occur, but potentially at a lower frequency than is currently believed. Although it is not possible to infer the clinical sensitivity of NP SARS-CoV-2 RT-PCR testing using these data, they may be used in combination with other reports to guide the use and interpretation of this common testing modality.
View details for DOI 10.1101/2020.05.03.20089151
View details for PubMedID 32511542
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Five-minute point-of-care testing for SARS-CoV-2: Not there yet.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
2020; 128: 104410
View details for DOI 10.1016/j.jcv.2020.104410
View details for PubMedID 32403009
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Patient-Derived Tumor Organoids Share Morphologic and Molecular Features with Carcinomas of Lung, Kidney, and Pancreas Primaries
ELSEVIER SCIENCE INC. 2020: S68
View details for Web of Science ID 000535952500128
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Merkel Cell Carcinoma of Lymph Node is Metastatic Cutaneous Merkel Cell Carcinoma
NATURE PUBLISHING GROUP. 2020: 824–26
View details for Web of Science ID 000518328801386
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A Multiplex SNaPshot Assay is a Rapid and Cost-Effective Method for Detecting POLE Mutations in Endometrial Carcinoma
NATURE PUBLISHING GROUP. 2020: 1040
View details for Web of Science ID 000518328802227
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Merkel Cell Carcinoma of Lymph Node is Metastatic Cutaneous Merkel Cell Carcinoma
NATURE PUBLISHING GROUP. 2020: 824–26
View details for Web of Science ID 000518328901386
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A Multiplex SNaPshot Assay is a Rapid and Cost-Effective Method for Detecting POLE Mutations in Endometrial Carcinoma
NATURE PUBLISHING GROUP. 2020: 1040
View details for Web of Science ID 000518328902227
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Analysis of Whole CDR3 TCR Repertoire after Hematopoietic Stem Cell Transplantation in Two Clinical Cohorts.
Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation
2020
Abstract
A major cause of morbidity and mortality for patients who undergo hematological stem cell transplantations (HSCT) is acute graft-versus-host disease (GVHD), a mostly T cell mediated disease. The examination of the T cell receptor (TCR) repertoire of HSCT patients and through the use of next generation nucleotide sequencing leads to the question of whether features of TCR repertoire reconstitution might reproducibly associate with GVHD.HYPOTHESIS: We hypothesized that the peripheral blood TCR repertoire of patients with steroid non-responsive, acute GVHD would be less diverse. We also hypothesized that patients with GVHD who shared HLA might also share common clones at the time of GVHD diagnosis, thereby potentially providing potential clinical indicators for treatment stratification. We further hypothesized that HSCT recipients with the same HLA mismatch might share a more similar TCR repertoire based on a potentially shared focus of alloreactive responses.METHOD: We studied two separate patient cohorts and two separate platforms to measure TCR repertoire. The first cohort of patients are from a multicenter, phase III, randomized, double-blinded clinical trial of patients who developed acute GVHD (NCT01002742). The second are samples from biobanks from two centers and the CIBMTR of patients who mismatched HSCT.CONCLUSION: There were no statistically significant differences in the TCR diversity of steroid responders and non-responders among patients with acute GVHD on the day of diagnosis. Most clones in the repertoire were unique to each patient, but a small number of clones were found to be both exclusive to, and shared, amongst GVHD non-responders. We were also able to show a strong correlation between the presence of VSS 20 and VSS29 and steroid responsiveness. Using the Bhattacharya coefficient, those patients who shared the same HLA mismatch were shown to be no more similar to one another than to those who had a completely different mismatch. Using two separate clinical cohorts and two separate platforms for analyzing the TCR repertoire, we have shown that the sampled human TCR repertoire is largely unique to each patient but showed glimmers of common clones of subsets of clones based on responsiveness to steroids in aGVHD on the day of diagnosis. These studies are informative for future strategies to assess for reproducible TCR responses in human alloreactivity and possible markers of GVHD responsiveness to therapy.
View details for DOI 10.1016/j.bbmt.2020.01.020
View details for PubMedID 32081787
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Increasing Clinical Trial Accrual via Automated Matching of Biomarker Criteria.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
2020; 25: 31–42
Abstract
Successful implementation of precision oncology requires both the deployment of nucleic acid sequencing panels to identify clinically actionable biomarkers, and the efficient screening of patient biomarker eligibility to on-going clinical trials and therapies. This process is typically performed manually by biocurators, geneticists, pathologists, and oncologists; however, this is a time-intensive, and inconsistent process amongst healthcare providers. We present the development of a feature matching algorithmic pipeline that identifies patients who meet eligibility criteria of precision medicine clinical trials via genetic biomarkers and apply it to patients undergoing treatment at the Stanford Cancer Center. This study demonstrates, through our patient eligibility screening algorithm that leverages clinical sequencing derived biomarkers with precision medicine clinical trials, the successful use of an automated algorithmic pipeline as a feasible, accurate and effective alternative to the traditional manual clinical trial curation.
View details for PubMedID 31797584
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Increasing Clinical Trial Accrual via Automated Matching of Biomarker Criteria
WORLD SCIENTIFIC PUBL CO PTE LTD. 2020: 31-42
View details for Web of Science ID 000702064500004
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Is Merkel Cell Carcinoma of Lymph Node Actually Metastatic Cutaneous Merkel Cell Carcinoma?
American journal of clinical pathology
2020
Abstract
The possibility of a so-called primary lymph node neuroendocrine carcinoma has been described in the literature. Here we evaluate cases fitting such a diagnosis and find that the cases demonstrate a convincing and pervasive pattern consistent with metastatic Merkel cell carcinoma.Six cases of primary lymph node Merkel cell carcinoma and one case of metastatic neuroendocrine carcinoma at a bony site, all with unknown primary, were sequenced using a combination of whole-exome and targeted panel methods. Sequencing results were analyzed for the presence of an ultraviolet (UV) mutational signature or off-target detection of Merkel cell polyomavirus (MCPyV).Four of six primary lymph node cases were positive for a UV mutational signature, with the remaining two cases positive for off-target alignment of MCPyV. One case of neuroendocrine carcinoma occurring at a bony site was also positive for a UV mutational signature.We find no evidence to corroborate the existence of so-called primary Merkel cell carcinoma of lymph node.
View details for DOI 10.1093/ajcp/aqaa051
View details for PubMedID 32445471
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Comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of SARS-CoV-2.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
2020; 129: 104427
Abstract
Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another.The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs.A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen's kappa coefficient.Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement.Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.
View details for DOI 10.1016/j.jcv.2020.104427
View details for PubMedID 32535398
View details for PubMedCentralID PMC7207111
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Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA.
The journal of applied laboratory medicine
2020
Abstract
Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). Limited data are available comparing the test performance characteristics of these assays.A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. Agreement between the two assays was assessed by overall, positive, and negative percent agreement and Cohen's kappa coefficient.A total of 104 (54 positive and 50 negative) clinical nasopharyngeal samples were tested by both assays. Using the Panther Fusion as a reference standard, the Xpert demonstrated an overall agreement of 99.0% (95% confidence interval (CI): 94.8 - 100), positive percent agreement of 98.1% (95% CI: 90.1 - 100), and a negative percent agreement of 100% (95% CI: 94.2 - 100). The kappa coefficient was 0.98 (95% CI: 0.94 - 1.0). One sample positive by the Panther Fusion with a cycle threshold (Ct) of 38.6 was found to be reproducibly negative by the Xpert assay.The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity.
View details for DOI 10.1093/jalm/jfaa135
View details for PubMedID 32761092
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Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
2020; 127: 104383
Abstract
Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and there is a need to assess their test performance relative to one another.The aim of this study was to compare the test performance of the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene.We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient.A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6.The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.
View details for DOI 10.1016/j.jcv.2020.104383
View details for PubMedID 32353760
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Large-Scale Testing of Asymptomatic Healthcare Personnel for Severe Acute Respiratory Syndrome Coronavirus 2.
Emerging infectious diseases
2020; 27 (1)
Abstract
Large-scale, 1-time testing of >12,000 asymptomatic healthcare personnel in California, USA, during April-June 2020 showed that prevalence of severe acute respiratory syndrome coronavirus 2 was low (<1%). Testing might identify asymptomatic and presymptomatic persons, including some with high viral burden, enabling prompt implementation of measures to limit nosocomial spread.
View details for DOI 10.3201/eid2701.203892
View details for PubMedID 33256889
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Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
2020
Abstract
Using data for 20,912 patients from two large academic health systems, we analyzed the frequency of SARS-CoV-2 RT-PCR test-discordance among individuals initially testing negative by nasopharyngeal swab who were retested on clinical grounds within 7 days. The frequency of subsequent positivity within this window was 3.5% and similar across institutions.
View details for DOI 10.1093/cid/ciaa722
View details for PubMedID 32506118
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Ex vivo drug screening defines novel drug sensitivity patterns for informing personalized therapy in myeloid neoplasms.
Blood advances
2020; 4 (12): 2768–78
Abstract
Precision medicine approaches such as ex vivo drug sensitivity screening (DSS) are appealing to inform rational drug selection in myelodysplastic syndromes (MDSs) and acute myeloid leukemia, given their marked biologic heterogeneity. We evaluated a novel, fully automated ex vivo DSS platform that uses high-throughput flow cytometry in 54 patients with newly diagnosed or treatment-refractory myeloid neoplasms to evaluate sensitivity (blast cytotoxicity and differentiation) to 74 US Food and Drug Administration-approved or investigational drugs and 36 drug combinations. After piloting the platform in 33 patients, we conducted a prospective feasibility study enrolling 21 patients refractory to hypomethylating agents (HMAs) to determine whether this assay could be performed within a clinically actionable time frame and could accurately predict clinical responses in vivo. When assayed for cytotoxicity, ex vivo drug sensitivity patterns were heterogeneous, but they defined distinct patient clusters with differential sensitivity to HMAs, anthracyclines, histone deacetylase inhibitors, and kinase inhibitors (P < .001 among clusters) and demonstrated synergy between HMAs and venetoclax (P < .01 for combinations vs single agents). In our feasibility study, ex vivo DSS results were available at a median of 15 days after bone marrow biopsy, and they informed personalized therapy, which frequently included venetoclax combinations, kinase inhibitors, differentiative agents, and androgens. In 21 patients with available ex vivo and in vivo clinical response data, the DSS platform had a positive predictive value of 0.92, negative predictive value of 0.82, and overall accuracy of 0.85. These data demonstrate the utility of this approach for identifying potentially useful and often novel therapeutic drugs for patients with myeloid neoplasms refractory to standard therapies.
View details for DOI 10.1182/bloodadvances.2020001934
View details for PubMedID 32569379
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Recipient-specific T-cell repertoire reconstitution in the gut following murine hematopoietic cell transplant.
Blood advances
2020; 4 (17): 4232–43
Abstract
Graft-versus-host disease (GVHD) is a complication of hematopoietic cell transplantation (HCT) caused by alloreactive T cells. Murine models of HCT are used to understand GVHD and T-cell reconstitution in GVHD target organs, most notably the gastrointestinal (GI) tract where the disease contributes most to patient mortality. T-cell receptor (TCR) repertoire sequencing was used to measure T-cell reconstitution from the same donor graft (C57BL/6 H-2b) in the GI tract of different recipients across a spectrum of matching, from syngeneic (C57BL/6), to minor histocompatibility (MHC) antigen mismatch BALB.B (H-2b), to major MHC mismatched B10.BR (H-2k) and BALB/c (H-2d). Although the donor T-cell pools had highly similar TCR, the TCR repertoire after HCT was very specific to recipients in each experiment independent of geography. A single invariant natural killer T clone was identifiable in every recipient group and was enriched in syngeneic recipients according to clonal count and confirmatory flow cytometry. Using a novel cluster analysis of the TCR repertoire, we could classify recipient groups based only on their CDR3 size distribution or TCR repertoire relatedness. Using a method for evaluating the contribution of common TCR motifs to relatedness, we found that reproducible sets of clones were associated with specific recipient groups within each experiment and that relatedness did not necessarily depend on the most common clones in allogeneic recipients. This finding suggests that TCR reconstitution is highly stochastic and likely does not depend on the evaluation of the most expanded TCR clones in any individual recipient but instead depends on a complex polyclonal architecture.
View details for DOI 10.1182/bloodadvances.2019000977
View details for PubMedID 32898248
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Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome.
Science immunology
2020; 5 (54)
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, can neutralize the virus. It is, however, unknown which features of the serological response may affect clinical outcomes of COVID-19 patients. We analyzed 983 longitudinal plasma samples from 79 hospitalized COVID-19 patients and 175 SARS-CoV-2-infected outpatients and asymptomatic individuals. Within this cohort, 25 patients died of their illness. Higher ratios of IgG antibodies targeting S1 or RBD domains of spike compared to nucleocapsid antigen were seen in outpatients who had mild illness versus severely ill patients. Plasma antibody increases correlated with decreases in viral RNAemia, but antibody responses in acute illness were insufficient to predict inpatient outcomes. Pseudovirus neutralization assays and a scalable ELISA measuring antibodies blocking RBD-ACE2 interaction were well correlated with patient IgG titers to RBD. Outpatient and asymptomatic individuals' SARS-CoV-2 antibodies, including IgG, progressively decreased during observation up to five months post-infection.
View details for DOI 10.1126/sciimmunol.abe0240
View details for PubMedID 33288645
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Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens.
Journal of clinical microbiology
2020
Abstract
Background: Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for diagnosis of SARS-CoV-2. The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use.Objectives: The aim of this study was to assess test performance of the Accula SARS-CoV-2 test.Study design: The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT) targeting the envelope (E) gene. Assay concordance was assessed by overall percent agreement, positive percent agreement (PPA), negative percent agreement (NPA), and Cohen's kappa coefficient.Results: Overall percent agreement between the assays was 84.0% (95% confidence interval [CI] 75.3 to 90.6%), PPA was 68.0% (95% CI 53.3 to 80.5%) and the kappa coefficient was 0.68 (95% CI 0.54 to 0.82). Sixteen specimens detected by the SHC-LDT were not detected by the Accula test, and showed low viral load burden with a median cycle threshold value of 37.7. NPA was 100% (95% CI 94.2 to 100%).Conclusion: Compared to the SHC-LDT, the Accula SARS-CoV-2 test showed excellent negative agreement. However, positive agreement was low for samples with low viral load. The false negative rate of the Accula POC test calls for a more thorough evaluation of POC test performance characteristics in clinical settings, and for confirmatory testing in individuals with moderate to high pre-test probability of SARS-CoV-2 who test negative on Accula.
View details for DOI 10.1128/JCM.01072-20
View details for PubMedID 32461285
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Complete and Prolonged Response to Immune Checkpoint Blockade in POLE-Mutated Colorectal Cancer.
JCO precision oncology
2019; 3: 1-5
View details for DOI 10.1200/PO.18.00214
View details for PubMedID 35100706
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Targeted deep sequencing of cell-free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology.
Cancer cytopathology
2019
Abstract
BACKGROUND: Liquid biopsy using cell-free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored.METHODS: We evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture-based next-generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty-one serous effusions from pleural (n=15), peritoneal (n=5), and pericardial (n=1) cavity were analyzed.RESULTS: The supernatants provided a median cfDNA concentration of 10.3ng/L. Notably, all effusions were sequenced successfully to a median depth >1000*, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin-fixed, paraffin-embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration (P=.5), depth of coverage (P=.6), or allele frequency of pathogenic mutations (P=.7).CONCLUSION: cfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.
View details for DOI 10.1002/cncy.22205
View details for PubMedID 31751001
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Increased Mortality and Bleeding in a Large Cohort of Patients on Heparin Anticoagulation Therapy with Discordant Anti-Factor Xa Activity and Activated Partial Thromboplastin Time (PTT); Implications for Clinical Management
AMER SOC HEMATOLOGY. 2019
View details for DOI 10.1182/blood-2019-132112
View details for Web of Science ID 000518218500781
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A Meta-Analysis of Genetic Abnormalities and Next Generation Sequencing of Primary Cases of Castleman Disease
AMER SOC HEMATOLOGY. 2019
View details for DOI 10.1182/blood-2019-131261
View details for Web of Science ID 000577164605300
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Clinical Utility of a Multi-Gene Next-Generation Sequencing Myeloid Panel in an Academic Hematology Practice
AMER SOC HEMATOLOGY. 2019
View details for DOI 10.1182/blood-2019-124445
View details for Web of Science ID 000577160401225
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Next Generation Sequencing-Based Characterization of T Cell Receptor Repertoire of Patients with Immune Thrombocytopenia
AMER SOC HEMATOLOGY. 2019
View details for DOI 10.1182/blood-2019-127590
View details for Web of Science ID 000577160405007
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A Feasibility Study of Biologically Focused Therapy for Myelodysplastic Syndrome Patients Refractory to Hypomethylating Agents
AMER SOC HEMATOLOGY. 2019
View details for DOI 10.1182/blood-2019-129473
View details for Web of Science ID 000577164602262
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Clinical Validation of an NGS-Based IGHV Somatic Hypermutation Assay
ELSEVIER SCIENCE INC. 2019: 1137
View details for Web of Science ID 000496996500075
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Antiphospholipid Antibodies in Patients With Lupus Anticoagulant Prozone Effect.
American journal of clinical pathology
2019
Abstract
OBJECTIVES: Lupus anticoagulant (LAC) is typically associated with thrombosis but also rarely with hemorrhage. Some patients exhibit a prozone effect on LAC testing. Antiphosphatidylserine/prothrombin (aPS/PT) antibodies may provide a mechanism for both hemorrhage and prozone effect. Our goal was to evaluate whether antibody specificities, isotypes, and titers were associated with LAC prozone effect, factor II levels, hemorrhage, and thrombosis.METHODS: Patients with prozone effect noted on LAC testing were entered into a database over 3 years. Factor II activity and aPS/PT antibody testing were performed when a sufficient residual sample was available.RESULTS: All patients with LAC prozone effect and antibody testing were positive for at least 1 class of aPS/PT antibodies. In addition, aPS/PT IgG titers were significantly associated with thrombosis and significantly inversely associated with factor II levels.CONCLUSIONS: In prozone effect patients, aPS/PT antibodies are associated with LAC prozone effect as well as thrombosis and decreased factor II levels.
View details for DOI 10.1093/ajcp/aqz151
View details for PubMedID 31598704
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IMPLEMENTATIONOF A SEMI-AUTOMATED VON WILLEBRAND FACTOR MULTIMER ASSAY (SEBIA HYDRAGEL 5) IN LABORATORY PRACTICE
WILEY. 2019: 80
View details for Web of Science ID 000487566000128
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Clonal Evolution and Changes in Two AML Patients Detected with A Novel Single-Cell DNA Sequencing Platform.
Scientific reports
2019; 9 (1): 11119
Abstract
Next-generation sequencing (NGS) is used to detect gene variants in genetically complex cell populations of cancer patient samples. Traditional bulk analysis can only provide average variant allele frequencies of the targeted genes across all sampled cells. It fails to resolve mutational co-occurrences and may miss rare cancer cells. Genome analysis at the single cell level offers the opportunity to more fully resolve clonal architecture. Peripheral blood mononuclear cells were sampled from acute myeloid leukemia patients longitudinally and single-cell DNA sequencing libraries were generated with a novel droplet-based microfluidics approach. Molecular profiling of single nucleotide variants across thousands of cells revealed genetic chimerism in patients after bone marrow transplantation (BMT). Importantly, hierarchical clustering analysis of single nucleotide variants (SNVs) uncovered a distinct oncogenic clone of cells carrying mutated tumor-suppressor and/or oncogene(s). This novel single-cell DNA sequencing approach enabled precise monitoring of engraftment and revealed clonal evolution of oncogenic cells during the progression and treatment of the disease.
View details for DOI 10.1038/s41598-019-47297-z
View details for PubMedID 31366893
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Indolent In Situ B-Cell Neoplasms With MYC Rearrangements Show Somatic Mutations in MYC and TNFRSF14 by Next-generation Sequencing.
The American journal of surgical pathology
2019
Abstract
Systemic high-grade B-cell lymphomas (HGBCLs) with MYC gene rearrangements are clinically aggressive. In situ lesions with indolent behavior have not been described to date. We have identified 2 cases of in situ B-cell neoplasms with MYC rearrangements (IS-BCN, MYC) occurring, and focally confined to ≤4 lymphoid follicles in otherwise healthy individuals and without clinical progression despite minimal intervention (surgical only). Morphologically similar to systemic HGBCLs, the low power view of these lesions showed a starry sky pattern with numerous mitotic figures. High power imaging demonstrated these cells to be medium-large in size with irregular nuclear contours, immature chromatin, and prominent nucleoli. Immunophenotypically these cells were light chain restricted, positive for CD20, CD10, c-Myc, and dim or negative for BCL2 with a Ki67 proliferative index of >95%. By fluorescence in situ hybridization studies, we detected MYC translocations in these cells but no rearrangements in BCL2 or BCL6. Microdissection of neoplastic cells in these patients followed by targeted next-generation sequencing identified a mutation in MYC, D2N, and an indel in TNFRSF14. Mutations in ID3 or TCF3 were not identified. Although rare, these lesions should be separated from HGBCLs involving follicles but with systemic spread which has been previously described. Unlike systemic lymphomas with MYC gene rearrangements, these in situ B-cell neoplasms with MYC rearrangements did not require systemic therapy and no progression has been seen in either patient beyond 1 year (29 and 16mo). Our work offers pathologic and biologic insight into the early process of B-cell neoplasia.
View details for DOI 10.1097/PAS.0000000000001338
View details for PubMedID 31368914
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Single-cell analysis of mutational heterogeneity in acute myeloid leukemia tumors with high-throughput droplet microfluidics
NATURE PUBLISHING GROUP. 2019: 568
View details for Web of Science ID 000489313104277
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Coexistence of BRAF V600E and TERT Promoter Mutations in Low-grade Serous Carcinoma of Ovary Recurring as Carcinosarcoma in a Lymph Node: Report of a Case
INTERNATIONAL JOURNAL OF GYNECOLOGICAL PATHOLOGY
2019; 38 (4): 386–92
View details for DOI 10.1097/PGP.0000000000000507
View details for Web of Science ID 000471670300012
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Complete and Prolonged Response to Immune Checkpoint Blockade in POLE-Mutated Colorectal Cancer
JCO PRECISION ONCOLOGY
2019; 3: 1–5
View details for DOI 10.1200/PO.18.00214
View details for Web of Science ID 000473546800001
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Revisiting diagnostic criteria for myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis: Borderline cases without anemia exist
INTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY
2019; 41 (3): 345–52
View details for DOI 10.1111/ijlh.12981
View details for Web of Science ID 000468370800013
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Update on diagnostic testing for platelet function disorders: What is practical and useful?
International journal of laboratory hematology
2019; 41 Suppl 1: 26–32
Abstract
INTRODUCTION: Platelet function disorders (PFD) are an important group of bleeding disorders that require validated and practical laboratory strategies for diagnosis.METHODS: This review summarizes the authors' experiences, current literature, and an international survey to evaluate the practices of diagnostic laboratories that offer tests for PFD.RESULTS: Blood counts, blood film review, and aggregation tests are the most commonly performed investigations for PFD and help determine whether there is thrombocytopenia and/or defective platelet function due to a variety of causes. The performance characteristics of tests for PFD, and the level of evidence that these tests detect bleeding problems, are important issues to determine where tests are useful for diagnostic or correlative purposes, or research only uses. Platelet aggregation assays, and quantitative analysis of platelet dense granule numbers, are tests with good performance characteristics that detect abnormalities associated with increased bleeding in a significant proportion of individuals referred for PFD investigations. Lumiaggregometry estimates of platelet adenosine triphosphate release show greater variability which limits the diagnostic usefulness. Diagnostic laboratories report that fiscal and other constraints, including a lack of high-quality evidence, limit their ability to offer an expanded test menu for PFD.CONCLUSION: PFD are clinically important bleeding disorders that remain challenging for diagnostic laboratories to investigate. While some PFD tests are well validated for diagnostic purposes, gaps in scientific evidence and resource limitations influence diagnostic laboratory decisions on which PFD tests to offer.
View details for PubMedID 31069975
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Development of Clinical Epigenome Profiling Assay and Computational Pipeline for FFPE Tumor Tissue
ELSEVIER SCIENCE INC. 2019: S51
View details for Web of Science ID 000568300200101
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Structural. Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue
JOURNAL OF MOLECULAR DIAGNOSTICS
2019; 21 (3): 375–83
View details for DOI 10.1016/j.jmoldx.2018.11.003
View details for Web of Science ID 000467350300002
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Update on diagnostic testing for platelet function disorders: What is practical and useful?
INTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY
2019; 41: 26–32
View details for DOI 10.1111/ijlh.12995
View details for Web of Science ID 000468349600006
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Next-Generation Sequencing for HER2 Status in Breast Cancer: Comparison with Immunohistochemistry and in situ Hybridization by 2018 Focused Update
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478081100217
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Targeted deep sequencing of cell-free DNA from body cavity fluids with malignant, suspicious, and benign cytology
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478081100461
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Molecular Profiling of Intraductal Tubulopapillary Neoplasm
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478081103213
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Targeted deep sequencing of cell-free DNA from body cavity fluids with malignant, suspicious, and benign cytology
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478915500443
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Molecular Profiling of Intraductal Tubulopapillary Neoplasm
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478915501405
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Next-Generation Sequencing for HER2 Status in Breast Cancer: Comparison with Immunohistochemistry and in situ Hybridization by 2018 Focused Update
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478915500217
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Indolent in situ High-Grade B-cell lymphoma with a MYC Translocation and Mutations Identified by Next Generation Sequencing
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478915501090
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Indolent in situ High-Grade B-cell lymphoma with a MYC Translocation and Mutations Identified by Next Generation Sequencing
NATURE PUBLISHING GROUP. 2019
View details for Web of Science ID 000478081102331
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Revisiting diagnostic criteria for myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis: Borderline cases without anemia exist.
International journal of laboratory hematology
2019
Abstract
INTRODUCTION: Myelodysplastic/myeloproliferative neoplasm with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T) is a rare disease in the 2016 revised World Health Organization (WHO) classification. Diagnostic criteria include the following: persistent thrombocytosis (>450*109 /L) with clustering of atypical megakaryocytes, refractory anemia, dyserythropoiesis with ring sideroblasts, and the presence of the spliceosome factor 3b subunit (SF3B1) mutation. It is unclear if anemia should be a required criterion for this diagnosis as cases which show all other features of MDS/MPN-RS-T but without anemia exist.METHODS: We searched for borderline cases of MDS/MPN-RS-T in which refractory anemia was absent at diagnosis in two major academic institutes.RESULTS: Three cases without anemia were identified. These cases all showed other classic morphologic and clinical features of MDS/MPN-RS-T, including thrombocytosis, atypical megakaryocytes with clustering, and characteristic SF3B1 and JAK2 V617F mutations.CONCLUSION: Given these findings, the requirement of refractory anemia as a diagnostic criterion for MDS/MPN-RS-T should be re-evaluated. Removal of refractory anemia as a diagnostic criterion would incorporate current borderline cases and extend the spectrum of this disorder.
View details for PubMedID 30811101
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Increased risk of lymphoid malignancy in patients with herpes zoster: a longitudinal follow-up study using a national cohort.
BMC cancer
2019; 19 (1): 1148
Abstract
The association between herpes zoster and the risk of lymphoid neoplasms in Asian populations has not yet been established. We performed a longitudinal follow-up study using a nationwide cohort to assess the risk of lymphoid neoplasms arising after herpes zoster infection in the adult Korean population.Data from participants ≥20 years of age who were registered in the Korean National Health Insurance Service-National Sample Cohort database between 2002 and 2013 were collected. We extracted the data of participants with herpes zoster (n = 59,495) as well as those of matched references at a ratio of 1:4 (n = 237,980) and investigated the subsequent occurrence of lymphoid neoplasms. A stratified Cox proportional hazards model was used to calculate unadjusted hazard ratios (HRs) as well as those adjusted for the Charlson comorbidity index score.The rate of lymphoid neoplasms was higher in the herpes zoster group (0.15% [90/59,495]) than in the reference group (0.08% [212/237,980], P < 0.001). The unadjusted and adjusted HRs of herpes zoster in patients with lymphoid neoplasms were 1.68 (95% confidence interval [CI] = 1.31-2.15) and 1.58 (95% CI = 1.23-2.02), respectively (P < 0.001 for both). On subgroup analyses according to age and sex, herpes zoster was associated with an increased risk of lymphoid neoplasms in all subgroups; the adjusted HRs were 1.53 (95% CI = 1.05-2.24) for patients < 60 years old, 1.58 (95% CI = 1.14-2.20) for patients ≥60 years old, 1.64 (95% CI = 1.16-2.31) for men, and 1.51 (95% CI = 1.06-2.16) for women (P < 0.05 for all). On subgroup analysis of lymphoid neoplasm subtypes, herpes zoster was associated with the risk of Hodgkin's disease (adjusted HR: 3.23 [95% CI = 1.17-8.93]) and multiple myeloma/malignant plasma cell neoplasms (adjusted HR: 2.17 [95% CI = 1.33-3.54]) (P < 0.05 for both).Herpes zoster is associated with lymphoid neoplasm development in the Korean population irrespective of age and sex. The risks of Hodgkin's disease and plasma cell neoplasms are significantly elevated in patients with herpes zoster.
View details for DOI 10.1186/s12885-019-6349-y
View details for PubMedID 31775678
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Morphologic, Immunophenotypic and Molecular Features of Hypermutation in Colorectal Carcinomas with Mutations in DNA Polymerase Ɛ (POLE).
Histopathology
2019
Abstract
Colorectal carcinomas (CRC) with mismatch repair (MMR) deficiency have increased tumor mutation burden and respond to immune checkpoint inhibitor therapy. The Cancer Genome Atlas identified hypermutated CRCs with somatic mutations in DNA polymerase ε (POLE) with mutation burdens exceeding that of MMR-deficient CRCs.To identify the morphologic, immunophenotypic and molecular features of POLE mutated CRCs, 63 consecutive MMR-intact CRCs were evaluated by Sanger sequencing for POLE exonuclease domain mutations in exons 9, 11, 13 and 14 and confirmed by next generation sequencing. Tumor immune microenvironment and immunoscores were assessed in POLE-mutated CRCs using immunohistochemistry to detect CD3+/CD8+ tumor-infiltrating lymphocytes and compared to 59 non-POLE mutated MMR-intact CRC, 10 non-POLE mutated MMR-deficient CRCs, and 223 normal colonic mucosa.4.8% CRC (4 MMR-intact primary and 1 MMR-intact metastasis) harbored POLE mutations in amino acid 286 in exon 9 (p.P286R) or exon 13 (p.V411L). POLE mutated CRCs arose in the transverse colon and rectum, were male-predominant, younger, and showed increased tumor-infiltrating lymphocytes and immune cells at the tumor-stromal interface. The patient with metastatic POLE mutated CRC was placed on PD-1 inhibitor treatment with marked and sustained response. These data indicate that POLE mutated CRCs have hypermutated phenotypes despite MMR-intact status, with mutation burdens higher than that in microsatellite unstable CRCs. Given the recent approval for treatment of microsatellite unstable cancer with immune checkpoint inhibitors, assessment of POLE status may help guide therapeutic decisions for hypermutated tumors with intact MMR that would otherwise be missed by routine testing.
View details for DOI 10.1111/his.13984
View details for PubMedID 31479159
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High-efficiency CRISPR induction of t(9;11) chromosomal translocations and acute leukemias in human blood stem cells.
Blood advances
2019; 3 (19): 2825–35
Abstract
Chromosomal rearrangements involving the mixed lineage leukemia (MLL) gene, also known as KMT2A, are often observed in human leukemias and are generally associated with a poor prognosis. To model these leukemias, we applied clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing to induce MLL chromosomal rearrangements in human hematopoietic stem and progenitor cells purified from umbilical cord blood. Electroporation of ribonucleoprotein complexes containing chemically modified synthetic single guide RNAs and purified Cas9 protein induced translocations between chromosomes 9 and 11 [t(9;11)] at an efficiency >1%. Transplantation of gene-edited cells into immune-compromised mice rapidly induced acute leukemias of different lineages and often with multiclonal origins dictated by the duration of in vitro culture prior to transplantation. Breakpoint junction sequences served as biomarkers to monitor clonal selection and progression in culture and in vivo. High-dimensional cell surface and intracellular protein analysis by mass cytometry (CyTOF) revealed that gene-edited leukemias recapitulated disease-specific protein expression observed in human patients and showed that MLL-rearranged (MLLr) mixed phenotype acute leukemias (MPALs) were more similar to acute myeloid leukemias (AMLs) than to acute lymphoblastic leukemias (ALLs). Therefore, highly efficient generation of MLL chromosomal translocations in primary human blood stem cells using CRISPR/Cas9 reliably models human acute MLLr leukemia and provides an experimental platform for basic and translational studies of leukemia biology and therapeutics.
View details for DOI 10.1182/bloodadvances.2019000450
View details for PubMedID 31582391
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Implementation of Whole-Blood Impedance Aggregometry for Heparin-Induced Thrombocytopenia Functional Assay and Case Discussion.
American journal of clinical pathology
2019; 152 (1): 50–58
Abstract
The diagnosis of heparin-induced thrombocytopenia (HIT) ideally requires a functional assay to confirm. 14C-serotonin release assay (SRA) as "gold standard" is technically challenging and unsuitable for routine use. We conducted a study to assess the performance of whole-blood impedance aggregometry (WBIA) as a simple and rapid HIT functional assay.Platelet factor 4 (PF4)/immunoglobulin G (IgG) antibody, WBIA, and SRA were tested on 70 patients suspected of having HIT. Patients with a 4Ts score of 4 or more, positive PF4/IgG, and positive SRA were considered HIT positive; others were designated HIT negative.WBIA had 85.7% (6/7) sensitivity and 98.4% (61/62) specificity, which were not statistically different compared with SRA. Sixty-two of 70 patients had concordant results (five positive and 57 negative) by both WBIA and SRA. Eight discordant cases revealed the importance of recognizing donor effect, interferences, and the presence of heparin-independent or non-heparin-dependent antibodies in functional assays.Implementation of WBIA could facilitate timely diagnosis and management of HIT.
View details for DOI 10.1093/ajcp/aqz013
View details for PubMedID 31165165
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Molecular profiling of clear cell adenocarcinoma of the urinary tract.
Virchows Archiv : an international journal of pathology
2019
Abstract
Clear cell adenocarcinoma (CCA) of the urinary tract is a rare type of malignancy whose molecular profiles remain undefined. Here we reported an integrated clinicopathologic and molecular profiling analysis of four cases of clear cell adenocarcinoma arising in the urethra or the bladder. Utilizing a clinically validated 130-gene exon-sequencing assay, we identified recurrent pathogenic PIK3CA (p. E545K) and KRAS (p.G12D) variants in three of four (75%) of the cases. In addition, an APC variant (P.S2310X), a TP53 variant (p.R273C), and a MYC amplification event were identified. The only CCA case without either PIK3CA or KRAS variants has a distinct pathogenesis through BK virus, demonstrated by positive BK virus PCR and SV40 immunohistochemistry. The novel finding of recurrent variants in the PI3K/AKT/mTOR pathway provides not only insights into oncogenesis but also potential clinical therapeutic targets for patients with clear cell adenocarcinoma of the urinary tract.
View details for DOI 10.1007/s00428-019-02634-5
View details for PubMedID 31372739
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Blood transcriptome and clonal T cell correlates of response and nonresponse to eltrombopag therapy in a cohort of patients with chronic immune thrombocytopenia.
Haematologica
2019
View details for DOI 10.3324/haematol.2019.226688
View details for PubMedID 31296576
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Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue.
The Journal of molecular diagnostics : JMD
2018
Abstract
The clinical management and therapy of many solid tumor malignancies is dependent on detection of medically actionable or diagnostically relevant genetic variation. However, a principal challenge for genetic assays from tumors is the fragmented and chemically damaged state of DNA in formalin-fixed, paraffin-embedded (FFPE) samples. From highly fragmented DNA and RNA there is no current technology for generating long-range DNA sequence data as is required to detect genomic structural variation or long-range genotype phasing. We have developed a high-throughput chromosome conformation capture approach for FFPE samples that we call "Fix-C", which is similar in concept to Hi-C. Fix-C enables structural variation detection from archival FFPE samples. This method was applied to 15 clinical adenocarcinoma and sarcoma positive control specimens spanning a broad range of tumor purities. In this panel, Fix-C analysis achieves a 90% concordance rate with FISH assays - the current clinical gold standard. Additionally, novel structural variation undetected by other methods could be identified and long-range chromatin configuration information recovered from these FFPE samples harboring highly degraded DNA. This powerful approach will enable detailed resolution of global genome rearrangement events during cancer progression from FFPE material and inform the development of targeted molecular diagnostic assays for patient care.
View details for PubMedID 30605765
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Clinical Implementation of Mutational Signature Analysis
ELSEVIER SCIENCE INC. 2018: 975
View details for Web of Science ID 000448637200267
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Tumor Molecular Profiling Aids in Determining Tissue of Origin and Therapy for Metastatic Adenocarcinoma in a Patient With Multiple Primary Malignancies.
JCO precision oncology
2018; 2: 1-4
View details for DOI 10.1200/PO.18.00177
View details for PubMedID 35135146
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Tumor Molecular Profiling Aids in Determining Tissue of Origin and Therapy for Metastatic Adenocarcinoma in a Patient With Multiple Primary Malignancies
JCO PRECISION ONCOLOGY
2018; 2
View details for DOI 10.1200/PO.18.00177
View details for Web of Science ID 000462187500001
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GENOMIC LANDSCAPE OF NON-DRIVER MUTATIONS IN MYELOPROLIFERATIVE NEOPLASMS: THE STANFORD EXPERIENCE
WILEY. 2018: 122
View details for Web of Science ID 000444677800226
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PLATELET TRANSCRIPTOMIC SIGNATURES IN MYELOPROLIFERATIVE NEOPLASMS
WILEY. 2018: E34
View details for Web of Science ID 000446055700086
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CASE REPORT: MONOCLONAL IGM & LAMBDA; COAGULATION INHIBITOR WITH PHOSPHATIDYLSERINE SPECIFICITY INTERFERING WITH PLASMA, BUT NOT WHOLE-BLOOD BASED COAGULATION TESTING
WILEY. 2018: E30
View details for Web of Science ID 000446055700078
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Single-cell analysis of mutational heterogeneity in acute myeloid leukemia tumors with high-throughput droplet microfluidics
AMER ASSOC CANCER RESEARCH. 2018
View details for DOI 10.1158/1538-7445.AM2018-5348
View details for Web of Science ID 000468819504334
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Structural Variation Detection by Proximity Ligation from FFPE Tumor Tissue
ELSEVIER SCIENCE INC. 2018: S8
View details for Web of Science ID 000568301800015
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MLL leukemia induction by t(9;11) chromosomal translocation in human hematopoietic stem cells using genome editing
BLOOD ADVANCES
2018; 2 (8): 832–45
Abstract
Genome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks. However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development. Here, we used transcription activator-like effector nucleases to generate t(9;11) chromosomal translocations encoding MLL-AF9 and reciprocal AF9-MLL fusion products in CD34+ human cord blood cells. Selected cytokine combinations enabled monoclonal outgrowth and immortalization of initially rare translocated cells, which were distinguished by elevated MLL target gene expression, high surface CD9 expression, and increased colony-forming ability. Subsequent transplantation into immune-compromised mice induced myeloid leukemias within 48 weeks, whose pathologic and molecular features extensively overlap with de novo patient MLL-rearranged leukemias. No secondary pathogenic mutations were revealed by targeted exome sequencing and whole genome RNA-sequencing analyses, suggesting the genetic sufficiency of t(9;11) translocation for leukemia development from human HSPCs. Thus, genome editing enables modeling of human acute MLL-rearranged leukemia in vivo, reflecting the genetic simplicity of this disease, and provides an experimental platform for biological and disease-modeling applications.
View details for PubMedID 29650777
View details for PubMedCentralID PMC5916000
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Coexistence of BRAF V600E and TERT Promoter Mutations in Low-grade Serous Carcinoma of Ovary Recurring as Carcinosarcoma in a Lymph Node: Report of a Case.
International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists
2018
Abstract
Low-grade serous carcinomas only rarely coexist with or progress to high-grade tumors. We present a case of low-grade serous carcinoma with transformation to carcinosarcoma on recurrence in the lymph node. Identical BRAF V600E and telomerase reverse transcriptase promoter mutations were identified in both the original and recurrent tumor. Given that telomerase reverse transcriptase promotor mutations are thought to play a role in progression of other tumor types, the function of telomerase reverse transcriptase mutations in BRAF mutated low-grade serous carcinoma deserves investigation.
View details for PubMedID 29620581
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Next-generation sequencing of idiopathic multicentric and unicentric Castleman disease and follicular dendritic cell sarcomas
BLOOD ADVANCES
2018; 2 (5): 481–91
Abstract
Castleman disease (CD) is a rare lymphoproliferative disorder subclassified as unicentric CD (UCD) or multicentric CD (MCD) based on clinical features and the distribution of enlarged lymph nodes with characteristic histopathology. MCD can be further subtyped based on human herpes virus 8 (HHV8) infection into HHV8-associated MCD, HHV8-/idiopathic MCD (iMCD), and polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin change (POEMS)-associated MCD. In a subset of cases of UCD, an associated follicular dendritic cell sarcoma (FDCS) may be seen. Although numerous reports of the clinical and histologic features of UCD, MCD, and FDCS exist, an understanding of the genetic and epigenetic landscape of these rare diseases is lacking. Given this paucity of knowledge, we analyzed 15 cases of UCD and 3 cases of iMCD by targeted next-generation sequencing (NGS; 405 genes) and 3 cases of FDCS associated with UCD hyaline vascular variant (UCD-HVV) by whole-exome sequencing. Common amplifications of ETS1, PTPN6, and TGFBR2 were seen in 1 iMCD and 1 UCD case; the iMCD case also had a somatic DNMT3A L295Q mutation. This iMCD patient also showed clinicopathologic features consistent with a specific subtype known as Castleman-Kojima disease (thrombocytopenia, anasarca, fever, reticulin fibrosis, and organomegaly [TAFRO] clinical subtype). Additionally, 1 case of UCD-HVV showed amplification of the cluster of histone genes on chromosome 6p. FDCS associated with UCD-HVV showed mutations and copy number changes in known oncogenes, tumor suppressors, and chromatin structural-remodeling proteins.
View details for PubMedID 29496669
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The Significance of Dim Cytoplasmic CD3 Expression in Acute Myeloid Leukemia: A Long-Term Retrospective Study Identifies an Association with Acute Promyelocytic Leukemia with FLT3-ITD Mutations
NATURE PUBLISHING GROUP. 2018: 529
View details for Web of Science ID 000429308603354
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A whole exome sequencing analysis of diffuse large B-cell lymphoma arising from topologically adjacent follicular lymphoma reveals an intimate and distant relationship
NATURE PUBLISHING GROUP. 2018: 533
View details for Web of Science ID 000459341002362
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The Significance of Dim Cytoplasmic CD3 Expression in Acute Myeloid Leukemia: A Long-Term Retrospective Study Identifies an Association with Acute Promyelocytic Leukemia with FLT3-ITD Mutations
NATURE PUBLISHING GROUP. 2018: 529
View details for Web of Science ID 000459341002354
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Molecular Characterization of Aggressive Estrogen Receptor Positive Breast Cancer Resistant to Palbociclib Therapy
NATURE PUBLISHING GROUP. 2018: 703
View details for Web of Science ID 000459341003278
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Detection of Large Chromosomal Abnormalities in Tumors through Analysis of Off-Target Next-Generation Sequencing (NGS) Read Data
NATURE PUBLISHING GROUP. 2018: 804
View details for Web of Science ID 000459341004013
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Validation and Application of Predicted Tumor Mutational Burden (pTMB) Using a 130-Gene Sequencing Panel in Lung Adenocarcinoma
NATURE PUBLISHING GROUP. 2018: 758–59
View details for Web of Science ID 000459341003440
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Molecular Characterization of Aggressive Estrogen Receptor Positive Breast Cancer Resistant to Palbociclib Therapy
NATURE PUBLISHING GROUP. 2018: 703
View details for Web of Science ID 000429308604325
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Validation and Application of Predicted Tumor Mutational Burden (pTMB) Using a 130-Gene Sequencing Panel in Lung Adenocarcinoma
NATURE PUBLISHING GROUP. 2018: 758–59
View details for Web of Science ID 000429308604486
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A whole exome sequencing analysis of diffuse large B-cell lymphoma arising from topologically adjacent follicular lymphoma reveals an intimate and distant relationship
NATURE PUBLISHING GROUP. 2018: 533
View details for Web of Science ID 000429308603362
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Detection of Large Chromosomal Abnormalities in Tumors through Analysis of Off-Target Next-Generation Sequencing (NGS) Read Data
NATURE PUBLISHING GROUP. 2018: 804
View details for Web of Science ID 000429308605111
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Detection of Clonal TRG and TRB Gene Rearrangements Using Next Generation Sequencing
ELSEVIER SCIENCE INC. 2017: 1055
View details for Web of Science ID 000414275900475
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Clinical Validation and Implementation of a Targeted Sequencing Panel for Myeloid Neoplasms
ELSEVIER SCIENCE INC. 2017: 958
View details for Web of Science ID 000414275900079
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Molecular and Clinicopathologic Features Associated with PD-L1 Expression in Lung Adenocarcinoma
ELSEVIER SCIENCE INC. 2017: 1009–10
View details for Web of Science ID 000414275900290
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in silico Long-Read Sequencing from FFPE Solid Tumor Tissue for Structural Variation Detection and Phasing in Archival Specimens
ELSEVIER SCIENCE INC. 2017: 1034–35
View details for Web of Science ID 000414275900390
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A novel TRIP11-FLT3 fusion in a patient with a myeloid/lymphoid neoplasm with eosinophilia
CANCER GENETICS
2017; 216: 10–15
Abstract
FLT3 fusions are associated with myeloid and lymphoid neoplasms with eosinophilia. We describe a patient presenting with clinicopathologic features of both chronic eosinophilic leukemia, not otherwise specified (CEL, NOS) and systemic mastocytosis (SM). The bone marrow demonstrated a myeloproliferative neoplasm with eosinophilia and aggregates of atypical mast cells. Cytogenetic analysis revealed a t(13;14)(q12;q32), which was subsequently molecularly characterized as a novel TRIP11-FLT3 rearrangement. A KIT D816V mutation was also identified. The patient rapidly transformed to T-lymphoblastic leukemia/lymphoma and expired shortly after diagnosis. This is the fifth FLT3 fusion gene described in the literature; the presence of both myeloid and lymphoid neoplasms implicates involvement of an early hematopoietic progenitor by rearranged FLT3. We suggest that leukemias and lymphomas with FLT3 fusion genes exhibit similar clinicopathologic features to, and should be included in, the WHO category of "Myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB, or FGFR1, or with PCM1-JAK2."
View details for PubMedID 29025582
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IDH2 Mutation in a Patient with Metastatic Colon Cancer
NEW ENGLAND JOURNAL OF MEDICINE
2017; 376 (20): 1991-1992
View details for DOI 10.1056/NEJMc1701072
View details for PubMedID 28514606
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IMPLEMENTATION OF WHOLEBLOOD IMPEDANCE AGGREGOMETRYFOR HEPARIN-INDUCED THROMBOCYTOPENIAFUNCTIONAL ASSAY
WILEY. 2017: 50
View details for Web of Science ID 000402838000083
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IMPROVING CLINICAL DECISION MAKING FOR HEPARINIZED PATIENTS WITH DISCORDANT ANTI-FACTOR XA ACTIVITY AND ACTIVATED PARTIAL THROMBOPLASTIN TIME.
WILEY. 2017: 40
View details for Web of Science ID 000402838000064
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NOVEL MARKERS FOR THE DIAGNOSIS OF ANTIPHOSPHOLIPID SYNDROME: ANTIBODIES AGAINST PHOSPHATIDYLSERINE/PROTHROMBIN COMPLEX
WILEY. 2017: 50
View details for Web of Science ID 000402838000082
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Identification of a Novel Somatic Mutation Leading to Allele Dropout for EGFR L858R Genotyping in Non-Small Cell Lung Cancer.
Molecular diagnosis & therapy
2017
Abstract
While PCR-based genotyping methods abound in molecular testing for lung cancer therapy, these approaches may not provide the robust sensitivity to detect accurate genotypes in a variable cancer genomic background.Here, we describe a study of a clinical tumor specimen containing a novel somatic single nucleotide variant that caused allele drop-out in EGFR L858R genotyping, resulting in a false-negative interpretation and impacting patient clinical management.We demonstrate that a subsequent unbiased next-generation sequencing approach correctly identified the driver mutation, and therefore may be more reliable for somatic variant detection.These findings magnify the potential pitfalls of PCR amplification-based approaches and stress the importance of unbiased and sensitive molecular testing strategies for therapeutic marker detection as molecular testing becomes the standard for determining clinical management of cancer patients.
View details for DOI 10.1007/s40291-017-0275-y
View details for PubMedID 28357677
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Repertoire of Murine T Cells in Target Tissues of MHC-Matched and -Mismatched Graft-Versus-Host Disease
ELSEVIER SCIENCE INC. 2017: S307–S308
View details for DOI 10.1016/j.bbmt.2016.12.230
View details for Web of Science ID 000540635000422
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The Significance of CD56 Expression and the RAM Immunophenotype, a Recurrent Immunophenotype Seen in Children, in Adult Acute Myeloid Leukemia
NATURE PUBLISHING GROUP. 2017: 358A–359A
View details for Web of Science ID 000393724401713
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Detection of Mutations in DNA Polymerase epsilon (POLE) in Colorectal Carcinoma with Intact Mismatch Repair Proteins: Immunotherapeutic Implications of Ultramutation
NATURE PUBLISHING GROUP. 2017: 173A
View details for Web of Science ID 000394467300687
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Detection of Mutations in DNA Polymerase epsilon (POLE) in Colorectal Carcinoma with Intact Mismatch Repair Proteins: Immunotherapeutic Implications of Ultramutation
NATURE PUBLISHING GROUP. 2017: 173A
View details for Web of Science ID 000393724400686
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A Study of Disseminated Intravascular Coagulation in Acute Leukemia Reveals Markedly Elevated D-Dimer Levels Are a Sensitive Indicator of Acute Promyelocytic Leukemia
NATURE PUBLISHING GROUP. 2017: 367A
View details for Web of Science ID 000394467302050
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A Study of Disseminated Intravascular Coagulation in Acute Leukemia Reveals Markedly Elevated D-Dimer Levels Are a Sensitive Indicator of Acute Promyelocytic Leukemia
NATURE PUBLISHING GROUP. 2017: 367A
View details for Web of Science ID 000393724401747
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A Retrospective Study of 305 Cases of Angioimmunoblastic T-Cell Lymphoma with Emphasis on Rare Lymphoplasmacytic and Plasma Cell Proliferations
NATURE PUBLISHING GROUP. 2017: 367A–368A
View details for Web of Science ID 000394467302051
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A Retrospective Study of 305 Cases of Angioimmunoblastic T-Cell Lymphoma with Emphasis on Rare Lymphoplasmacytic and Plasma Cell Proliferations
NATURE PUBLISHING GROUP. 2017: 367A–368A
View details for Web of Science ID 000393724401748
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The Significance of CD56 Expression and the RAM Immunophenotype, a Recurrent Immunophenotype Seen in Children, in Adult Acute Myeloid Leukemia
NATURE PUBLISHING GROUP. 2017: 358A–359A
View details for Web of Science ID 000394467302016
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Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use
JOURNAL OF MOLECULAR DIAGNOSTICS
2017; 19 (1): 72-83
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10(-3). A single library could identify >93% of the clones with frequency ≥10(-3) in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10(-3) and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
View details for DOI 10.1016/j.jmoldx.2016.07.009
View details for Web of Science ID 000390983100008
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A study of disseminated intravascular coagulation in acute leukemia reveals markedly elevated D-dimer levels are a sensitive indicator of acute promyelocytic leukemia.
International journal of laboratory hematology
2017
Abstract
While the presence of disseminated intravascular coagulation (DIC) has been implicated in worse clinical outcome in acute leukemia, the relationship between different subtypes of acute leukemia and the clinicopathologic features of DIC has not been systematically well studied.In this study, we retrospectively reviewed 149 cases of newly diagnosed acute leukemia and assessed the utility of evaluating red blood cell morphologic features, and coagulation parameters in determining the presence of DIC as well as differentiating subtypes of acute leukemia.Review of our cohort demonstrates a novel finding, that elevated D-dimer concentrations ≥19 000 ng/mL fibrinogen equivalent units (FEU) are a sensitive diagnostic indicator of acute promyelocytic leukemia (APL) with moderate specificity, sensitivity 96%, specificity 92% in acute leukemia subtyping. Similar to other studies, APL showed an increased incidence of DIC (P < 0.01) compared to other subtypes of acute leukemia. Surprisingly, the presence of schistocytes on the peripheral blood smear was not a statistically significant indicator of DIC, sensitivity of 36% and specificity of 89%. Finally, the presence of DIC was not a significant indicator of poorer prognosis amongst all patients with AML.Overall we identify elevated D-dimer concentrations ≥19 000 ng/mL FEU are a sensitive indicator of acute promyelocytic leukemia (APL), with a sensitivity of 96% and specificity of 92% in the subtyping of acute leukemias, and that the presence of schistocytes in peripheral blood smears is not a diagnostically sensitive screening test for DIC with a sensitivity of 36%.
View details for PubMedID 28422420
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Comprehensive Genomic Profiling of Malignant Effusions in Patients with Metastatic Lung Adenocarcinoma.
The Journal of molecular diagnostics : JMD
2017
Abstract
Cytology samples are being increasingly utilized for comprehensive molecular testing. Although fine-needle aspirates are adequate substrates for high-throughput sequencing, the suitability of malignant body fluids remains largely unexplored. Herein, we investigated the adequacy and utility of performing targeted next-generation sequencing (NGS) on malignant effusions from patients with metastatic lung adenocarcinoma. Thirty-two effusion samples that were submitted for hybrid capture-based NGS using a clinically validated solid tumor genotyping panel were examined. All cases showed ≥5% tumor cellularity; however, 28 (88%) provided sufficient DNA for NGS (≥1 ng/μL). The sequencing reads showed satisfactory quality control statistics, and the variant allele frequencies were correlated with tumor cellularity. Furthermore, pathogenic or likely pathogenic genomic alterations were identified in 26/28 samples (93%), whereas clinically actionable alterations were present in 18 (64%). Notably, nine patients had additional molecular testing performed on preceding/subsequent biopsies, and the results across multiple samples were compared. In two patients, the NGS-based fluid analysis identified clinically actionable alterations that were not detected by other hotspot testing. In four patients treated with tyrosine kinase inhibitors, malignant fluid sequencing confirmed driver alterations from prior testing and revealed new resistance mechanisms. Hence, given adequate DNA input and tumor cellularity, comprehensive genomic profiling of malignant effusions may be used to establish mutational status at diagnosis and inform treatment resistance during targeted therapy.
View details for PubMedID 29269277
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Identification of a Novel MPL Loss of Function Mutation in a Patient with Cyclic Thrombocytopenia and Characterization of This Syndrome
AMER SOC HEMATOLOGY. 2016
View details for Web of Science ID 000394452300114
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Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use.
journal of molecular diagnostics
2016
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10(-3). A single library could identify >93% of the clones with frequency ≥10(-3) in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10(-3) and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
View details for DOI 10.1016/j.jmoldx.2016.07.009
View details for PubMedID 27815002
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Targeted Next-Generation Sequencing-Based Mutation Profiling of Fine Needle Aspiration Samples: Utility and Technical Adequacy
ELSEVIER SCIENCE INC. 2016: 999
View details for Web of Science ID 000387201000275
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Detection of POLE Exonuclease Domain Mutations by Targeted Genomic Profiling in Hypermutated, Microsatellite Stable Colorectal Carcinoma
ELSEVIER SCIENCE INC. 2016: 1006
View details for Web of Science ID 000387201000301
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Development of a Cloud-Based Comprehensive Cancer Transcriptome Profiling Pipeline for Clinical Diagnostics
ELSEVIER SCIENCE INC. 2016: 989
View details for Web of Science ID 000387201000232
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Value of NGS-Based T-Cell Clonality Analysis in Cases of Mycosis Fungoides with Discrepant Fragment Size-Based Tissue and Blood Results
ELSEVIER SCIENCE INC. 2016: 951
View details for Web of Science ID 000387201000079
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A study of the mutational landscape of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma.
Modern pathology
2016; 29 (10): 1212-1220
Abstract
Pediatric-type follicular lymphoma and pediatric marginal zone lymphoma are two of the rarest B-cell lymphomas. These lymphomas occur predominantly in the pediatric population and show features distinct from their more common counterparts in adults: adult-type follicular lymphoma and adult-type nodal marginal zone lymphoma. Here we report a detailed whole-exome deep sequencing analysis of a cohort of pediatric-type follicular lymphomas and pediatric marginal zone lymphomas. This analysis revealed a recurrent somatic variant encoding p.Lys66Arg in the transcription factor interferon regulatory factor 8 (IRF8) in 3 of 6 cases (50%) of pediatric-type follicular lymphoma. This specific point mutation was not detected in pediatric marginal zone lymphoma or in adult-type follicular lymphoma. Additional somatic point mutations in pediatric-type follicular lymphoma were observed in genes involved in transcription, intracellular signaling, and cell proliferation. In pediatric marginal zone lymphoma, no recurrent mutation was identified; however, somatic point mutations were observed in genes involved in cellular adhesion, cytokine regulatory elements, and cellular proliferation. A somatic variant in AMOTL1, a recurrently mutated gene in splenic marginal zone lymphoma, was also identified in a case of pediatric marginal zone lymphoma. The overall non-synonymous mutational burden was low in both pediatric-type follicular lymphoma and pediatric marginal zone lymphoma (4.6 mutations per exome). Altogether, these findings support a distinctive genetic basis for pediatric-type follicular lymphoma and pediatric marginal zone lymphoma when compared with adult subtypes and to one another. Moreover, identification of a recurrent point mutation in IRF8 provides insight into a potential driver mutation in the pathogenesis of pediatric-type follicular lymphoma with implications for novel diagnostic or therapeutic strategies.Modern Pathology advance online publication, 24 June 2016; doi:10.1038/modpathol.2016.102.
View details for DOI 10.1038/modpathol.2016.102
View details for PubMedID 27338637
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Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans.
Molecular genetics & genomic medicine
2016; 4 (5): 513-520
Abstract
African Americans have a higher incidence of venous thromboembolism (VTE) than European descent individuals. However, the typical genetic risk factors in populations of European descent are nearly absent in African Americans, and population-specific genetic factors influencing the higher VTE rate are not well characterized.We performed a candidate gene analysis on an exome-sequenced African American family with recurrent VTE and identified a variant in Protein S (PROS1) V510M (rs138925964). We assessed the population impact of PROS1 V510M using a multicenter African American cohort of 306 cases with VTE compared to 370 controls. Additionally, we compared our case cohort to a background population cohort of 2203 African Americans in the NHLBI GO Exome Sequencing Project (ESP).In the African American family with recurrent VTE, we found prior laboratories for our cases indicating low free Protein S levels, providing functional support for PROS1 V510M as the causative mutation. Additionally, this variant was significantly enriched in the VTE cases of our multicenter case-control study (Fisher's Exact Test, P = 0.0041, OR = 4.62, 95% CI: 1.51-15.20; allele frequencies - cases: 2.45%, controls: 0.54%). Similarly, PROS1 V510M was also enriched in our VTE case cohort compared to African Americans in the ESP cohort (Fisher's Exact Test, P = 0.010, OR = 2.28, 95% CI: 1.26-4.10).We found a variant, PROS1 V510M, in an African American family with VTE and clinical laboratory abnormalities in Protein S. Additionally, we found that this variant conferred increased risk of VTE in a case-control study of African Americans. In the ESP cohort, the variant is nearly absent in ESP European descent subjects (n = 3, allele frequency: 0.03%). Additionally, in 1000 Genomes Phase 3 data, the variant only appears in African descent populations. Thus, PROS1 V510M is a population-specific genetic risk factor for VTE in African Americans.
View details for DOI 10.1002/mgg3.226
View details for PubMedID 27652279
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Gender and duration of disease differentiate responses to rituximab-dexamethasone therapy in adults with immune thrombocytopenia
AMERICAN JOURNAL OF HEMATOLOGY
2016; 91 (9): 907–11
Abstract
Adults often develop chronic immune thrombocytopenia (ITP) for which treatment order is uncertain. Rituximab and three cycles of dexamethasone (4R + 3Dex) improve treatment responses and short-term disease control but long-term outcome is not known. In adults with ITP treated with 4R + 3D, we sought long-term outcome and associated prognostic variables. Forty-nine adults treated at Weill-Cornell received 4R + 3Dex. Their clinical characteristics were reviewed. Duration was median time to treatment failure; Kaplan-Meier estimates were developed. Vbeta Tcell receptor (VBTCR) repertoire was obtained after treatment in 36 patients. Patients were adults with ITP 18-64 years old, median age 37. The 27 females were twice as likely to have an ongoing response to 4R + 3Dex (44.1%) as males (19.6%; P = 0.009). For ITP duration <12 months, 52.7% of patients had continuing responses to 4R + 3Dex compared to 15.3% of patients with diagnosis >12 months (P = 0.02). Females with ITP duration of <12 months had continuing responses in 78.6%, compared to males with <12 months duration of ITP (21.2%). For patients with disease duration <12 months, 67% of females had continuing responses, compared to 31% of males (P = 0.004). Post-treatment polyclonal VBTCR was seen in 9/10 continuing responders (six female, three male) but only 13/26 relapsers/nonresponders (P = 0.068). Durable remissions after treatment with 4R + 3Dex were more frequent in female patients with <12 months of ITP duration and those with polyclonal VBTCR after treatment, emphasizing the roles of duration of disease, gender and T cells in chronic ITP. Differences in pathophysiology of ITP by gender and by duration of ITP require further study. Am. J. Hematol. 91:907-911, 2016. © 2016 Wiley Periodicals, Inc.
View details for PubMedID 27220625
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DESCRIPTION AND LABORATORY VALIDATION OF A NOVEL ALGORITHM FOR CALCULATION OF TEG PLATELET MAPPING (TM) WHEN ATYPICAL ACTIVATOR F TRACING" OCCURS
WILEY-BLACKWELL. 2016: E428
View details for Web of Science ID 000385237100145
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Germ line variants predispose to both JAK2 V617F clonal hematopoiesis and myeloproliferative neoplasms.
Blood
2016; 128 (8): 1121-1128
Abstract
We conducted a genome-wide association study (GWAS) to identify novel predisposition alleles associated with Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs) and JAK2 V617F clonal hematopoiesis in the general population. We recruited a web-based cohort of 726 individuals with polycythemia vera, essential thrombocythemia, and myelofibrosis and 252 637 population controls unselected for hematologic phenotypes. Using a single-nucleotide polymorphism (SNP) array platform with custom probes for the JAK2 V617F mutation (V617F), we identified 497 individuals (0.2%) among the population controls who were V617F carriers. We performed a combined GWAS of the MPN cases plus V617F carriers in the control population (n = 1223) vs the remaining controls who were noncarriers for V617F (n = 252 140). For these MPN cases plus V617F carriers, we replicated the germ line JAK2 46/1 haplotype (rs59384377: odds ratio [OR] = 2.4, P = 6.6 × 10(-89)), previously associated with V617F-positive MPN. We also identified genome-wide significant associations in the TERT gene (rs7705526: OR = 1.8, P = 1.1 × 10(-32)), in SH2B3 (rs7310615: OR = 1.4, P = 3.1 × 10(-14)), and upstream of TET2 (rs1548483: OR = 2.0, P = 2.0 × 10(-9)). These associations were confirmed in a separate replication cohort of 446 V617F carriers vs 169 021 noncarriers. In a joint analysis of the combined GWAS and replication results, we identified additional genome-wide significant predisposition alleles associated with CHEK2, ATM, PINT, and GFI1B All SNP ORs were similar for MPN patients and controls who were V617F carriers. These data indicate that the same germ line variants endow individuals with a predisposition not only to MPN, but also to JAK2 V617F clonal hematopoiesis, a more common phenomenon that may foreshadow the development of an overt neoplasm.
View details for DOI 10.1182/blood-2015-06-652941
View details for PubMedID 27365426
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ROS: novel regulators of thrombopoiesis
BLOOD
2016; 128 (5): 613-?
View details for DOI 10.1182/blood-2016-06-718544
View details for Web of Science ID 000383843000004
View details for PubMedID 27492312
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Prozone Effect in the Diagnosis of Lupus Anticoagulant for the Lupus Anticoagulant-Hypoprothrombinemia Syndrome.
American journal of clinical pathology
2016; 146 (2): 262-267
Abstract
The main clinical sequela of a lupus anticoagulant is increased thrombosis risk. However, bleeding due to lupus anticoagulant-hypoprothrombinemia syndrome is a rare but well-described manifestation of antiphospholipid syndrome. The association of acute acquired hypoprothrombinemia is caused by a lupus anticoagulant's specificity to prothrombin, which results in clearance of prothrombin and bleeding due to hypoprothrombinemia (usually <10% of normal). Severe life-threatening bleeding is most frequently reported in children with systemic lupus erythematosus or in healthy children after viral infection. In such cases, steroid therapy is usually effective in controlling the bleeding problems and improving prothrombin levels.We report one pediatric patient with a lupus anticoagulant who had acute hemorrhagic diathesis.The diagnosis in this case was complicated by the presence of a prozone effect in lupus anticoagulant testing. The prozone effect (also known as hook effect) refers to situations where very high concentrations of antibody mask detection, typically in antigen-antibody reactions, which depend on visualization of agglutination. Decreasing the antibody/antigen ratio results in detectable antigen-antibody complexes.We report for the first time a variation on this theme in a patient with a lupus anticoagulant-type antiphospholipid antibody and hypoprothrombinemia, which corrected with immunosuppression and restoration of normal prothrombin levels.
View details for DOI 10.1093/ajcp/aqw106
View details for PubMedID 27473743
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Template for Reporting Results of Monitoring Tests for Patients With Chronic Myelogenous Leukemia (BCR-ABL1(+)).
Archives of pathology & laboratory medicine
2016; 140 (7): 672-674
View details for DOI 10.5858/arpa.2015-0399-CP
View details for PubMedID 26653363
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Template for Reporting Results of Biomarker Testing of Specimens From Patients With Myeloproliferative Neoplasms.
Archives of pathology & laboratory medicine
2016; 140 (7): 675-677
View details for DOI 10.5858/arpa.2015-0400-CP
View details for PubMedID 26653364
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LABORATORY ADHERENCE TO ISTH GUIDELINES ON PLATELET AGGREGATION TESTING. INITIAL REVIEW OF RESULTS FROM AN INTERNATIONAL SURVEY.
WILEY-BLACKWELL. 2016: 74–75
View details for Web of Science ID 000383521500175
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Clinical activity of ponatinib in a patient with FGFR1-rearranged mixed-phenotype acute leukemia.
Leukemia
2016; 30 (4): 947-950
View details for DOI 10.1038/leu.2015.136
View details for PubMedID 26055304
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Measuring the Effect of Dipyridamole and Clopidogrel Using Thromboelastography/Platelet Mapping (R): Is There Evidence of a Meaningful Dose-Response Relationship in Children Supported with the Berlin Heart EXCOR Ventricular Assist Device?
ELSEVIER SCIENCE INC. 2016: S47
View details for DOI 10.1016/j.healun.2016.01.127
View details for Web of Science ID 000374718100104
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Isolated Follicles Enriched for Centroblasts and Lacking t(14;18)/BCL2 in Lymphoid Tissue: Diagnostic and Clinical Implications
PLOS ONE
2016; 11 (3)
Abstract
We sought to address the significance of isolated follicles that exhibit atypical morphologic features that may be mistaken for lymphoma in a background of reactive lymphoid tissue. Seven cases that demonstrated centroblast-predominant isolated follicles and absent BCL2 staining in otherwise-normal lymph nodes were studied. Four of seven cases showed clonal B-cell proliferations amid a polyclonal B cell background; all cases lacked the IGH-BCL2 translocation and BCL2 protein expression. Although three patients had invasive breast carcinoma at other sites, none were associated with systemic lymphoma up to 44 months after diagnosis. The immunoarchitectural features of these highly unusual cases raise the question of whether a predominance of centroblasts and/or absence of BCL2 expression could represent a precursor lesion or atypical reactive phenomenon. Differentiating such cases from follicular lymphoma or another mimic is critical, lest patients with indolent proliferations be exposed to unnecessarily aggressive treatment.
View details for DOI 10.1371/journal.pone.0151735
View details for Web of Science ID 000372582800093
View details for PubMedCentralID PMC4798531
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Clonal architecture of CXCR4 WHIM-like mutations in Waldenstrom Macroglobulinaemia
BRITISH JOURNAL OF HAEMATOLOGY
2016; 172 (5): 735-744
Abstract
CXCR4(WHIM) somatic mutations are distinctive to Waldenström Macroglobulinaemia (WM), and impact disease presentation and treatment outcome. The clonal architecture of CXCR4(WHIM) mutations remains to be delineated. We developed highly sensitive allele-specific polymerase chain reaction (AS-PCR) assays for detecting the most common CXCR4(WHIM) mutations (CXCR4(S338X C>A and C>G) ) in WM. The AS-PCR assays detected CXCR4(S338X) mutations in WM and IgM monoclonal gammopathy of unknown significance (MGUS) patients not revealed by Sanger sequencing. By combined AS-PCR and Sanger sequencing, CXCR4(WHIM) mutations were identified in 44/102 (43%), 21/62 (34%), 2/12 (17%) and 1/20 (5%) untreated WM, previously treated WM, IgM MGUS and marginal zone lymphoma patients, respectively, but no chronic lymphocytic leukaemia, multiple myeloma, non-IgM MGUS patients or healthy donors. Cancer cell fraction analysis in WM and IgM MGUS patients showed CXCR4(S338X) mutations were primarily subclonal, with highly variable clonal distribution (median 35·1%, range 1·2-97·5%). Combined AS-PCR and Sanger sequencing revealed multiple CXCR4(WHIM) mutations in many individual WM patients, including homozygous and compound heterozygous mutations validated by deep RNA sequencing. The findings show that CXCR4(WHIM) mutations are more common in WM than previously revealed, and are primarily subclonal, supporting their acquisition after MYD88(L265P) in WM oncogenesis. The presence of multiple CXCR4(WHIM) mutations within individual WM patients may be indicative of targeted CXCR4 genomic instability.
View details for DOI 10.1111/bjh.13897
View details for PubMedID 26659815
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Somatic Mutational Landscape of Inflammatory Bowel Disease-Associated Signet Ring Cell Colorectal Carcinoma
NATURE PUBLISHING GROUP. 2016: 456A
View details for Web of Science ID 000370302503280
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Comparative Study of Isocitrate Dehydrogenase 1 Mutations in Intraheptatic Cholangiocarcinoma by Immunohistochemistry and Pyrosequencing
NATURE PUBLISHING GROUP. 2016: 443A–444A
View details for Web of Science ID 000369270702496
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Somatic Mutational Landscape of Inflammatory Bowel Disease-Associated Signet Ring Cell Colorectal Carcinoma
NATURE PUBLISHING GROUP. 2016: 456A
View details for Web of Science ID 000369270702545
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Comparative Study of Isocitrate Dehydrogenase 1 Mutations in Intraheptatic Cholangiocarcinoma by Immunohistochemistry and Pyrosequencing
NATURE PUBLISHING GROUP. 2016: 443A–444A
View details for Web of Science ID 000370302503231
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Isolated Follicles Enriched for Centroblasts and Lacking t(14;18)/BCL2 in Lymphoid Tissue: Diagnostic and Clinical Implications.
PloS one
2016; 11 (3)
Abstract
We sought to address the significance of isolated follicles that exhibit atypical morphologic features that may be mistaken for lymphoma in a background of reactive lymphoid tissue. Seven cases that demonstrated centroblast-predominant isolated follicles and absent BCL2 staining in otherwise-normal lymph nodes were studied. Four of seven cases showed clonal B-cell proliferations amid a polyclonal B cell background; all cases lacked the IGH-BCL2 translocation and BCL2 protein expression. Although three patients had invasive breast carcinoma at other sites, none were associated with systemic lymphoma up to 44 months after diagnosis. The immunoarchitectural features of these highly unusual cases raise the question of whether a predominance of centroblasts and/or absence of BCL2 expression could represent a precursor lesion or atypical reactive phenomenon. Differentiating such cases from follicular lymphoma or another mimic is critical, lest patients with indolent proliferations be exposed to unnecessarily aggressive treatment.
View details for DOI 10.1371/journal.pone.0151735
View details for PubMedID 26991267
View details for PubMedCentralID PMC4798531
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Factor V Leiden
AMERICAN JOURNAL OF HEMATOLOGY
2016; 91 (1): 46–49
Abstract
Factor V Leiden (FVLeiden ) is a common hereditary thrombophilia that causes activated protein C (APC) resistance. This review describes many of the most fascinating features of FVLeiden , including background features, mechanisms of hypercoagulability, the founder mutation concept, the "FVLeiden paradox," synergistic interaction with other thrombotic risk factors, the intertwined relationship between FVLeiden and APC resistance testing, and other, uncommon mutations implicated in causing APC resistance. In addition, there are several conditions where laboratory tests for APC resistance and FVLeiden are or can be discrepant, including lupus anticoagulants, anticoagulants such as direct thrombin inhibitors (dabigatran, argatroban, and bivalirudin) and rivaroxaban, as well as pseudohomozygous, pseudo-wildtype, liver transplant, and bone marrow transplant patients. The laboratory test error rate for FVLeiden is also presented.
View details for PubMedID 26492443
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The Clonal Architecture of CXCR4mutations in Waldenstrom's Macroglobulinemia Shows Highly Variable Subclonal Distribution, and Multiple Mutations within Individual Patients Indicative of Targeted Genomic Instability
AMER SOC HEMATOLOGY. 2015
View details for Web of Science ID 000368019004286
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The VarScan2's SNVs-Near-Indel Filter: Is It Necessary?
ELSEVIER SCIENCE INC. 2015: 801
View details for Web of Science ID 000363830000216
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Next-Generation Sequencing for Detection of Clonal TRG Gene Rearrangements Shows Improved Specificity and Positive Predictive Value Compared to Fragment Analysis Using BIOMED-2 Primers and Capillary Electrophoresis
ELSEVIER SCIENCE INC. 2015: 770
View details for Web of Science ID 000363830000086
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Potential Pitfalls with TruSeq Amplicon: Cancer Panel Variant Detection
ELSEVIER SCIENCE INC. 2015: 852
View details for Web of Science ID 000363830000423
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IBRUTINIB IN PREVIOUSLY TREATED PATIENTS WITH WALDENSTROM'S MACROGLOBULINEMIA IS HIGHLY ACTIVE, PRODUCES DURABLE RESPONSES, AND IS IMPACTED BY MYD88 AND CXCR4 MUTATION STATUS
FERRATA STORTI FOUNDATION. 2015: 311
View details for Web of Science ID 000361204902289
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Next-generation sequencing of acute myeloid leukemia identifies the significance of TP53, U2AF1, ASXL1, and TET2 mutations
MODERN PATHOLOGY
2015; 28 (5): 706-714
Abstract
We assessed the frequency and clinicopathologic significance of 19 genes currently identified as significantly mutated in myeloid neoplasms, RUNX1, ASXL1, TET2, CEBPA, IDH1, IDH2, DNMT3A, FLT3, NPM1, TP53, NRAS, EZH2, CBL, U2AF1, SF3B1, SRSF2, JAK2, CSF3R, and SETBP1, across 93 cases of acute myeloid leukemia (AML) using capture target enrichment and next-generation sequencing. Of these cases, 79% showed at least one nonsynonymous mutation, and cases of AML with recurrent genetic abnormalities showed a lower frequency of mutations versus AML with myelodysplasia-related changes (P<0.001). Mutational analysis further demonstrated that TP53 mutations are associated with complex karyotype AML, whereas ASXL1 and U2AF1 mutations are associated with AML with myelodysplasia-related changes. Furthermore, U2AF1 mutations were specifically associated with trilineage morphologic dysplasia. Univariate analysis demonstrated that U2AF1 and TP53 mutations are associated with absence of clinical remission, poor overall survival (OS), and poor disease-free survival (DFS; P<0.0001), whereas TET2 and ASXL1 mutations are associated with poor OS (P<0.03). In multivariate analysis, U2AF1 and TP53 mutations retained independent prognostic significance in OS and DFS, respectively. Our results demonstrate unique relationships between mutations in AML, clinicopathologic prognosis, subtype categorization, and morphologic dysplasia.Modern Pathology advance online publication, 21 November 2014; doi:10.1038/modpathol.2014.160.
View details for DOI 10.1038/modpathol.2014.160
View details for Web of Science ID 000353774200010
View details for PubMedID 25412851
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Ibrutinib in Previously Treated Waldenstrom's Macroglobulinemia
NEW ENGLAND JOURNAL OF MEDICINE
2015; 372 (15): 1430-1440
Abstract
MYD88(L265P) and CXCR4(WHIM) mutations are highly prevalent in Waldenström's macroglobulinemia. MYD88(L265P) triggers tumor-cell growth through Bruton's tyrosine kinase, a target of ibrutinib. CXCR4(WHIM) mutations confer in vitro resistance to ibrutinib.We performed a prospective study of ibrutinib in 63 symptomatic patients with Waldenström's macroglobulinemia who had received at least one previous treatment, and we investigated the effect of MYD88 and CXCR4 mutations on outcomes. Ibrutinib at a daily dose of 420 mg was administered orally until disease progression or the development of unacceptable toxic effects.After the patients received ibrutinib, median serum IgM levels decreased from 3520 mg per deciliter to 880 mg per deciliter, median hemoglobin levels increased from 10.5 g per deciliter to 13.8 g per deciliter, and bone marrow involvement decreased from 60% to 25% (P<0.01 for all comparisons). The median time to at least a minor response was 4 weeks. The overall response rate was 90.5%, and the major response rate was 73.0%; these rates were highest among patients with MYD88(L265P)CXCR4(WT) (with WT indicating wild-type) (100% overall response rate and 91.2% major response rate), followed by patients with MYD88(L265P)CXCR4(WHIM) (85.7% and 61.9%, respectively) and patients with MYD88(WT)CXCR4(WT) (71.4% and 28.6%). The estimated 2-year progression-free and overall survival rates among all patients were 69.1% and 95.2%, respectively. Treatment-related toxic effects of grade 2 or higher included neutropenia (in 22% of the patients) and thrombocytopenia (in 14%), which were more common in heavily pretreated patients; postprocedural bleeding (in 3%); epistaxis associated with the use of fish-oil supplements (in 3%); and atrial fibrillation associated with a history of arrhythmia (5%).Ibrutinib was highly active, associated with durable responses, and safe in pretreated patients with Waldenström's macroglobulinemia. MYD88 and CXCR4 mutation status affected responses to this drug. (Funded by Pharmacyclics and others; ClinicalTrials.gov number, NCT01614821.).
View details for DOI 10.1056/NEJMoa1501548
View details for PubMedID 25853747
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Mast Cells in Systemic Mastocytosis Have Distinctly Brighter CD45 Expression by Flow Cytometry
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
2015; 143 (4): 527-534
Abstract
We sought to determine the significance of bright CD45 expression on mast cells in cases of systemic mastocytosis vs mast cells in bone marrows uninvolved by systemic mastocytosis and compare this CD45 expression with CD25 and CD2 expression on mast cells.Multiparameter flow cytometry was performed on 31 cases of systemic mastocytosis and 70 bone marrow cases that were not involved by systemic mastocytosis. Bright expression of CD45 was defined as more than 20% of CD117+ mast cells showing brighter CD45 expression than the average expression level of lymphocytes.Mast cells with bright CD45 expression were seen in 26 systemic mastocytosis cases and three bone marrows uninvolved by systemic mastocytosis (sensitivity, 84%; specificity, 96%). CD25 alone had a greater sensitivity (100%) but lower specificity (93%) compared with bright CD45 for identifying abnormal mast cells, while CD2 alone had lower sensitivity but higher specificity. To reach a specificity of 100%, CD25 together with bright CD45 on mast cells was the optimal combination to detect cases of systemic mastocytosis.A combination of bright CD45 and CD25 appears to specifically identify abnormal mast cells in cases of systemic mastocytosis. Further studies will be necessary to confirm these results.
View details for DOI 10.1309/AJCPZ3J4GEEYIRRA
View details for PubMedID 25780004
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Mast Cells in Systemic Mastocytosis Have Distinctly Brighter CD45 Expression by Flow Cytometry
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
2015; 143 (4): 527-534
View details for DOI 10.1309/AJCPZ3J4GEEYIRRA
View details for Web of Science ID 000919500200008
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Thromboelastography/Platelet Mapping (R) and Aspirin: Is There Evidence of a Meaningful Dose-Response Relationship in Children Supported With the Berlin Heart EXCOR Ventricular Assist Device?
ELSEVIER SCIENCE INC. 2015: S77
View details for DOI 10.1016/j.healun.2015.01.202
View details for Web of Science ID 000353251500186
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The utility of IgM, CD21, HGAL and LMO2 in the diagnosis of pediatric follicular lymphoma
HUMAN PATHOLOGY
2015; 46 (4): 629-633
Abstract
Pediatric follicular lymphoma (pFL) is a rare neoplasm with features differing from follicular lymphoma arising in adults. Here, we describe a rare case of pFL that showed morphologic features partially overlapping with progressive transformation of germinal centers and reactive follicular hyperplasia. As typical of pFL, neoplastic B cells within follicles did not express B-cell leukemia/lymphoma 2 (BCL2). However, this case showed additional distinctive abnormal findings, which contributed to the diagnosis: (1) diffuse and uniform staining of immunoglobulin M (IgM) on cells within and outside of follicles, (2) abnormally dim expression of CD21 on follicular dendritic cells, and (3) expression of human germinal center-associated lymphoma (HGAL) and LIM domain only 2 (LMO2) on B cells in interfollicular and follicular areas. This case demonstrates the utility of these abnormal features, which can be seen in adult- or usual-type follicular lymphoma, in the diagnosis of pFL. Further studies are necessary to evaluate the significance of these findings in other cases of pFL.
View details for DOI 10.1016/j.humpath.2014.12.016
View details for Web of Science ID 000352117000020
View details for PubMedID 25701230
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Effects of Thrombopoietin Mimetics on Patients with Chronic ITP: Perspectives from Blood Transcriptome Profiling Analysis
AMER SOC HEMATOLOGY. 2014
View details for Web of Science ID 000349233800107
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Molecular Immunoglobulin/T-Cell Receptor Clonality Analysis by Bidirectional Amplicon Sequencing on MiSeq with a Phasing Primer Design Strategy
ELSEVIER SCIENCE INC. 2014: 714–15
View details for Web of Science ID 000343794200083
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Next-Generation Molecular Diagnostic Testing of Cystic Fibrosis Using Complementary Long Padlock Probes
ELSEVIER SCIENCE INC. 2014: 712
View details for Web of Science ID 000343794200071
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Standardization of BCR-ABL1 Quantitation: Successes and Challenges, the Stanford Experience
ELSEVIER SCIENCE INC. 2014: 714
View details for Web of Science ID 000343794200080
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An Unusual Case of Classical Hodgkin Lymphoma Expressing Multiple T-Cell Antigens: Contributions of Molecular Studies to Diagnosis in Hematopathology
ELSEVIER SCIENCE INC. 2014: 721
View details for Web of Science ID 000343794200110
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Ameloblastoma driver mutations revealed by next-generation sequencing of formalin-fixed paraffin-embedded specimens
AMER ASSOC CANCER RESEARCH. 2014
View details for DOI 10.1158/1538-7445.AM2014-3436
View details for Web of Science ID 000349910200435
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Immunoglobulin and T cell receptor gene high-throughput sequencing quantifies minimal residual disease in acute lymphoblastic leukemia and predicts post-transplantation relapse and survival.
Biology of blood and marrow transplantation
2014; 20 (9): 1307-1313
Abstract
Minimal residual disease (MRD) quantification is an important predictor of outcome after treatment for acute lymphoblastic leukemia (ALL). Bone marrow ALL burden ≥ 10(-4) after induction predicts subsequent relapse. Likewise, MRD ≥ 10(-4) in bone marrow before initiation of conditioning for allogeneic (allo) hematopoietic cell transplantation (HCT) predicts transplantation failure. Current methods for MRD quantification in ALL are not sufficiently sensitive for use with peripheral blood specimens and have not been broadly implemented in the management of adults with ALL. Consensus-primed immunoglobulin (Ig), T cell receptor (TCR) amplification and high-throughput sequencing (HTS) permit use of a standardized algorithm for all patients and can detect leukemia at 10(-6) or lower. We applied the LymphoSIGHT HTS platform (Sequenta Inc., South San Francisco, CA) to quantification of MRD in 237 samples from 29 adult B cell ALL patients before and after allo-HCT. Using primers for the IGH-VDJ, IGH-DJ, IGK, TCRB, TCRD, and TCRG loci, MRD could be quantified in 93% of patients. Leukemia-associated clonotypes at these loci were identified in 52%, 28%, 10%, 35%, 28%, and 41% of patients, respectively. MRD ≥ 10(-4) before HCT conditioning predicted post-HCT relapse (hazard ratio [HR], 7.7; 95% confidence interval [CI], 2.0 to 30; P = .003). In post-HCT blood samples, MRD ≥10(-6) had 100% positive predictive value for relapse with median lead time of 89 days (HR, 14; 95% CI, 4.7 to 44, P < .0001). The use of HTS-based MRD quantification in adults with ALL offers a standardized approach with sufficient sensitivity to quantify leukemia MRD in peripheral blood. Use of this approach may identify a window for clinical intervention before overt relapse.
View details for DOI 10.1016/j.bbmt.2014.04.018
View details for PubMedID 24769317
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Identification of recurrent SMO and BRAF mutations in ameloblastomas.
Nature genetics
2014; 46 (7): 722-725
Abstract
Here we report the discovery of oncogenic mutations in the Hedgehog and mitogen-activated protein kinase (MAPK) pathways in over 80% of ameloblastomas, locally destructive odontogenic tumors of the jaw, by genomic analysis of archival material. Mutations in SMO (encoding Smoothened, SMO) are common in ameloblastomas of the maxilla, whereas BRAF mutations are predominant in tumors of the mandible. We show that a frequently occurring SMO alteration encoding p.Leu412Phe is an activating mutation and that its effect on Hedgehog-pathway activity can be inhibited by arsenic trioxide (ATO), an anti-leukemia drug approved by the US Food and Drug Administration (FDA) that is currently in clinical trials for its Hedgehog-inhibitory activity. In a similar manner, ameloblastoma cells harboring an activating BRAF mutation encoding p.Val600Glu are sensitive to the BRAF inhibitor vemurafenib. Our findings establish a new paradigm for the diagnostic classification and treatment of ameloblastomas.
View details for DOI 10.1038/ng.2986
View details for PubMedID 24859340
- STAT3 mutations are present in aggressive B-cell lymphomas including a subset of diffuse large B-cell lymphomas with CD30 expression. Haematologica 2014; 99 (7): e105-7
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Identification of recurrent SMO and BRAF mutations in ameloblastomas
NATURE GENETICS
2014; 46 (7): 722-725
Abstract
Here we report the discovery of oncogenic mutations in the Hedgehog and mitogen-activated protein kinase (MAPK) pathways in over 80% of ameloblastomas, locally destructive odontogenic tumors of the jaw, by genomic analysis of archival material. Mutations in SMO (encoding Smoothened, SMO) are common in ameloblastomas of the maxilla, whereas BRAF mutations are predominant in tumors of the mandible. We show that a frequently occurring SMO alteration encoding p.Leu412Phe is an activating mutation and that its effect on Hedgehog-pathway activity can be inhibited by arsenic trioxide (ATO), an anti-leukemia drug approved by the US Food and Drug Administration (FDA) that is currently in clinical trials for its Hedgehog-inhibitory activity. In a similar manner, ameloblastoma cells harboring an activating BRAF mutation encoding p.Val600Glu are sensitive to the BRAF inhibitor vemurafenib. Our findings establish a new paradigm for the diagnostic classification and treatment of ameloblastomas.
View details for DOI 10.1038/ng.2986
View details for Web of Science ID 000338093800013
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High sensitivity and specificity of a new functional flow cytometry assay for clinically significant heparin-induced thrombocytopenia antibodies
INTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY
2014; 36 (2): 135-143
Abstract
Heparin-induced thrombocytopenia (HIT) is a life-threatening condition, in which the anticoagulant heparin, platelet factor 4 (PF4), and platelet-activating antibodies form complexes with prothrombotic properties. Laboratory tests to support clinical diagnosis are subdivided into functional, platelet activation assays, which lack standardization, or immunological assays, which have moderate specificity toward HIT. In this study, clinical performance of HITAlert, a novel in vitro diagnostic (IVD) registered platelet activation assay, was tested in a large cohort of HIT-suspected patients and compared with immunological assays.From 346 HIT-suspected patients (single center), clinical data including 4T pretest probability results, citrated platelet-poor plasmas, and sera were collected, allowing direct comparison of clinical observations with HITAlert results. HITAlert performance was compared with PF4 IgG ELISA (246 patients, three centers) and PF4 PaGIA (298 patients, single center).HITAlert showed high sensitivity (88.2%) and specificity (99.1%) when compared with clinical diagnosis. Agreement of HITAlert with PF4 ELISA- and PF4 PaGIA-positive patients is low (52.7 and 23.2%, respectively), while agreement with PF4 IgG ELISA- and PF4 PaGIA-negative patients is very high (98.1 and 99.1%, respectively).HITAlert performance is excellent when compared with clinical HIT diagnosis, making it a suitable assay for rapid testing of platelet activation due to anticoagulant therapy.
View details for DOI 10.1111/ijlh.12136
View details for Web of Science ID 000332777000004
View details for PubMedID 23981347
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Mutational Profiling of Ameloblastoma Identifies Common Gain-of-Function Mutations
NATURE PUBLISHING GROUP. 2014: 324A
View details for Web of Science ID 000331502201650
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Mutational Profiling of Ameloblastoma Identifies Common Gain-of-Function Mutations
NATURE PUBLISHING GROUP. 2014: 324A
View details for Web of Science ID 000331155801553
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A Balanced Look at the Implications of Genomic (and Other "Omics") Testing for Disease Diagnosis and Clinical Care.
Genes
2014; 5 (3): 748-766
Abstract
The tremendous increase in DNA sequencing capacity arising from the commercialization of "next generation" instruments has opened the door to innumerable routes of investigation in basic and translational medical science. It enables very large data sets to be gathered, whose interpretation and conversion into useful knowledge is only beginning. A challenge for modern healthcare systems and academic medical centers is to apply these new methods for the diagnosis of disease and the management of patient care without unnecessary delay, but also with appropriate evaluation of the quality of data and interpretation, as well as the clinical value of the insights gained. Most critically, the standards applied for evaluating these new laboratory data and ensuring that the results and their significance are clearly communicated to patients and their caregivers should be at least as rigorous as those applied to other kinds of medical tests. Here, we present an overview of conceptual and practical issues to be considered in planning for the integration of genomic methods or, in principle, any other type of "omics" testing into clinical care.
View details for DOI 10.3390/genes5030748
View details for PubMedID 25257203
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STAT3 mutations are frequent in CD30+ T-cell lymphomas and T-cell large granular lymphocytic leukemia.
Leukemia
2013; 27 (11): 2244-2247
View details for DOI 10.1038/leu.2013.104
View details for PubMedID 23563237
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VIETNAMESE NON-SMALL CELL LUNG CANCER PATIENTS IN CALIFORNIA: MOLECULAR PROFILES AND CLINICAL CHARACTERISTICS
LIPPINCOTT WILLIAMS & WILKINS. 2013: S208–S209
View details for Web of Science ID 000339624901009
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Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes.
Haematologica
2013; 98 (11): 1689-1696
Abstract
In order to identify novel somatic mutations associated with classic BCR/ABL1-negative myeloproliferative neoplasms, we performed high-coverage genome sequencing of DNA from peripheral blood granulocytes and cultured skin fibroblasts from a patient with MPL W515K-positive primary myelofibrosis. The primary myelofibrosis genome had a low somatic mutation rate, consistent with that observed in similar hematopoietic tumor genomes. Interfacing of whole-genome DNA sequence data with RNA expression data identified three somatic mutations of potential functional significance: a nonsense mutation in CARD6, implicated in modulation of NF-kappaB activation; a 19-base pair deletion involving a potential regulatory region in the 5'-untranslated region of BRD2, implicated in transcriptional regulation and cell cycle control; and a non-synonymous point mutation in KIAA0355, an uncharacterized protein. Additional mutations in three genes (CAP2, SOX30, and MFRP) were also evident, albeit with no support for expression at the RNA level. Re-sequencing of these six genes in 178 patients with polycythemia vera, essential thrombocythemia, and myelofibrosis did not identify recurrent somatic mutations in these genes. Finally, we describe methods for reducing false-positive variant calls in the analysis of hematologic malignancies with a low somatic mutation rate. This trial is registered with ClinicalTrials.gov (NCT01108159).
View details for DOI 10.3324/haematol.2013.092379
View details for PubMedID 23872309
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Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes.
Haematologica
2013; 98 (11): 1689-1696
Abstract
In order to identify novel somatic mutations associated with classic BCR/ABL1-negative myeloproliferative neoplasms, we performed high-coverage genome sequencing of DNA from peripheral blood granulocytes and cultured skin fibroblasts from a patient with MPL W515K-positive primary myelofibrosis. The primary myelofibrosis genome had a low somatic mutation rate, consistent with that observed in similar hematopoietic tumor genomes. Interfacing of whole-genome DNA sequence data with RNA expression data identified three somatic mutations of potential functional significance: a nonsense mutation in CARD6, implicated in modulation of NF-kappaB activation; a 19-base pair deletion involving a potential regulatory region in the 5'-untranslated region of BRD2, implicated in transcriptional regulation and cell cycle control; and a non-synonymous point mutation in KIAA0355, an uncharacterized protein. Additional mutations in three genes (CAP2, SOX30, and MFRP) were also evident, albeit with no support for expression at the RNA level. Re-sequencing of these six genes in 178 patients with polycythemia vera, essential thrombocythemia, and myelofibrosis did not identify recurrent somatic mutations in these genes. Finally, we describe methods for reducing false-positive variant calls in the analysis of hematologic malignancies with a low somatic mutation rate. This trial is registered with ClinicalTrials.gov (NCT01108159).
View details for DOI 10.3324/haematol.2013.092379
View details for PubMedID 23872309
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Minimal residual disease quantification using consensus primers and high- throughput IGH sequencing predicts post-transplant relapse in chronic lymphocytic leukemia
LEUKEMIA
2013; 27 (8): 1659-1665
Abstract
Quantification of minimal residual disease (MRD) following allogeneic hematopoietic cell transplantation (allo-HCT) predicts post-transplant relapse in patients with chronic lymphocytic leukemia (CLL). We utilized an MRD-quantification method that amplifies immunoglobulin heavy chain (IGH) loci using consensus V and J segment primers followed by high-throughput sequencing (HTS), enabling quantification with a detection limit of one CLL cell per million mononuclear cells. Using this IGH-HTS approach, we analyzed MRD patterns in over 400 samples from 40 CLL patients who underwent reduced-intensity allo-HCT. Nine patients relapsed within 12 months post-HCT. Of the 31 patients in remission at 12 months post-HCT, disease-free survival was 86% in patients with MRD <10(-4) and 20% in those with MRD 10(-4) (relapse hazard ratio (HR) 9.0; 95% confidence interval (CI) 2.5-32; P<0.0001), with median follow-up of 36 months. Additionally, MRD predicted relapse at other time points, including 9, 18 and 24 months post-HCT. MRD doubling time <12 months with disease burden 10(-5) was associated with relapse within 12 months of MRD assessment in 50% of patients, and within 24 months in 90% of patients. This IGH-HTS method may facilitate routine MRD quantification in clinical trials.Leukemia advance online publication, 12 March 2013; doi:10.1038/leu.2013.52.
View details for DOI 10.1038/leu.2013.52
View details for Web of Science ID 000322823200006
View details for PubMedID 23419792
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Oxidative stress and immune thrombocytopenia.
Seminars in hematology
2013; 50 (3): e1-4
Abstract
Immune thrombocytopenia (ITP) is an autoimmune disorder characterized by increased platelet destruction or decreased platelet production. The mechanism of the disease has been extensively studied so that we now have a much improved understanding of the pathophysiology; however, the trigger of the autoimmunity remains unclear. More recently, oxidative stress was identified to be involved in the pathogenesis of ITP and provides a new hypothesis for the initiation of autoimmunity in patients with ITP. In this review, oxidative stress and its impact on autoimmunity, particularly ITP, will be covered.
View details for DOI 10.1053/j.seminhematol.2013.06.011
View details for PubMedID 23953344
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A distinct evolution of the T-cell repertoire categorizes treatment refractory gastrointestinal acute graft-versus-host disease.
Blood
2013; 121 (24): 4955-4962
Abstract
Steroid refractory gastrointestinal (GI) acute graft versus host disease (aGVHD) is a major cause of mortality in hematopoietic stem cell transplantation (HCT) without immune markers to establish a diagnosis or guide therapy. We found that T cell receptor β (TCRβ) CDR3 repertoire sequencing reveals patterns that could eventually serve as a disease biomarker of T cell alloreactivity in aGVHD. We identified T cell clones in GI biopsies in a heterogeneous group of 15 allogeneic HCT patients with GI aGVHD symptoms. Seven steroid-refractory aGVHD patients showed a more conserved TCRβ clonal structure between different biopsy sites in the GI tract than eight primary-therapy responsive patients. Tracking GI clones identified at endoscopy longitudinally in the blood also revealed an increased clonal expansion in patients with steroid-refractory disease. Immune repertoire sequencing-based methods could enable a novel personalized way to guide diagnosis and therapy in diseases where T cell activity is a major determinant.
View details for DOI 10.1182/blood-2013-03-489757
View details for PubMedID 23652802
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A distinct evolution of the T-cell repertoire categorizes treatment refractory gastrointestinal acute graft-versus-host disease
BLOOD
2013; 121 (24): 4955-4962
Abstract
Steroid refractory gastrointestinal (GI) acute graft versus host disease (aGVHD) is a major cause of mortality in hematopoietic stem cell transplantation (HCT) without immune markers to establish a diagnosis or guide therapy. We found that T cell receptor β (TCRβ) CDR3 repertoire sequencing reveals patterns that could eventually serve as a disease biomarker of T cell alloreactivity in aGVHD. We identified T cell clones in GI biopsies in a heterogeneous group of 15 allogeneic HCT patients with GI aGVHD symptoms. Seven steroid-refractory aGVHD patients showed a more conserved TCRβ clonal structure between different biopsy sites in the GI tract than eight primary-therapy responsive patients. Tracking GI clones identified at endoscopy longitudinally in the blood also revealed an increased clonal expansion in patients with steroid-refractory disease. Immune repertoire sequencing-based methods could enable a novel personalized way to guide diagnosis and therapy in diseases where T cell activity is a major determinant.
View details for DOI 10.1182/blood-2013-03-489757
View details for Web of Science ID 000321896300024
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Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations.
American journal of surgical pathology
2013; 37 (6): 796-803
Abstract
Somatic mutations, often translocations or single nucleotide variations, are pathognomonic for certain types of cancers and are increasingly of clinical importance for diagnosis and prediction of response to therapy. Conventional clinical assays only evaluate 1 mutation at a time, and targeted tests are often constrained to identify only the most common mutations. Genome-wide or transcriptome-wide high-throughput sequencing (HTS) of clinical samples offers an opportunity to evaluate for all clinically significant mutations with a single test. Recently a "desktop version" of HTS has become available, but most of the experience to date is based on data obtained from high-quality DNA from frozen specimens. In this study, we demonstrate, as a proof of principle, that translocations in sarcomas can be diagnosed from formalin-fixed paraffin-embedded (FFPE) tissue with desktop HTS. Using the first generation MiSeq platform, full transcriptome sequencing was performed on FFPE material from archival blocks of 3 synovial sarcomas, 3 myxoid liposarcomas, 2 Ewing sarcomas, and 1 clear cell sarcoma. Mapping the reads to the "sarcomatome" (all known 83 genes involved in translocations and mutations in sarcoma) and using a novel algorithm for ranking fusion candidates, the pathognomonic fusions and the exact breakpoints were identified in all cases of synovial sarcoma, myxoid liposarcoma, and clear cell sarcoma. The Ewing sarcoma fusion gene was detectable in FFPE material only with a sequencing platform that generates greater sequencing depth. The results show that a single transcriptome HTS assay, from FFPE, has the potential to replace conventional molecular diagnostic techniques for the evaluation of clinically relevant mutations in cancer.
View details for DOI 10.1097/PAS.0b013e31827ad9b2
View details for PubMedID 23598961
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Indolent T-Lymphoblastic Proliferation (iT-LBP): A Review of Clinical and Pathologic Features and Distinction from Malignant T-Lymphoblastic Lymphoma
ADVANCES IN ANATOMIC PATHOLOGY
2013; 20 (3): 137-140
Abstract
In recent years, a new pathologic entity has emerged: indolent T-lymphoblastic proliferation (iT-LBP). iT-LBPs share immunophenotypic similarities with T-lymphoblastic lymphoma; however, T-lymphoblastic proliferations are clinically indolent, and unlike the malignant counterpart, these expansions of nonclonal terminal deoxynucleotidyl transferase (TdT)+ T cells do not require treatment. Here we review the clinical and pathologic features, which are required for an accurate diagnosis of an iT-LBP. We demonstrate specific criteria can be used to accurately diagnose iT-LBP, notably: (1) confluent groups of TdT+ T cells in a biopsy specimen, (2) relative preservation of surrounding normal lymphoid architecture, (3) TdT+ T cells without morphologic atypia, (4) absence of thymic epithelium, (5) nonclonal TdT+ T cells, (6) immunophenotype of developmentally normal immature thymic T cells, and (7) clinical evidence of indolence (follow-up >6 mo without progression).
View details for DOI 10.1097/PAP.0b013e31828d17ec
View details for Web of Science ID 000317588700001
View details for PubMedID 23574769
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CLINICAL UTILITY OF ENDOGENOUS THROMBIN POTENTIAL IN MONITORING PATIENTS TREATED WITH UNFRACTIONATED HEPARIN
WILEY-BLACKWELL. 2013: 69–69
View details for Web of Science ID 000318286300136
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Sequential azacitidine plus lenalidomide combination for elderly patients with untreated acute myeloid leukemia.
Haematologica
2013; 98 (4): 591-596
Abstract
There are limited treatment options for older patients with acute myeloid leukemia and prognosis of these patients remains poor, thereby warranting development of novel therapies. We evaluated the efficacy and safety of azacitidine in combination with lenalidomide as front-line therapy for older patients with acute myeloid leukemia. Patients ≥ 60 years of age with untreated acute myeloid leukemia received azacitidine 75 mg/m2 for 7 days followed by escalating doses of lenalidomide daily for 21 days starting on day 8 of each cycle every 6 weeks. Patients received continued therapy until disease progression, unacceptable toxicity, or completion of 12 cycles. Forty-two patients (median age, 74 years) were enrolled with equal distribution according to European LeukemiaNet risk. The overall response rate was 40% (rate of complete remission with or without complete recovery of blood counts = 28%). The median time to complete remission with or without complete recovery of blood counts was 12 weeks, and duration of this status was 28 weeks (range, 4 - >104 weeks). Therapy-related acute myeloid leukemia and a high score on the Hematopoietic Cell Transplantation Comorbidity Index were negative predictors of response. Early death was noted in 17% of patients. Grades ≥ 3 toxicities were uncommon and most adverse events were gastrointestinal, fatigue and myelosuppression. In conclusion, a sequential combination of azacitidine plus lenalidomide has clinical activity in older patients with acute myeloid leukemia, and further studies of this combination are underway.
View details for DOI 10.3324/haematol.2012.076414
View details for PubMedID 23242596
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Discordant aPTT and anti-Xa values and outcomes in hospitalized patients treated with intravenous unfractionated heparin.
Annals of pharmacotherapy
2013; 47 (2): 151-158
Abstract
Both the activated partial thromboplastin time (aPTT) and anti-Xa assay can be used to monitor unfractionated heparin (UFH). Following implementation of an anti-Xa method for heparin dosing protocols in our hospital, we became aware of many patients with discordant aPTT and anti-Xa values.To determine the frequency of discordant aPTT and anti-Xa values in a large cohort of hospitalized patients treated with UFH, as well as the demographics, coagulation status, indication for UFH, and clinical outcomes in this population.All aPTT and anti-Xa values from adults hospitalized between February and August 2009 at Stanford Hospital who were treated with UFH were analyzed. All samples were drawn simultaneously. A polynomial fit correlating aPTT and anti-Xa with a 99% confidence limit was designed. Paired aPTT/anti-Xa values were grouped according to whether the paired values fell within or outside of the concordant area. Patients were placed into groups based on concordance status, and clinical outcomes were assessed.A total of 2321 paired values from 539 patients were studied; 42% of data pairs had a high aPTT value relative to the anti-Xa value. Patients with elevated baseline prothrombin time/international normalized ratio or aPTT frequently demonstrated disproportionate relative prolongation of the aPTT. Patients with at least 2 consecutive high aPTT to anti-Xa values had increased 21-day major bleeding (9% vs 3%; p = 0.0316) and 30-day mortality (14% dead vs 5% dead at 30 days; p = 0.0202) compared with patients with consistently concordant values.aPTT and anti-Xa values are frequently discordant when used to measure UFH in hospitalized patients. A disproportionate prolongation of the aPTT relative to the anti-Xa was the most common discordant pattern in our study. Patients with relatively high aPTT to anti-Xa values appear to be at increased risk of adverse outcomes. Monitoring both aPTT and Xa values may have utility in managing such patients.
View details for DOI 10.1345/aph.1R635
View details for PubMedID 23386070
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Desktop Transcriptome Sequencing from Archival Tissue To Identify Clinically Relevant Translocations
NATURE PUBLISHING GROUP. 2013: 438A
View details for Web of Science ID 000314444402452
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Desktop Transcriptome Sequencing from Archival Tissue To Identify Clinically Relevant Translocations
102nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP)
NATURE PUBLISHING GROUP. 2013: 438A–438A
View details for Web of Science ID 000314789302442
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The Expansion of Gastrointestinal-Associated alpha beta T Cell Clones in Peripheral Blood Associates with Severe Steroid Refractory GVHD
BMT Tandem Meetings
ELSEVIER SCIENCE INC. 2013: S334–S335
View details for Web of Science ID 000314441900449
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Impaired B Cell Clonotype Diversification After Allogeneic Hematopoietic Cell Transplantation Predicts Graft-Versus-Host Disease
BMT Tandem Meetings
ELSEVIER SCIENCE INC. 2013: S148–S149
View details for Web of Science ID 000314441900072
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2-Hydroxyglutarate in IDH mutant acute myeloid leukemia: predicting patient responses, minimal residual disease and correlations with methylcytosine and hydroxymethylcytosine levels
LEUKEMIA & LYMPHOMA
2013; 54 (2): 408-410
View details for DOI 10.3109/10428194.2012.701009
View details for Web of Science ID 000313285400034
View details for PubMedID 22680765
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The Expansion of Gastrointestinal-associated alpha beta T Cell Clones in Peripheral Blood Over Time Is a Disease Feature of Severe Acute Graft-Versus-Host Disease
54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000313838901092
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Azacitidine Plus Lenalidomide for Untreated AML Patients Ineligible for Conventional Chemotherapy
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000313838906082
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The Role of Oxidative Stress in Pediatric Immune Thrombocytopenia
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000314049602365
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A Germline Variant in the TERT Gene Is a Novel Predisposition Allele Associated with Myeloproliferative Neoplasms
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000313838900250
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Correlation of Symptom Assessment with Genotyping Analysis of Saliva Samples in a Large Cohort of Myeloproliferative Neoplasm Patients
54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000314049602145
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Estimation of JAK2 V617F Prevalence by Detection of the Mutation in Saliva Samples From Online MPN and General Population Cohorts
54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000314049602140
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Whole Genome Sequence Analysis of Primary Myelofibrosis.
54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000313838905376
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TdT(+) T-lymphoblastic Populations Are Increased in Castleman Disease, in Castleman Disease in Association With Follicular Dendritic Cell Tumors, and in Angioimmunoblastic T-cell Lymphoma
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
2012; 36 (11): 1619-1628
Abstract
T-lymphoblastic lymphoma is an aggressive neoplasm requiring prompt clinical treatment. Conversely, indolent T-lymphoblastic proliferation mimics T-lymphoblastic lymphoma but consists of a proliferation of non-neoplastic TdT+ T cells, requiring no treatment. Recently, we identified several cases of indolent T-lymphoblastic proliferations in extrathymic lymphoid tissues: 1 in a patient suffering from Castleman disease (CD) associated with a follicular dendritic cell sarcoma/tumor, 1 in a patient with a history of angioimmunoblastic T-cell lymphoma (AITL), and 1 in association with acinic cell carcinoma. Interestingly, in the case of the patient with a history of AITL, these TdT+ T cells were seen in multiple anatomic sites over the span of 5 years. Here we review these 3 cases and extend our findings by demonstrating that TdT+ T-lymphoblastic populations are increased in lymph nodes of patients with CD (P=0.011), CD in association with follicular dendritic cell tumors, and AITL (P<0.01) compared with other T-cell or B-cell lymphomas or reactive lymph nodes. Finally, analysis of 352 nonhematolymphoid tumors including carcinomas, melanomas, and sarcomas demonstrates that TdT+ T cells are not increased in these tumors. Our studies not only present several detailed cases of indolent T-lymphoblastic proliferations, but also correlate these populations with specific hematologic diseases.
View details for DOI 10.1097/PAS.0b013e318264e223
View details for Web of Science ID 000310059600004
View details for PubMedID 23060347
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USING A FUNCTIONAL FLOW CYTOMETRIC ASSAY (HITALERT) TO SUPPORT CLINICAL HEPARIN-INDUCED THROMBOCYTOPENIA (HIT) DIAGNOSIS
WILEY-BLACKWELL. 2012: 394
View details for Web of Science ID 000310386300054
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Prophylactic rituximab after allogeneic transplantation decreases B-cell alloimmunity with low chronic GVHD incidence
BLOOD
2012; 119 (25): 6145-6154
Abstract
B cells are involved in the pathogenesis of chronic GVHD (cGVHD). We hypothesized that prophylactic anti-B-cell therapy delivered 2 months after transplantation would decrease allogeneic donor B-cell immunity and possibly the incidence of cGVHD. Therefore, in the present study, patients with high-risk chronic lymphocytic leukemia (n = 22) and mantle-cell lymphoma (n = 13) received a total lymphoid irradiation of 80 cGy for 10 days and antithymocyte globulin 1.5 mg/kg/d for 5 days. Rituximab (375 mg/m(2)) was infused weekly on days 56, 63, 70, and 77 after transplantation. The incidence of acute GVHD was 6%. The cumulative incidence of cGVHD was 20%. Nonrelapse mortality was 3%. Rituximab treatment after allogeneic transplantation significantly reduced B-cell allogeneic immunity, with complete prevention of alloreactive H-Y Ab development in male patients with female donors (P = .01). Overall survival and freedom from progression at 4 years for chronic lymphocytic leukemia patients were 73% and 47%, respectively; for mantle-cell lymphoma patients, they were 69% and 53%, respectively.
View details for DOI 10.1182/blood-2011-12-395970
View details for PubMedID 22563089
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Aggressive EBV-associated Lymphoproliferative Disorder: A Prodrome to Diffuse Large B-cell Lymphoma?
APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY
2012; 20 (3): 325-330
Abstract
A 19-year-old male patient presented with intermittent high fever and left cervical lymphadenopathy. The lymph node biopsy findings were interpreted as "Epstein-Barr virus (EBV)-associated lymphoproliferative disorder consistent with infectious mononucleosis." No molecular studies were performed at that time. The patient was followed without treatment. Five months later, the patient again presented with fever, lymphadenopathy, and splenomegaly. The lymph node biopsy showed features of a diffuse large B-cell lymphoma. Molecular studies on this lymph node biopsy showed a clonal EBV population, although polymerase chain reaction studies failed to reveal a clonal B-cell or T-cell population. A concurrent bone marrow biopsy showed features consistent with hemophagocytic syndrome. He had elevated ferritin, soluble interleukin-2 receptors and persistent EBV viremia. The patient responded to Rituxan for a short period with undetectable EBV levels. Subsequent right cervical lymph node, liver, and jejunal biopsies showed involvement by diffuse large B-cell lymphoma and the patient expired soon thereafter.
View details for Web of Science ID 000303140100012
View details for PubMedID 22505014
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The Risk of Using a Patient's Medical Record to Determine Platelet Function Inhibition by Aspirin Therapy
WILEY-BLACKWELL. 2012: S183–S184
View details for Web of Science ID 000302999500124
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Comparison of Aptt and anti-Xa Activity with Patient Outcomes in a Large Cohort of Hospitalized Patients Treated with Unfractionated Heparin
WILEY-BLACKWELL. 2012: S174–S174
View details for Web of Science ID 000302999500099
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Controversies in Heparin Monitoring
AMERICAN JOURNAL OF HEMATOLOGY
2012; 87: S137-S140
View details for DOI 10.1002/ajh.23210
View details for Web of Science ID 000302999500024
View details for PubMedID 22495972
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Safety, efficacy and biological predictors of response to sequential azacitidine and lenalidomide for elderly patients with acute myeloid leukemia
LEUKEMIA
2012; 26 (5): 893-901
Abstract
Acute myeloid leukemia (AML) is a disease of the elderly. Poor outcomes with standard therapies necessitate novel approaches. Outpatient regimens sufficiently potent and well tolerated to induce remissions and enable continuation therapy may be beneficial. In this phase-1 study, we determined the maximum tolerated dose (MTD) and the efficacy for sequential azacitidine and lenalidomide as remission induction and continuation therapy in elderly, previously untreated patients. We investigated the impact on global DNA methylation and bone marrow cytokines, and sought biological predictors of response. Eighteen patients were enrolled. The MTD was not reached. Median follow-up was 8.2 months (10.3 months for survivors). Common adverse events included fatigue, injection site reactions, constipation, nausea, pruritus and febrile neutropenia. Ten patients responded (56%), and the rate of complete remissions (CRs) or CRs with incomplete recovery of blood counts for evaluable patients was 44% (7/16). The median response duration was 6.2 months. DNA demethylation and changes in bone marrow cytokines were observed; responders had a unique cytokine profile and a trend towards lower methylation levels. Sequential azacitidine and lenalidomide was well tolerated with encouraging clinical and biological activity in previously untreated elderly AML patients. This trial is registered at ClinicalTrials.gov (NCT00890929).
View details for DOI 10.1038/leu.2011.294
View details for Web of Science ID 000303883500005
View details for PubMedID 22033493
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UNIVERSAL MINIMAL RESIDUAL DISEASE QUANTIFICATION USING CONSENSUS PRIMERS AND HIGH-THROUGHPUT IGH SEQUENCING PREDICTS POST-TRANSPLANT CLL RELAPSE BETTER THAN PATIENT-SPECIFIC PCR
BMT Tandem Meeting
ELSEVIER SCIENCE INC. 2012: S288–S288
View details for Web of Science ID 000299398600228
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Tailored temozolomide therapy according to MGMT methylation status for elderly patients with acute myeloid leukemia
AMERICAN JOURNAL OF HEMATOLOGY
2012; 87 (1): 45-50
Abstract
Temozolomide sensitivity is determined by methylation of the O(6)-methylguanine-DNA methyltransferase (MGMT) promoter. This study assessed whether the temozolomide dose can be tailored by MGMT promoter status and whether protracted, low-dose temozolomide can "prime" blasts in patients with unmethylated MGMT (unMGMT). Elderly patients with high-risk AML were stratified by MGMT methylation. Patients with methylated MGMT (mMGMT) received temozolomide 200 mg/m(2) orally for 7 days every 4 weeks, while patients with unMGMT received temozolomide 100 mg/m(2) orally for 14 days followed by 200 mg/m(2) orally for 7 days every 6weeks. Of 36 patients (median age, 75 years), 31 (86%) had an unMGMT promoter. Overall response rate for the entire cohort was 36%. Patients with mMGMT and unMGMT had similar response rates (40% vs. 29%). Median duration of response and overall survival (OS) among responders were 29 and 35 weeks, respectively. Induction deaths (ID) occurred in 25% of patients, mostly caused by disease progression. Hematological toxicities were the most common adverse event. Toxicities were similar between patients on conventional versus protracted schedules. High HCT-CI scores were predictive of lower CR rate, higher ID, and shorter OS, while bone marrow blast count <50% at screening predicted for improved responses. Temozolomide, dosed according to MGMT methylation status, demonstrated modest clinical activity in elderly patients with AML, especially in those presenting with fewer comorbidities and low disease burden. The trial was registered on www.ClinicalTrials.gov as #NCT00611247.
View details for DOI 10.1002/ajh.22191
View details for Web of Science ID 000298257700010
View details for PubMedID 22052619
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High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2011; 108 (52): 21194-21199
Abstract
The primary cause of poor outcome following allogeneic hematopoietic cell transplantation (HCT) for chronic lymphocytic leukemia (CLL) is disease recurrence. Detection of increasing minimal residual disease (MRD) following HCT may permit early intervention to prevent clinical relapse; however, MRD quantification remains an uncommon diagnostic test because of logistical and financial barriers to widespread use. Here we describe a method for quantifying CLL MRD using widely available consensus primers for amplification of all Ig heavy chain (IGH) genes in a mixture of peripheral blood mononuclear cells, followed by high-throughput sequencing (HTS) for disease-specific IGH sequence quantification. To achieve accurate MRD quantification, we developed a systematic bioinformatic methodology to aggregate cancer clone sequence variants arising from systematic and random artifacts occurring during IGH-HTS. We then compared the sensitivity of IGH-HTS, flow cytometry, and allele-specific oligonucleotide PCR for MRD quantification in 28 samples collected from 6 CLL patients following allogeneic HCT. Using amplimer libraries generated with consensus primers from patient blood samples, we demonstrate the sensitivity of IGH-HTS with 454 pyrosequencing to be 10(-5), with a high correlation between quantification by allele-specific oligonucleotide PCR and IGH-HTS (r = 0.85). From the same dataset used to quantify MRD, IGH-HTS also allowed us to profile IGH repertoire reconstitution after HCT-information not provided by the other MRD methods. IGH-HTS using consensus primers will broaden the availability of MRD quantification in CLL and other B cell malignancies, and this approach has potential for quantitative evaluation of immune diversification following transplant and nontransplant therapies.
View details for DOI 10.1073/pnas.1118357109
View details for Web of Science ID 000298479900065
View details for PubMedID 22160699
View details for PubMedCentralID PMC3248502
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A novel splice donor mutation in the thrombopoietin gene leads to exon 2 skipping in a Filipino family with hereditary thrombocythemia.
Blood
2011; 118 (26): 6988-6990
View details for DOI 10.1182/blood-2011-10-386177
View details for PubMedID 22194398
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A novel splice donor mutation in the thrombopoietin gene leads to exon 2 skipping in a Filipino family with hereditary thrombocythemia
BLOOD
2011; 118 (26): 6988-?
View details for DOI 10.1182/blood-2011-10-386177
View details for Web of Science ID 000298401000038
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Clonally identical Hodgkin's disease develops after allogeneic hematopoietic cell transplant for CLL
BONE MARROW TRANSPLANTATION
2011; 46 (12): 1576-1578
View details for DOI 10.1038/bmt.2010.340
View details for Web of Science ID 000298326500015
View details for PubMedID 21258419
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High-Throughput Immunoglobulin Gene Sequencing Quantifies Minimal Residual Disease in CLL with 10e-6 Sensitivity and Strongly Predicts Relapse After Allogeneic Hematopoietic Cell Transplantation
53rd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2011: 1090–91
View details for Web of Science ID 000299597103408
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2-Hydroxyglutarate in IDH mutant AML: Predicting Patient Responses, Minimal Residual Disease and Correlations with Methylcytosine and Hydroxymethylcytosine Levels
AMER SOC HEMATOLOGY. 2011: 1073–74
View details for Web of Science ID 000299597103375
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Massively Parallel Immunoglobulin Gene Sequencing Provides Ultra-Sensitive Minimal Residual Disease Detection and Predicts Post-Transplant Relapse in Acute Lymphoblastic Leukemia by Three to Six Months
AMER SOC HEMATOLOGY. 2011: 1752–53
View details for Web of Science ID 000299597106272
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Prolonged aPTT Relative to Anti-Xa Is Associated with Increased 30-Day Mortality in Hospitalized Patients Treated with Unfractionated Heparin
53rd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2011: 559–59
View details for Web of Science ID 000299597101517
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Immature T-Cell Populations in Lymph Nodes of Castleman Disease and Angioimmunoblastic T-Cell Lymphoma Suggest Alternate Sites of T-Cell Development
53rd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2011: 1395–96
View details for Web of Science ID 000299597104588
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Refining the diagnosis of T-cell large granular lymphocytic leukemia by combining distinct patterns of antigen expression with T-cell clonality studies
LEUKEMIA
2011; 25 (9): 1439-1443
Abstract
T-cell large granular lymphocytic (LGL) leukemia is a complex diagnosis, requiring persistent clonal expansions of LGLs, and cytopenias. Often the diagnosis is unclear as non-clonal expansions of LGLs commonly occur in reactive conditions. To better understand T-LGL leukemia, we performed a comprehensive clinicopathologic analysis of 85 patients with LGL expansions. Interestingly, distinct CD8+(dim)/CD57+ populations, seen by flow cytometry, were significantly associated with clonal T-LGL leukemia (P < 0.001) as well as neutropenia (median absolute neutrophil count (ANC) 1.45 vs 3.19 × 10(9)/l; P = 0.0017). Furthermore, cases with distinct CD8+(dim)/CD57+ populations and monoclonal T cells had even lower ANCs (median ANC 1.41 × 10(9)/l; P = 0.001) compared with cases without these dual criteria. Additionally, complete or partial loss of CD5 expression was independently associated with clonal T-LGL leukemia (P<0.001) and neutropenia (median ANC 1.41 vs 2.70 × 10(9)/l; P = 0.002). This study describes specific immunophenotypic parameters to better define clonal cases of T-LGL leukemia associated with significant neutropenia.
View details for DOI 10.1038/leu.2011.107
View details for Web of Science ID 000294665400008
View details for PubMedID 21617700
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Evaluation of a Gene Expression Microarray-based Assay to Determine Tissue Type of Origin on a Diverse Set of 49 Malignancies
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
2011; 35 (7): 1030-1037
Abstract
The Tissue of Origin Frozen (TOO-FRZ) assay from Pathwork Diagnostics has been cleared by the Food and Drug Administration as a diagnostic study for malignancies of unknown primary. The goal of this study was to evaluate the performance of TOO-FRZ on a diverse collection of malignancies. We collected a diverse set of 49 malignancies. We classified each case into 1 of 4 groups: common morphology from a tissue type included in the TOO-FRZ assay (n=29), uncommon morphology from a tissue type included in the TOO-FRZ assay (n=10), tumor from a tissue type not included in the TOO-FRZ assay (n=3), and malignancies of unknown primary (n=7). We found strong diagnostic performance for common morphologies from tissue types on the TOO-FRZ [overall accuracy=26 of 29 (90%, 95% CI, 73% to 97%)], with perfect performance in all tissue types except gastric (0 of 2) and pancreatic (1 of 2) tissues. There was a significant decline in performance for uncommon morphologies from tissue types included in the TOO-FRZ assay [6 of 10 (60%) cases with an indeterminate result, 1 of 10 (10%) cases with an incorrect prediction, and 3 of 10 (30%) with a correct prediction] and for tumors from tissue types not included in the assay (incorrect prediction in 2 of 3 cases). For the 7 malignancies of unknown primary in our study set, the TOO-FRZ provided a likely clinically useful result in only 2 of 7 cases. These results provide an insight into the strengths and limitations of this molecular assay for the surgical pathologist, and our findings suggest future directions for research in this area.
View details for DOI 10.1097/PAS.0b013e3182178b59
View details for Web of Science ID 000291676200011
View details for PubMedID 21602661
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Sequential azacitidine and lenalidomide in elderly acute myeloid leukemia: completed results of the phase I study
AMER SOC CLINICAL ONCOLOGY. 2011
View details for DOI 10.1200/jco.2011.29.15_suppl.6505
View details for Web of Science ID 000208880302012
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Mutagenesis of Varicella-Zoster Virus Glycoprotein I (gI) Identifies a Cysteine Residue Critical for gE/gI Heterodimer Formation, gI Structure, and Virulence in Skin Cells
JOURNAL OF VIROLOGY
2011; 85 (9): 4095-4110
Abstract
Varicella-zoster virus (VZV) is the alphaherpesvirus that causes chicken pox (varicella) and shingles (zoster). The two VZV glycoproteins gE and gI form a heterodimer that mediates efficient cell-to-cell spread. Deletion of gI yields a small-plaque-phenotype virus, ΔgI virus, which is avirulent in human skin using the xenograft model of VZV pathogenesis. In the present study, 10 mutant viruses were generated to determine which residues were required for the typical function of gI. Three phosphorylation sites in the cytoplasmic domain of gI were not required for VZV virulence in vivo. Two deletion mutants mapped a gE binding region in gI to residues 105 to 125. A glycosylation site, N116, in this region did not affect virulence. Substitution of four cysteine residues highly conserved in the Alphaherpesvirinae established that C95 is required for gE/gI heterodimer formation. The C95A and Δ105-125 (with residues 105 to 125 deleted) viruses had small-plaque phenotypes with reduced replication kinetics in vitro similar to those of the ΔgI virus. The Δ105-125 virus was avirulent for human skin in vivo. In contrast, the C95A mutant replicated in vivo but with significantly reduced kinetics compared to those of the wild-type virus. In addition to abolished gE/gI heterodimer formation, gI from the C95A or the Δ105-125 mutant was not recognized by monoclonal antibodies that detect the canonical conformation of gI, demonstrating structural disruption of gI in these viruses. This alteration prevented gI incorporation into virus particles. Thus, residues C95 and 105 to 125 are critical for gI structure required for gE/gI heterodimer formation, virion incorporation, and ultimately, effective viral spread in human skin.
View details for DOI 10.1128/JVI.02596-10
View details for Web of Science ID 000289618600005
View details for PubMedID 21345964
View details for PubMedCentralID PMC3126246
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The role of vanin-1 and oxidative stress-related pathways in distinguishing acute and chronic pediatric ITP
BLOOD
2011; 117 (17): 4569-4579
Abstract
Pediatric immune thrombocytopenia (ITP) is usually self-limited. However, approximately 20% of children develop chronic ITP, which can be associated with significant morbidity because of long-term immunosuppression and splenectomy in refractory cases. To explore the molecular mechanism of chronic ITP compared with acute ITP, we studied 63 pediatric patients with ITP. Gene expression analysis of whole blood revealed distinct signatures for acute and chronic ITP. Oxidative stress-related pathways were among the most significant chronic ITP-associated pathways. Overexpression of VNN1, an oxidative stress sensor in epithelial cells, was most strongly associated with progression to chronic ITP. Studies of normal persons demonstrated VNN1 expression in a variety of blood cells. Exposure of blood mononuclear cells to oxidative stress inducers elicited dramatic up-regulation of VNN1 and down-regulation of PPARγ, indicating a role for VNN1 as a peripheral blood oxidative stress sensor. Assessment of redox state by tandem mass spectrometry demonstrated statistically significant lower glutathione ratios in patients with ITP versus healthy controls; lower glutathione ratios were also seen in untreated patients with ITP compared with recently treated patients. Our work demonstrates distinct patterns of gene expression in acute and chronic ITP and implicates oxidative stress pathways in the pathogenesis of chronic pediatric ITP.
View details for DOI 10.1182/blood-2010-09-304931
View details for PubMedID 21325602
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Distinct Populations of CD8+/CD57+ Large Granular Lymphocytes Are Associated with T-Cell Monoclonality and Define a Subset of Clinically and Pathologically Significant Patients: A Case-Control Study of 70 Patients with Large Granular Lymphocytic Proliferations
NATURE PUBLISHING GROUP. 2011: 312A
View details for Web of Science ID 000291285000768
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Distinct Populations of CD8+/CD57+ Large Granular Lymphocytes Are Associated with T-Cell Monoclonality and Define a Subset of Clinically and Pathologically Significant Patients: A Case-Control Study of 70 Patients with Large Granular Lymphocytic Proliferations.
NATURE PUBLISHING GROUP. 2011: 312A
View details for Web of Science ID 000287282301483
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Varicella-Zoster Virus Glycoprotein E Is a Critical Determinant of Virulence in the SCID Mouse-Human Model of Neuropathogenesis
JOURNAL OF VIROLOGY
2011; 85 (1): 98-111
Abstract
Varicella-zoster virus (VZV) is a neurotropic alphaherpesvirus. VZV infection of human dorsal root ganglion (DRG) xenografts in immunodeficient mice models the infection of sensory ganglia. We examined DRG infection with recombinant VZV (recombinant Oka [rOka]) and the following gE mutants: gEΔ27-90, gEΔCys, gE-AYRV, and gE-SSTT. gEΔ27-90, which lacks the gE domain that interacts with a putative receptor insulin-degrading enzyme (IDE), replicated as extensively as rOka, producing infectious virions and significant cytopathic effects within 14 days of inoculation. Since neural cells express IDE, the gE/IDE interaction was dispensable for VZV neurotropism. In contrast, gEΔCys, which lacks gE/gI heterodimer formation, was significantly impaired at early times postinfection; viral genome copy numbers increased slowly, and infectious virus production was not detected until day 28. Delayed replication was associated with impaired cell-cell spread in ganglia, similar to the phenotype of a gI deletion mutant (rOkaΔgI). However, at later time points, infection of satellite cells and other supportive nonneuronal cells resulted in extensive DRG tissue damage and cell loss such that cytopathic changes observed at day 70 were more severe than those for rOka-infected DRG. The replication of gE-AYRV, which is impaired for trans-Golgi network (TGN) localization, and the replication of gE-SSTT, which contains mutations in an acidic cluster, were equivalent to that of rOka, causing significant cytopathic effects and infectious virus production by day 14; genome copy numbers were equivalent to those of rOka. These experiments suggest that the gE interaction with cellular IDE, gE targeting to TGN sites of virion envelopment, and phosphorylation at SSTT are dispensable for VZV DRG infection, whereas the gE/gI interaction is critical for VZV neurovirulence.
View details for DOI 10.1128/JVI.01902-10
View details for Web of Science ID 000285095800008
View details for PubMedID 20962081
View details for PubMedCentralID PMC3014186
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Development of Antibodies to Human Thrombin and Factor V in a Patient Exposed to Topical Bovine Thrombin
PEDIATRIC BLOOD & CANCER
2010; 55 (6): 1195-1197
Abstract
Bovine topical thrombin is commonly used for local hemostasis in pediatric surgery. Acquired inhibitors to coagulation factors, particularly to factor V and bovine thrombin, have been infrequently reported in the pediatric population. We report a 3-year-old male who developed a coagulopathy and clinical bleeding after cardiothoracic surgery, during which bovine topical thrombin was used for local hemostasis. Laboratory tests revealed elevated prothrombin, partial thromboplastin, and thrombin times, and a low factor V activity level. He was found to have both human-thrombin and factor V inhibitors, among the first reported cases of these combined inhibitors secondary to bovine topical thrombin. He was treated with intravenous immunoglobulin and steroids with a rapid and durable response.
View details for DOI 10.1002/pbc.22699
View details for PubMedID 20979176
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Development of North American Consensus Guidelines for Medical Laboratories That Perform and Interpret Platelet Function Testing Using Light Transmission Aggregometry
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
2010; 134 (6): 955-963
Abstract
Platelet function testing is important for the diagnostic evaluation of common and rare bleeding disorders. Our study goals were to promote best practices and reduce unnecessary testing variances by developing North American guidelines on platelet function testing. Guidelines were developed by consensus for expert recommendations (minimum level for approval, 70%) that included recommendations on the evaluation and interpretation of light transmission platelet aggregometry (LTA). To assess consensus, medical opinions on recommendations were gathered from diagnostic laboratories that perform LTA, in collaboration with the Quality Management Program-Laboratory Services (QMP-LS) in Ontario, Canada (10 laboratories), and the North American Specialized Coagulation Laboratory Association (NASCOLA; 47 laboratories, 5 overlapping the QMP-LS group). Adequate consensus was achieved for all and 89% of recommendations for the QMP-LS and NASCOLA groups, respectively. The recommendations adopted provide North American laboratories with additional guidance on platelet function testing, including how to interpret LTA abnormalities.
View details for DOI 10.1309/AJCP9V3RRVNZMKDS
View details for Web of Science ID 000284440100013
View details for PubMedID 21088160
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Temozolomide In Acute Myeloid Leukemia: A MGMT Promoter Methylation Status-Based Treatment Stratification
52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2010: 1357–58
View details for Web of Science ID 000289662203644
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Distinct CD8(+)/CD57(+) Large Granular Lymphocytic Populations Seen by Flow Cytometry Are Associated with Monoclonal T-Cell Populations, a Retrospective Case-Control Study of Large Granular Lymphocytic Leukemia
AMER SOC HEMATOLOGY. 2010: 1116
View details for Web of Science ID 000289662203039
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Identification of Novel LNK Mutations In Patients with Chronic Myeloproliferative Neoplasms and Related Disorders
52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2010: 143–44
View details for Web of Science ID 000289662200316
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Identification of a Novel Splice Donor Mutation In the Thrombopoietin Gene In a Philippine Family with Hereditary Thrombocythemia
52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2010: 1272–72
View details for Web of Science ID 000289662203418
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High-Throughput VDJ Sequencing Is Superior to Quantitative PCR and Flow Cytometry for the Quantification of Minimal Residual Disease In Chronic Lymphocytic Leukemia After Hematopoietic Cell Transplantation.
52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)
AMER SOC HEMATOLOGY. 2010: 552–52
View details for Web of Science ID 000289662201393
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Heparin-induced thrombocytopenia: Current status and diagnostic challenges
AMERICAN JOURNAL OF HEMATOLOGY
2010; 85 (9): 700-706
Abstract
Heparin-induced thrombocytopenia (HIT) is a fairly common and potentially catastrophic complication of heparin therapy. Diagnosing HIT remains a challenge, as the patients at risk often have other reasons for thrombocytopenia and/or thrombosis. HIT is considered a clinicopathologic disorder whose diagnosis is generally made on the basis of both clinical criteria and the presence of "HIT antibodies" in the patient's serum or plasma. There are two basic laboratory approaches to detect HIT antibodies. The immunoassays detect antibodies based on their binding properties, whereas the functional assays detect antibodies based on their platelet-activating properties. Prompt and accurate diagnosis of HIT is imperative, as overdiagnosis exposes patients to alternative anticoagulants and their associated bleeding risks, whereas under- or delayed diagnosis leaves patients vulnerable to the thromboembolic sequelae of HIT, which can be life threatening. A critical interpretation of laboratory results by the clinician is an essential component of diagnosing HIT. This requires a keen understanding of the current concepts in the pathophysiologic mechanisms of the disease, and the application of these concepts when interpreting the results of both the functional and immunoassays. Equally important is an awareness of the strengths and weaknesses, as well as the current lack of standardization and proficiency testing, of these assays.
View details for DOI 10.1002/ajh.21770
View details for Web of Science ID 000281601900012
View details for PubMedID 20665476
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Complete donor T-cell engraftment 30 days after allogeneic transplantation predicts molecular remission in high-risk chronic lymphocytic leukaemia
BRITISH JOURNAL OF HAEMATOLOGY
2010; 150 (5): 637-639
View details for DOI 10.1111/j.1365-2141.2010.08252.x
View details for Web of Science ID 000281060700020
View details for PubMedID 20528878
View details for PubMedCentralID PMC2935248
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Novel mutations in the inhibitory adaptor protein LNK drive JAK-STAT signaling in patients with myeloproliferative neoplasms
BLOOD
2010; 116 (6): 988-992
Abstract
Dysregulated Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling due to activation of tyrosine kinases is a common feature of myeloid malignancies. Here we report the first human disease-related mutations in the adaptor protein LNK, a negative regulator of JAK-STAT signaling, in 2 patients with JAK2 V617F-negative myeloproliferative neoplasms (MPNs). One patient exhibited a 5 base-pair deletion and missense mutation leading to a premature stop codon and loss of the pleckstrin homology (PH) and Src homology 2 (SH2) domains. A second patient had a missense mutation (E208Q) in the PH domain. BaF3-MPL cells transduced with these LNK mutants displayed augmented and sustained thrombopoietin-dependent growth and signaling. Primary samples from MPN patients bearing LNK mutations exhibited aberrant JAK-STAT activation, and cytokine-responsive CD34(+) early progenitors were abnormally abundant in both patients. These findings indicate that JAK-STAT activation due to loss of LNK negative feedback regulation is a novel mechanism of MPN pathogenesis.
View details for DOI 10.1182/blood-2010-02-270108
View details for Web of Science ID 000280881700021
View details for PubMedID 20404132
View details for PubMedCentralID PMC2924231
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Hereditary diffuse gastric cancer due to a previously undescribed CDH1 splice site mutation
HUMAN PATHOLOGY
2010; 41 (8): 1200-1203
Abstract
Our patient was a 52-year-old man who was diagnosed with signet ring cell gastric adenocarcinoma. An extensive family history of gastric cancer raised suspicion for hereditary diffuse gastric cancer. Sequencing of the patient's CDH1 gene revealed a novel point mutation in a strictly conserved splice site within intron 6, c.833-2 A > G. This mutation was predicted to result in loss of function due to defective RNA splicing. To characterize the pathogenic mechanism of this mutation, we amplified the patient's CDH1 gene products by reverse transcriptase polymerase chain reaction. Primers flanking the region of the mutation detected 3 distinct transcripts. In addition to the wild-type product, a larger product consistent with activation of a cryptic splice site within intron 6 and a smaller product shown to result from exon 7 skipping were detected. In summary, we have identified a novel CDH1 mutation in a large hereditary diffuse gastric cancer kindred and identified its pathogenic mechanism.
View details for DOI 10.1016/j.humpath.2010.01.022
View details for PubMedID 20624523
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Future research in ITP: an ICIS consensus
3rd Intercontinental-Cooperative-ITP-Study-Group Expert Meeting
SPRINGER. 2010: S19–S23
Abstract
While much has been learned about the basic immunology and clinical characteristics of immune thrombocytopenia, many important questions remain with regard to pathogenesis, disease progression, identification of novel therapeutic targets and approaches, and clinical trials that rationalize and optimize use of existing therapies. The answers to these questions are likely to impact our understanding of the pathogenesis and therapeutic targets of autoimmune disease in general.
View details for DOI 10.1007/s00277-010-0917-1
View details for Web of Science ID 000279682100005
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Future research in ITP: an ICIS consensus.
Annals of hematology
2010; 89: 19-23
Abstract
While much has been learned about the basic immunology and clinical characteristics of immune thrombocytopenia, many important questions remain with regard to pathogenesis, disease progression, identification of novel therapeutic targets and approaches, and clinical trials that rationalize and optimize use of existing therapies. The answers to these questions are likely to impact our understanding of the pathogenesis and therapeutic targets of autoimmune disease in general.
View details for PubMedID 20309690
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Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements
JOURNAL OF IMMUNOLOGY
2010; 184 (12): 6986-6992
Abstract
Individual variation in the Ig germline gene repertoire leads to individual differences in the combinatorial diversity of the Ab repertoire, but the study of such variation has been problematic. The application of high-throughput DNA sequencing to the study of rearranged Ig genes now makes this possible. The sequencing of thousands of VDJ rearrangements from an individual, either from genomic DNA or expressed mRNA, should allow their germline IGHV, IGHD, and IGHJ repertoires to be inferred. In addition, where previously mere glimpses of diversity could be gained from sequencing studies, new large data sets should allow the rearrangement frequency of different genes and alleles to be seen with clarity. We analyzed the DNA of 108,210 human IgH chain rearrangements from 12 individuals and determined their individual IGH genotypes. The number of reportedly functional IGHV genes and allelic variants ranged from 45 to 60, principally because of variable levels of gene heterozygosity, and included 14 previously unreported IGHV polymorphisms. New polymorphisms of the IGHD3-16 and IGHJ6 genes were also seen. At heterozygous loci, remarkably different rearrangement frequencies were seen for the various IGHV alleles, and these frequencies were consistent between individuals. The specific alleles that make up an individual's Ig genotype may therefore be critical in shaping the combinatorial repertoire. The extent of genotypic variation between individuals is highlighted by an individual with aplastic anemia who appears to lack six contiguous IGHD genes on both chromosomes. These deletions significantly alter the potential expressed IGH repertoire, and possibly immune function, in this individual.
View details for DOI 10.4049/jimmunol.1000445
View details for Web of Science ID 000278516700047
View details for PubMedID 20495067
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Comprehensive and Efficient HBB Mutation Analysis for Detection of beta-Hemoglobinopathies in a Pan-Ethnic Population
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
2010; 133 (5): 700-707
Abstract
Current methods that assay hemoglobin beta-globin chain variants can have limited clinical sensitivity when applied techniques identify only a predefined panel of mutations. Even sequence-based assays may be limited depending on which gene regions are investigated. We sought to develop a clinically practical yet inclusive molecular assay to identify beta-globin mutations in multicultural populations. We highlight the beta-globin mutation detection assay (beta-GMDA), an extensive gene sequencing assay. The polymerase chain reaction (PCR) primers are located to encompass virtually all hemoglobin beta locus (HBB) mutations. In addition, this assay is able to detect, by gap PCR, a common large deletion (Delta619 base pair), which would be missed by sequencing alone. We describe our 5-year experience with the beta-GMDA and indicate its capability for detecting homozygous, heterozygous, and compound heterozygous sequence changes, including previously unknown HBB variants. The beta-GMDA offers superior sensitivity and ease of use with comprehensive detection of HBB mutations that result in beta-globin chain variants.
View details for DOI 10.1309/AJCP7HQ2KWGHECIO
View details for Web of Science ID 000277476500004
View details for PubMedID 20395516
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Comprehensive and Efficient HBB Mutation Analysis for Detection of beta-Hemoglobinopathies in a Pan-Ethnic Population
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
2010; 133 (5): 700-707
View details for DOI 10.1309/AJCP7HQ2KWGHECIO
View details for Web of Science ID 000932237600004
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Combined Use of PCR-Based TCRG and TCRB Clonality Tests on Paraffin-Embedded Skin Tissue in the Differential Diagnosis of Mycosis Fungoides and Inflammatory Dermatoses
JOURNAL OF MOLECULAR DIAGNOSTICS
2010; 12 (3): 320-327
Abstract
The distinction between mycosis fungoides (MF) and inflammatory dermatoses (ID) by clinicopathologic criteria can be challenging. There is limited information regarding the performance characteristics and utility of TCRG and TCRB clonality assays in diagnosis of MF and ID from paraffin-embedded tissue sections. In this study, PCR tests were performed with both TCRG and TCRB BIOMED-2 clonality methods followed by capillary electrophoresis and Genescan analysis using DNA samples from 35 MF and 96 ID patients with 69 and 133 paraffin-embedded specimens, respectively. Performance characteristics were determined for each test individually and in combination. TCRG and TCRB tests demonstrated identical sensitivity (64%) and specificity (84%) when analyzed as individual assays. The positive predictive value, negative predictive value, and change of posttest MF probability over a range of MF pretest probabilities were obtained. These data were used to construct an algorithm for sequential use of TCRG and TCRB. As single tests, commercially available BIOMED-2 PCR-based TCRG and TCRB clonality tests on paraffin-embedded tissue have no significant difference in terms of sensitivity and specificity. Combined use of the two tests in patients with intermediate pretest probabilities as proposed in the algorithm could improve test utility.
View details for DOI 10.2353/jmoldx.2010.090123
View details for Web of Science ID 000277531700009
View details for PubMedID 20203005
View details for PubMedCentralID PMC2860468
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Presentation of Extranodal Natural Killer T-Cell Lymphoma, Nasal Type, With Poorly Circumscribed Erythematous Patches
JOURNAL OF CLINICAL ONCOLOGY
2010; 28 (6): E94-E95
View details for DOI 10.1200/JCO.2009.24.3428
View details for Web of Science ID 000274653200030
View details for PubMedID 19933911
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Acute Myeloid Leukemia (AML) with Monosomal Karyotype Is Characterized by Absence of NPM1 and FLT3 Mutations, Worse Clinical Outcome and Usually Falls within AML with Myelodysplasia-Related Changes (MRC)
NATURE PUBLISHING GROUP. 2010: 328A
View details for Web of Science ID 000274582502144
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Acute Myeloid Leukemia (AML) with Monosomal Karyotype Is Characterized by Absence of NPM1 and FLT3 Mutations, Worse Clinical Outcome and Usually Falls within AML with Myelodysplasia-Related Changes (MRC)
NATURE PUBLISHING GROUP. 2010: 328A
View details for Web of Science ID 000274337301479
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Design and Evaluation of a Real-Time PCR Assay for Quantification of JAK2 V617F and Wild-Type JAK2 Transcript Levels in the Clinical Laboratory
JOURNAL OF MOLECULAR DIAGNOSTICS
2010; 12 (1): 58-64
Abstract
The somatic mutation JAK2 V617F is associated with BCR-ABL1-negative myeloproliferative neoplasms. Detection of this mutation aids diagnosis of these neoplasms, and quantification of JAK2 V617F may provide a method to monitor response to therapy. For these reasons, we designed a clinical assay that uses allele-specific PCR and real-time detection with hydrolysis probes for the quantification of JAK2 V617F, wild-type JAK2, and GAPDH transcripts. Mutant and wild-type JAK2 were quantified by using external plasmid standards that contain the relevant JAK2 V617F or JAK2 sequence, respectively. We tested 55 peripheral blood specimens from patients with suspected myeloproliferative neoplasms and 55 peripheral blood specimens from patients not known to have myeloproliferative neoplasms. Low-level, nonspecific amplification was detected in reactions containing a high copy number of plasmid standards and in specimens from patients not known to have myeloproliferative neoplasms, necessitating the use of a laboratory-established mutant to wild-type cutoff. The limit of detection established by using cell line dilutions is 0.1%, and this method identified three JAK2 V617F-positive patients who were not detected by a less sensitive method. The assay characteristics and our initial evaluation indicate this method can be used for the detection and quantification of JAK2 V617F, which should be useful for diagnosis of myeloproliferative neoplasms and potentially for monitoring minimal residual disease in future trials of therapies targeted to myeloproliferative neoplasms.
View details for DOI 10.2353/jmoldx.2010.090068
View details for Web of Science ID 000273664100009
View details for PubMedID 19959796
View details for PubMedCentralID PMC2797719
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Anti-Glycoprotein H Antibody Impairs the Pathogenicity of Varicella-Zoster Virus in Skin Xenografts in the SCID Mouse Model
JOURNAL OF VIROLOGY
2010; 84 (1): 141-152
Abstract
Varicella-zoster virus (VZV) infection is usually mild in healthy individuals but can cause severe disease in immunocompromised patients. Prophylaxis with varicella-zoster immunoglobulin can reduce the severity of VZV if given shortly after exposure. Glycoprotein H (gH) is a highly conserved herpesvirus protein with functions in virus entry and cell-cell spread and is a target of neutralizing antibodies. The anti-gH monoclonal antibody (MAb) 206 neutralizes VZV in vitro. To determine the requirement for gH in VZV pathogenesis in vivo, MAb 206 was administered to SCID mice with human skin xenografts inoculated with VZV. Anti-gH antibody given at 6 h postinfection significantly reduced the frequency of skin xenograft infection by 42%. Virus titers, genome copies, and lesion size were decreased in xenografts that became infected. In contrast, administering anti-gH antibody at 4 days postinfection suppressed VZV replication but did not reduce the frequency of infection. The neutralizing anti-gH MAb 206 blocked virus entry, cell fusion, or both in skin in vivo. In vitro, MAb 206 bound to plasma membranes and to surface virus particles. Antibody was internalized into vacuoles within infected cells, associated with intracellular virus particles, and colocalized with markers for early endosomes and multivesicular bodies but not the trans-Golgi network. MAb 206 blocked spread, altered intracellular trafficking of gH, and bound to surface VZV particles, which might facilitate their uptake and targeting for degradation. As a consequence, antibody interference with gH function would likely prevent or significantly reduce VZV replication in skin during primary or recurrent infection.
View details for DOI 10.1128/JVI.01338-09
View details for Web of Science ID 000272564300013
View details for PubMedID 19828615
View details for PubMedCentralID PMC2798403
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Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing
SCIENCE TRANSLATIONAL MEDICINE
2009; 1 (12)
Abstract
The complex repertoire of immune receptors generated by B and T cells enables recognition of diverse threats to the host organism. In this work, we show that massively parallel DNA sequencing of rearranged immune receptor loci can provide direct detection and tracking of immune diversity and expanded clonal lymphocyte populations in physiological and pathological contexts. DNA was isolated from blood and tissue samples, a series of redundant primers was used to amplify diverse DNA rearrangements, and the resulting mixtures of barcoded amplicons were sequenced using long-read ultra deep sequencing. Individual DNA molecules were then characterized on the basis of DNA segments that had been joined to make a functional (or nonfunctional) immune effector. Current experimental designs can accommodate up to 150 samples in a single sequence run, with the depth of sequencing sufficient to identify stable and dynamic aspects of the immune repertoire in both normal and diseased circumstances. These data provide a high-resolution picture of immune spectra in normal individuals and in patients with hematological malignancies, illuminating, in the latter case, both the initial behavior of clonal tumor populations and the later suppression or re-emergence of such populations after treatment.
View details for DOI 10.1126/scitranslmed.3000540
View details for Web of Science ID 000277263200001
View details for PubMedID 20161664
View details for PubMedCentralID PMC2819115
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Increased VNN1/PPARG Gene Expression Ratio Is Correlated with Developing Chronic ITP and Oxidative Stress Exposure to PBMC in Vitro
51st Annual Meeting and Exposition of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2009: 368–68
View details for Web of Science ID 000272725801073
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Critical Values in the Coagulation Laboratory: Results of a Survey of the North American Specialized Coagulation Laboratory Association
AMER SOC HEMATOLOGY. 2009: 576
View details for Web of Science ID 000272725801595
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AML Patients with Monosomal Karyotype Are Characterized by Absence of NPM1 and FLT3 Mutations and Worse Clinical Outcome.
AMER SOC HEMATOLOGY. 2009: 1035
View details for Web of Science ID 000272725803193
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Clinical Assay Design for Detection of CEBPA Mutations in Patients with Acute Myeloid Leukemia
AMER SOC INVESTIGATIVE PATHOLOGY, INC. 2009: 627
View details for Web of Science ID 000271681400060
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Interim results of protracted low doses of temozolomide in high-risk acute myeloid leukemia
45th Annual Meeting of the American-Society-of-Clinical-Oncology (ASCO)
AMER SOC CLINICAL ONCOLOGY. 2009
View details for Web of Science ID 000276606605042
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Baseline status of O (6)-methylguanine-DNA-methyltransferase (MGMT) promoter methylation and effect of protracted doses of temozolomide on MGMT in acute leukemia.
AMER ASSOC CANCER RESEARCH. 2009
View details for Web of Science ID 000209702702111
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Glycogen synthase kinase 3 beta missplicing contributes to leukemia stem cell generation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009; 106 (10): 3925-3929
Abstract
Recent evidence suggests that a rare population of self-renewing cancer stem cells (CSC) is responsible for cancer progression and therapeutic resistance. Chronic myeloid leukemia (CML) represents an important paradigm for understanding the genetic and epigenetic events involved in CSC production. CML progresses from a chronic phase (CP) in hematopoietic stem cells (HSC) that harbor the BCR-ABL translocation, to blast crisis (BC), characterized by aberrant activation of beta-catenin within granulocyte-macrophage progenitors (GMP). A major barrier to predicting and inhibiting blast crisis transformation has been the identification of mechanisms driving beta-catenin activation. Here we show that BC CML myeloid progenitors, in particular GMP, serially transplant leukemia in immunocompromised mice and thus are enriched for leukemia stem cells (LSC). Notably, cDNA sequencing of Wnt/beta-catenin pathway regulatory genes, including adenomatous polyposis coli, GSK3beta, axin 1, beta-catenin, lymphoid enhancer factor-1, cyclin D1, and c-myc, revealed a novel in-frame splice deletion of the GSK3beta kinase domain in the GMP of BC samples that was not detectable by sequencing in blasts or normal progenitors. Moreover, BC CML progenitors with misspliced GSK3beta have enhanced beta-catenin expression as well as serial engraftment potential while reintroduction of full-length GSK3beta reduces both in vitro replating and leukemic engraftment. We propose that CP CML is initiated by BCR-ABL expression in an HSC clone but that progression to BC may include missplicing of GSK3beta in GMP LSC, enabling unphosphorylated beta-catenin to participate in LSC self-renewal. Missplicing of GSK3beta represents a unique mechanism for the emergence of BC CML LSC and might provide a novel diagnostic and therapeutic target.
View details for DOI 10.1073/pnas.0900189106
View details for Web of Science ID 000264036900051
View details for PubMedID 19237556
View details for PubMedCentralID PMC2646624
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Clinical characterization of acute myeloid leukemia with myelodysplasia-related changes as defined by the 2008 WHO classification system
50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium
AMER SOC HEMATOLOGY. 2009: 1906–8
Abstract
Although some studies have validated the 2001 World Health Organization (WHO) classification of acute myeloid leukemia (AML), including the importance of multilineage dysplasia, others have suggested that multilineage dysplasia correlates with unfavorable cytogenetics but has no independent impact on prognosis. In 2008, the revised WHO classification has expanded this category into "AML with myelodysplasia-related changes" (AML-MRC). We evaluated the clinical, pathologic, cytogenetic, and molecular features of 100 AML patients using the 2008 WHO criteria. Patients underwent genetic screening for NPM1, FLT3-ITD, FLT3-D835, and CEBPA mutations. Compared with patients with AML, not otherwise specified, patients with AML-MRC were significantly older (P= .014), presented with a lower hemoglobin (P= .044), more frequently expressed CD14 (P= .048), and exhibited a decreased frequency of CEBPA mutations (P= .001). Multivariate analysis indicated that patients with AML-MRC had a significantly worse overall survival, progression-free survival, and complete response compared with AML-not otherwise specified (all P< .001). These data support the clinical, morphologic, and cytogenetic criteria for this 2008 WHO AML category.
View details for DOI 10.1182/blood-2008-10-182782
View details for Web of Science ID 000263723700007
View details for PubMedID 19131546
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Laboratory Practice Guidelines for Detecting and Reporting BCR-ABL Drug Resistance Mutations in Chronic Myelogenous Leukemia and Acute Lymphoblastic Leukemia A Report of the Association for Molecular Pathology
JOURNAL OF MOLECULAR DIAGNOSTICS
2009; 11 (1): 4-11
Abstract
The BCR-ABL tyrosine kinase produced by the t(9;22)(q34;q11) translocation, also known as the Philadelphia chromosome, is the initiating event in chronic myeloid leukemia (CML) and Ph+ acute lymphoblastic leukemia (ALL). Targeting of BCR-ABL with tyrosine kinase inhibitors (TKIs) has resulted in rapid clinical responses in the vast majority of patients with CML and Philadelphia chromosome+ ALL. However, long-term use of TKIs occasionally results in emergence of therapy resistance, in part through the selection of clones with mutations in the BCR-ABL kinase domain. We present here an overview of the current practice in monitoring for such mutations, including the methods used, the clinical and laboratory criteria for triggering mutational analysis, and the guidelines for reporting BCR-ABL mutations. We also present a proposal for a public database for correlating mutational status with in vitro and in vivo responses to different TKIs to aid in the interpretation of mutation studies.
View details for DOI 10.2353/jmoldx.2009.080095
View details for PubMedID 19095773
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High-Throughput Immune Receptor Sequencing for Diagnosis, Prognosis and Monitoring of Lymphoid Malignancies
NATURE PUBLISHING GROUP. 2009: 368A
View details for Web of Science ID 000262486301670
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Acute Myeloid Leukemia with Myelodysplasia-Related Changes as Defined by the 2008 WHO Classification System
NATURE PUBLISHING GROUP. 2009: 291A
View details for Web of Science ID 000262371501315
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High-Throughput Immune Receptor Sequencing for Diagnosis, Prognosis and Monitoring of Lymphoid Malignancies
NATURE PUBLISHING GROUP. 2009: 368A
View details for Web of Science ID 000262371501669
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Acute Myeloid Leukemia with Myelodysplasia-Related Changes as Defined by the 2008 WHO Classification System
98th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology
NATURE PUBLISHING GROUP. 2009: 291A–291A
View details for Web of Science ID 000262486301315
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Molecular stratification of patients with normal karyotype acute myeloid leukemia based on initial assessment of FLT3-internal tandem duplication status at first complete remission
LEUKEMIA & LYMPHOMA
2009; 50 (5): 851-853
View details for DOI 10.1080/10428190902838400
View details for Web of Science ID 000266201800029
View details for PubMedID 19452323
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Clinical Characterization of Acute Myeloid Leukemia with Myelodysplasia-Related Changes as Defined by the 2008 WHO Classification System
50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium
AMER SOC HEMATOLOGY. 2008: 341–42
View details for Web of Science ID 000262104701146
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Complete Donor Chimerism Predicts Molecular Remission in High Risk CLL Following Nonmyeloablative Transplantation
AMER SOC HEMATOLOGY. 2008: 1127–28
View details for Web of Science ID 000262104703719
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Tailored Temozolomide Therapy for Elderly Patients with Acute Myeloid Leukemia.
AMER SOC HEMATOLOGY. 2008: 351
View details for Web of Science ID 000262104701178
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Elevated Vanin 1 and Advillin Expression Is Associated with Progression to Chronic ITP in Children
50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium
AMER SOC HEMATOLOGY. 2008: 152–53
View details for Web of Science ID 000262104700398
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High-Throughput Sequencing for Diagnosis, Prognosis and Monitoring of Lymphoid Malignancies.
50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium
AMER SOC HEMATOLOGY. 2008: 1294–94
View details for Web of Science ID 000262104704397
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Design and Validation of a Real-Time PCR Assay for Quantification of JAK2 V617F and Wild-type JAK2 Transcript Levels
14th Annual Meeting of the Association-for-Molecular-Pathology
ELSEVIER SCIENCE INC. 2008: 581–81
View details for Web of Science ID 000260533600084
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Superficial venous thrombosis associated with congenital absence of the inferior vena cava and previous episode of deep venous thrombosis
AMERICAN JOURNAL OF HEMATOLOGY
2008; 83 (3): 250-252
Abstract
Congenital malformations of the inferior vena cava (IVC) are uncommon and may be associated with an increased risk of venous thrombosis. We report the case of a man with congenital absence of the IVC and remote history of deep venous thrombosis who now presents with severe abdominal wall superficial thrombophlebitis. To our knowledge, this is the first report of a patient with IVC absence who has developed both deep and superficial venous thromboses.
View details for DOI 10.1002/ajh.21089
View details for Web of Science ID 000253559700018
View details for PubMedID 17918250
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Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers
JOURNAL OF MOLECULAR DIAGNOSTICS
2008; 10 (1): 67-77
Abstract
Clinical workup of metastatic malignancies of unknown origin is often arduous and expensive and is reported to be unsuccessful in 30 to 60% of cases. Accurate classification of uncertain primary cancers may improve with microarray-based gene expression testing. We evaluated the analytical performance characteristics of the Pathwork tissue of origin test, which uses expression signals from 1668 probe sets in a gene expression microarray, to quantify the similarity of tumor specimens to 15 known tissues of origin. Sixty archived tissue specimens from poorly and undifferentiated tumors (metastatic and primary) were analyzed at four laboratories representing a wide range of preanalytical conditions (eg, personnel, reagents, instrumentation, and protocols). Cross-laboratory comparisons showed highly reproducible results between laboratories, with correlation coefficients between 0.95 to 0.97 for measurements of similarity scores, and an average 93.8% overall concordance between laboratories in terms of final tissue calls. Bland-Altman plots (mean coefficients of reproducibility of 32.48+/-3.97) and kappa statistics (kappa >0.86) also indicated a high level of agreement between laboratories. We conclude that the Pathwork tissue of origin test is a robust assay that produces consistent results in diverse laboratory conditions reflecting the preanalytical variations found in the everyday clinical practice of molecular diagnostics laboratories.
View details for DOI 10.2353/jmoldx.2008.070099
View details for Web of Science ID 000252521200009
View details for PubMedID 18083688
View details for PubMedCentralID PMC2175545
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Significance of NPM1 and FLT3 mutations in acute myeloid leukemia with multilineage dysplasia: Does NPM1 identify a lower risk group?
NATURE PUBLISHING GROUP. 2008: 281A
View details for Web of Science ID 000252181101411
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Significance of NPM1 and FLT3 mutations in acute myeloid leukemia with multilineage dysplasia: Does NPM1 identify a lower risk group?
97th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology
NATURE PUBLISHING GROUP. 2008: 281A–281A
View details for Web of Science ID 000252180201412
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Gene expression and pathway analysis of immune thrombocytopenic purpura
BRITISH JOURNAL OF HAEMATOLOGY
2008; 140 (1): 99-103
Abstract
A global expression profile of peripheral blood from patients with immune thrombocytopenic purpura (ITP) was performed that identified an ITP-specific signature, which also included interferon (IFN)-induced genes. Several genes correlated with ITP have been shown to be associated with expression signatures in systemic lupus erythematosis and rheumatoid arthritis, indicating an overlap with other autoimmune disorders. Pathway analysis demonstrated that IFN signalling, death receptor and protein ubiquitination pathways were associated with ITP. These results provide the first glimpse of the genes and pathways consistently aberrant in ITP, identifying new targets for investigations of pathogenesis and treatment of ITP.
View details for DOI 10.1111/j.1365-2141.2007.06881.x
View details for PubMedID 18005267
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Laboratory testing for heparin-induced thrombocytopenia is inconsistent in North America: A survey of North American specialized coagulation laboratories
THROMBOSIS AND HAEMOSTASIS
2007; 98 (6): 1357-1361
Abstract
Heparin-induced thrombocytopenia (HIT) is a serious complication of heparin therapy. As HIT is considered a clinico-pathologic entity, laboratory practices have an important role in diagnosing or excluding HIT. It was the objective of this study to assess the current status of laboratory testing for HIT in North America. An online survey consisting of 67 questions related to laboratory testing for HIT was developed by the North American Specialized Coagulation Laboratory Association (NASCOLA), and distributed to its 59 members. The survey included queries about HIT test ordering practices, HIT immunoassay and activation assays performed, and reporting practices. Data was collected from the 44 NASCOLA laboratories who responded. Of these sites, 88% performed immunoassays for HIT, commonly using commercial assays. However, sites varied in practices related to use of controls, immunoglobulin class of antibody detected, and in result interpretation and reporting. Platelet activation assays for HIT were performed by 36% of sites, commonly using assays of serotonin release (50%) or heparin-induced platelet aggregation (43%). Sites varied in the use of washed platelets versus platelet-rich plasma, controls, and heparin concentrations. This survey is the first comprehensive assessment of patterns of practice in HIT testing among diagnostic coagulation laboratories in North America. We observed site-specific variability of testing methods encompassing all stages of testing, including pre-analytical handling, testing methodologies, and result interpretation and reporting. The variability in HIT platelet activation assay methods among institutions indicates a need for proficiency testing to assess assay performance, and for consensus guidelines on HIT laboratory testing.
View details for DOI 10.1160/TH07-06-0401
View details for Web of Science ID 000251687400031
View details for PubMedID 18064336
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Effect of Ginkgo biloba (EGb 761) aggregation and platelet and aspirin on platelet analysis among older adults at risk of cardiovascular disease: a randomized clinical trial
BLOOD COAGULATION & FIBRINOLYSIS
2007; 18 (8): 787-793
Abstract
Several case reports have implicated Ginkgo biloba in clinically adverse bleeding disorders. Ginkgo biloba has been reported to increase pain-free walking distance among patients with peripheral artery disease (PAD). Standard PAD therapy includes 325 mg/day aspirin. The objective of this study was to examine potential adverse effects of concomitant aspirin and Ginkgo biloba on platelet function. Ginkgo biloba (EGb 761, 300 mg/day) was compared with placebo for effects on measures of platelet aggregation among adults consuming 325 mg/day aspirin in a randomized, double-blind, placebo-controlled, parallel design trial of 4-week duration. Participants were adults, age 69 +/- 10 years, with PAD or risk factors for cardiovascular disease. Outcome measures included platelet function analysis (PFA-100 analyzer) using ADP as an agonist (n = 26 placebo; n = 29 ginkgo), and platelet aggregation using ADP, epinephrine, collagen and ristocetin as agonists (n = 21 placebo; n = 23 ginkgo). Participants kept daily logs of bleeding or bruising episodes. There were no clinically or statistically significant differences between treatment groups for any agonists, for either PFA-100 analysis or platelet aggregation. Reports of bleeding or bruising were infrequent and similar for both study groups. In conclusion, in older adults with PAD or cardiovascular disease risk, a relatively high dose of Ginkgo biloba combined with 325 mg/day daily aspirin did not have a clinically or statistically detectable impact on indices of coagulation examined over 4 weeks, compared with the effect of aspirin alone. No adverse bleeding events were observed, although the trial was limited to a small sample size.
View details for Web of Science ID 000251271200012
View details for PubMedID 17982321
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Missplicing of glycogen synthase kinase 3 beta: A potential mechanism of blast crisis chronic myeloid leukemia stem cell generation
49th Annual Meeting of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2007: 238A–239A
View details for Web of Science ID 000251100801044
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Large granular lymphocyte leukemia: Clonality reconsidered.
AMER SOC HEMATOLOGY. 2007: 912A
View details for Web of Science ID 000251100804139
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T-cell clonality analysis in biopsy specimens from two different skin sites shows high specificity in the diagnosis of patients with suggested mycosis fungoides
43rd Annual Meeting of the American-Society-of-Dermatopathology
MOSBY-ELSEVIER. 2007: 782–90
Abstract
The diagnosis of mycosis fungoides (MF) is often difficult because of significant clinical and histopathologic overlap with inflammatory dermatoses. T-cell receptor (TCR)gamma chain rearrangement by polymerase chain reaction (PCR) (TCR-PCR) is a helpful adjuvant tool in this setting, but several of the inflammatory dermatoses in the differential diagnosis of MF may contain a clonal T-cell proliferation.We examined whether analysis for T-cell clonality and comparison of the clones with the standardized BIOMED-2 PCR multiplex primers for the TCRgamma chain from two anatomically distinct skin sites improves diagnostic accuracy.We examined two biopsy specimens each from 10 patients with unequivocal MF, from 18 patients with inflammatory dermatoses, and from 18 patients who could initially not be definitively given a diagnosis based on clinical and histopathologic criteria.Eight of 10 patients with unequivocal MF had an identical clone in both biopsy specimens. Two of 18 patients with inflammatory dermatoses were found to have a clone in one of the biopsy specimens. On further follow-up of the 18 patients with morphologically nondiagnostic biopsy specimens, 13 of 18 were later confirmed to have MF and 5 of 18 had inflammatory dermatoses. Eleven of 13 patients with MF had an identical clone in both biopsy specimens; two of 13 had a polyclonal amplification pattern in both biopsy specimens. Four of 5 patients with inflammatory dermatoses had no clone in either biopsy specimen. One patient with an inflammatory dermatosis had an identical clone in both specimens. The sensitivity of TCR-PCR analysis to evaluate for an identical clone at different anatomic skin sites (dual TCR-PCR) is 82.6% and the specificity is 95.7%.The number of patients in the study group was limited.These data suggest that dual TCR-PCR is a very promising technique with high specificity in distinguishing MF from inflammatory dermatoses.
View details for DOI 10.1016/j.jaad.2007.06.004
View details for Web of Science ID 000250387100004
View details for PubMedID 17646032
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Analysis of dystrophin gene alterations in Duchenne and Becker muscular dystrophy patients using a custom comparative genomic hybridization array
AMER SOC INVESTIGATIVE PATHOLOGY, INC. 2007: 650
View details for Web of Science ID 000250849300017
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Identification of an intronic SNP leading to allele dropout during validation of a CDH1 sequencing assay: Implications for designing PCR-based assays
AMER SOC INVESTIGATIVE PATHOLOGY, INC. 2007: 656–57
View details for Web of Science ID 000250849300044
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Analytical performance of a microarray-based gene expression test to determine tissue of origin in uncertain primary cancers
AMER SOC INVESTIGATIVE PATHOLOGY, INC. 2007: 685
View details for Web of Science ID 000250849300166
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Identification of an intronic single nucleotide polymorphism leading to allele dropout during validation of a CDH1 sequencing assay: implications for designing polymerase chain reaction-based assays
GENETICS IN MEDICINE
2007; 9 (11): 752-760
Abstract
The CDH1 gene encodes the cell adhesion protein E-cadherin, and CDH1 germline mutations are associated with hereditary diffuse gastric cancer. Identification of individuals at high risk of developing diffuse gastric cancer affords the opportunity for endoscopic screening or elective prophylactic gastrectomy. We set out to develop a CDH1 sequencing assay for clinical use.All exons of the CDH1 gene were amplified and sequenced with published and modified primers.While validating the assay, we encountered a case in which a single nucleotide polymorphism located in intron 15 led to allele dropout and therefore to a false-negative result. The polymorphism leading to allele dropout was located within a primer-binding sequence, five bases away from the 3' end of the primer. A frameshift mutation in exon 15 was detected by an alternative primer that binds away from the polymorphic site. A search of the University of California Santa Cruz single nucleotide polymorphism database revealed other polymorphisms located within primer-binding sites. A total of 12 primers in nine primer sets were modified to minimize allele dropout risk.The approach of designing primers to avoid known single nucleotide polymorphisms can be generalized to the design of any polymerase chain reaction-based assay and should be employed whenever possible.
View details for DOI 10.1097/GIM.0b013e318159a369
View details for PubMedID 18007144
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Antithrombotic therapy and pregnancy: consensus report and recommendations for prevention and treatment of venous thromboembolism and adverse pregnancy outcomes
AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY
2007; 197 (5)
Abstract
Venous thromboembolism and adverse pregnancy outcomes are potential complications of pregnancy. Numerous studies have evaluated both the risk factors for and the prevention and management of these outcomes in pregnant patients. This consensus group was convened to provide concise recommendations, based on the currently available literature, regarding the use of antithrombotic therapy in pregnant patients at risk for venous thromboembolic events and adverse pregnancy outcomes.
View details for DOI 10.1016/j.ajog.2007.04.022
View details for Web of Science ID 000250915500004
View details for PubMedID 17980177
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Aberrant infection and persistence of varicella-zoster virus in human dorsal root ganglia in vivo absence of glycoprotein I
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2007; 104 (35): 14086-14091
Abstract
Varicella-zoster virus (VZV) causes varicella, establishes latency in sensory ganglia, and reactivates as herpes zoster. Human dorsal root ganglia (DRGs) xenografts in immunodeficient mice provide a model for evaluating VZV neuropathogenesis. Our investigation of the role of glycoprotein I (gI), which is dispensable in vitro, examines the functions of a VZV gene product during infection of human neural cells in vivo. Whereas intact recombinant Oka (rOka) initiated a short replicative phase followed by persistence in DRGs, the gI deletion mutant, rOkaDeltagI, showed prolonged replication with no transition to persistence up to 70 days after infection. Only a few varicella-zoster nucleocapsids and cytoplasmic virions were observed in neurons, and the major VZV glycoprotein, gE, was retained in the rough endoplasmic reticulum in the absence of gI. VZV neurotropism was not disrupted when DRG xenografts were infected with rOka mutants lacking gI promoter elements that bind cellular transactivators, specificity factor 1 (Sp1) and upstream stimulatory factor (USF). Because gI is essential and Sp1 and USF contribute to VZV pathogenesis in skin and T cells in vivo, these DRG experiments indicate that the genetic requirements for VZV infection are less stringent in neural cells in vivo. The observations demonstrate that gI is important for VZV neurotropism and suggest that a strategy to reduce neurovirulence by deleting gI could prolong active infection in human DRGs.
View details for DOI 10.1073/pnas.0706023104
View details for Web of Science ID 000249187500042
View details for PubMedID 17709745
View details for PubMedCentralID PMC1955823
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Testing for maternal cell contamination in prenatal samples - A comprehensive survey of current diagnostic practices in 35 molecular diagnostic laboratories
JOURNAL OF MOLECULAR DIAGNOSTICS
2007; 9 (3): 394-400
Abstract
The potential presence of maternal cell contamination (MCC) in chorionic villus or amniotic fluid samples poses a serious preanalytical risk for prenatal misdiagnosis. The aim of this study was to identify current diagnostic practices in the absence of comprehensive practice guidelines. Thirty-five clinical molecular laboratories that conduct prenatal testing agreed to participate in a clinical practice survey. The survey included questions about sample requirements, test indications, assay type, test performance and limitations, criteria and management of uninformative test results, reporting, and billing. Sixty percent of participating laboratories performed testing on direct and cultured amniotic fluid, whereas forty percent tested cultured cells only. Most also accepted chorionic villus samples. Although MCC testing of fetal samples is recommended in guidelines by the American College of Medical Genetics, only 60% of surveyed laboratories performed it without exception. Commercially available assays were used by 75% of participating laboratories, and at least five identity markers were evaluated at 87% of the laboratories. The reported lower limit of MCC detection ranged from 1 to 20% but was not determined in all laboratories. MCC testing was performed in the majority of molecular diagnostic laboratories, but guidelines for standardization are needed to ensure optimal and accurate prenatal patient care.
View details for DOI 10.2353/jmoldx.2007.070017
View details for Web of Science ID 000247691200015
View details for PubMedID 17591939
View details for PubMedCentralID PMC1899411
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Recalcitrant cutaneous langerhans cell histiocytosis in a child with T-cell acute lymphoblastic leukemia
WILEY-LISS. 2007: 757–58
View details for Web of Science ID 000246239900056
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International standardized approach for flow cytometric residual disease monitoring in chronic lymphocytic leukaemia
LEUKEMIA
2007; 21 (5): 956-964
Abstract
The eradication of minimal residual disease (MRD) in chronic lymphocytic leukaemia (CLL) predicts for improved outcome. However, the wide variety of MRD techniques makes it difficult to interpret and compare different clinical trials. Our aim was to develop a standardized flow cytometric CLL-MRD assay and compare it to real-time quantitative allele-specific oligonucleotide (RQ-ASO) Immunoglobulin heavy chain gene (IgH) polymerase chain reaction (PCR). Analysis of 728 paired blood and marrow samples demonstrated high concordance (87%) for patients off-therapy. Blood analysis was equally or more sensitive than marrow in 92% of samples but marrow analysis was necessary to detect MRD within 3 months of alemtuzumab therapy. Assessment of 50 CLL-specific antibody combinations identified three (CD5/CD19 with CD20/CD38, CD81/CD22 and CD79b/CD43) with low inter-laboratory variation and false-detection rates. Experienced operators demonstrated an accuracy of 95.7% (specificity 98.8%, sensitivity 91.1%) in 141 samples with 0.01-0.1% CLL. There was close correlation and 95% concordance with RQ-ASO IgH-PCR for detection of CLL above 0.01%. The proposed flow cytometry approach is applicable to all sample types and therapeutic regimes, and sufficiently rapid and sensitive to guide therapy to an MRD-negativity in real time. These techniques may be used as a tool for assessing response and comparing the efficacy of different therapeutic approaches.
View details for DOI 10.1038/sj.leu.2404584
View details for Web of Science ID 000245999900014
View details for PubMedID 17361231
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Clinical evaluation of a novel oncologic tissue of origin assay based on gene expression microarray.
ASSOC CLINICAL SCIENTISTS. 2007: 197–97
View details for Web of Science ID 000246264700023
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Severe coagulation factor V deficiency associated with an interstitial deletion of chromosome 1q
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
2007; 5 (3): 626-628
View details for Web of Science ID 000244277800034
View details for PubMedID 17166249
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Safety and efficacy of a ginkgo biloba-containing dietary supplement on cognitive function, quality of life, and platelet function in healthy, cognitively intact older adults
JOURNAL OF THE AMERICAN DIETETIC ASSOCIATION
2007; 107 (3): 422-432
Abstract
To determine if a ginkgo biloba-containing supplement improves cognitive function and quality of life, alters primary hemostasis, and is safe in healthy, cognitively intact older adults.Four-month, randomized, double-blind, placebo-controlled parallel design.Ninety men and women (age range 65 to 84 years) were recruited to a university clinic. Eligibility included those without dementia or depression, not taking psychoactive medications or medications or supplements that alter hemostasis.Ninety subjects were randomly assigned to placebo or a ginkgo biloba-based supplement containing 160 mg ginkgo biloba, 68 mg gotu kola, and 180 mg decosahexaenoic acid per day for 4 months.Assessments included: six standardized cognitive function tests, the SF-36 Quality of Life questionnaire, the Platelet Function Analyzer-100 (Dade Behring, Eschbom, Germany), and the monitoring of adverse events.Baseline characteristics and study hypotheses were tested using analysis of covariance. Tests were two-tailed with a 0.05 significance level.Seventy-eight subjects (87%) completed both baseline and 4-month testing (n=36 in placebo group, n=42 in ginkgo biloba group). At baseline, the participants' cognitive function was above average. One of six cognitive tests indicated significant protocol differences at 4 months (P=0.03), favoring the placebo. There were no significant differences in quality of life, platelet function, or adverse events.These finding do not support the use of a ginkgo biloba-containing supplement for improving cognitive function or quality of life in cognitively intact, older, healthy adults. However, high baseline scores may have contributed to the null findings. The ginkgo biloba product seems safe and did not alter platelet function, though additional studies are needed to evaluate the interaction of varying doses of ginkgo biloba and ginkgo biloba-containing supplements with medications and supplements that alter hemostasis.
View details for DOI 10.1016/j.jada.2006.12.011
View details for Web of Science ID 000244551100016
View details for PubMedID 17324660
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Molecular characterization and subcellular localization of Tyr478del: a pathogenic in-frame deletion in coagulation factor V
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
2007; 5 (2): 431-433
View details for Web of Science ID 000243563000038
View details for PubMedID 17269939
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Rituximab infusion two months after total lymphoid irradiation-antithymocyte globulin (TLI-ATG) nonmyeloablative transplantation maintains B-cell disease control with minimal GVHD
Tandem BMT Meeting 2007
ELSEVIER SCIENCE INC. 2007: 103–
View details for Web of Science ID 000244028300284
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T-cell clonality analysis in biopsies from two different sites improves specificity of diagnosis in patients with suspected mycosis fungoides
BLACKWELL PUBLISHING. 2007: 82
View details for Web of Science ID 000243233600026
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Gene expression profile of idiopathic thrombocytopenic purpura (ITP) reveals elevated expression of interferon regulated genes.
48th Annual Meeting of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2006: 211A–211A
View details for Web of Science ID 000242440000703
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Severe factor V deficiency associated with chromosome 1q deletion.
AMER SOC HEMATOLOGY. 2006: 310A
View details for Web of Science ID 000242440001302
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Rituximab infusion two months after nonmyeloablative transplantation maintains B-cell disease control with minimal GVHD.
48th Annual Meeting of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2006: 823A–823A
View details for Web of Science ID 000242440003696
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Microsatellite instability testing: Comparison of the Promega MSI Analysis System, the Bethesda panel, and immunohistochemistry
AMER SOC INVESTIGATIVE PATHOLOGY, INC. 2006: 665
View details for Web of Science ID 000241811800199
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Testing for maternal cell contamination in prenatal samples: a comprehensive survey of current diagnostic practices in 35 molecular diagnostic laboratories in the US
AMER SOC INVESTIGATIVE PATHOLOGY, INC. 2006: 622–23
View details for Web of Science ID 000241811800019
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Gene expression profile of idiopathic thrombocytopenic purpura (ITP)
2nd Expert Meeting of the Intercontinental-Childhood-ITP-Study-Group (ICIS)
WILEY PERIODICALS, INC. 2006: 675–77
Abstract
To search for novel mechanisms that contribute to the pathophysiology of idiopathic thrombocytopenic purpura (ITP), we determined the whole blood gene expression profile in five ITP patients and five control samples. Using DNA microarrays that contained 24,473 unique putative genes, we found 176 cDNAs that were strongly correlated with ITP. These included a cluster of interferon-regulated genes and TLR7, as well many less-well characterized genes which are candidates for further study. We believe this approach is likely to yield new insights into our understanding of the molecular pathophysiology of ITP.
View details for DOI 10.1002/pbc.20981
View details for Web of Science ID 000240405600010
View details for PubMedID 16933260
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Maintenance rituximab following induction chemoimmunotherapy may prolong progression-free survival in mantle cell lymphoma: a pilot study from the Wisconsin Oncology Network
ANNALS OF ONCOLOGY
2006; 17 (9): 1418-1423
Abstract
There is no standard first line treatment for mantle cell lymphoma.This was a multicenter phase II pilot study of rituximab and modified hyper-fractionated cyclophosphamide, vincristine doxorubicin, dexamethasone (modified R-hyperCVAD) administered every 28 days for four to six cycles followed by rituximab maintenance therapy consisting of four weekly doses every 6 months for 2 years. Unlike traditional hyperCVAD regimens, no methotrexate or cytarabine was administered.Of 22 patients, the overall response rate was 77% and the complete response rate was 64%. With a median follow-up time of 37 months in surviving patients, the median PFS was 37 months and the median OS was not reached. The achievement of a molecular remission did not correlate with improved outcome. The major toxicity was expected myelosuppression. Two patients died during induction treatment. There were no major adverse effects during maintenance therapy.In a multicenter trial, modified R-hyperCVAD was tolerable and effective induction therapy for untreated MCL. Maintenance rituximab appeared to prolong PFS without increasing toxicity.
View details for DOI 10.1093/annonc/mdl127
View details for Web of Science ID 000240587900012
View details for PubMedID 16766582
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Detection of the JAK2 V617F mutation by LightCycler PCR and probe dissociation analysis
JOURNAL OF MOLECULAR DIAGNOSTICS
2006; 8 (3): 330-334
Abstract
A point mutation in the JAK2 gene, a member of the tyrosine kinase family, was recently identified and shown to be associated with several myeloproliferative disorders. Several studies identified the same JAK2 point mutation (1,849G>T), resulting in the substitution of a valine to phenylalanine at codon 617 (V617F). We developed a simple and sensitive method to detect this mutation via polymerase chain reaction and probe dissociation analysis using the LightCycler platform, and we compared this method to existing restriction fragment-length polymorphism, direct sequencing, and amplification refractory mutation system methods. We found that the LightCycler method offered advantages of speed, reliability, and more straightforward interpretation over the restriction fragment-length polymorphism and sequencing approaches.
View details for DOI 10.2353/jmoldx.2006.050130
View details for Web of Science ID 000239106800006
View details for PubMedID 16825505
View details for PubMedCentralID PMC1867612
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First molecular characterization of a patient with combined factor V and factor VII deficiency
THROMBOSIS AND HAEMOSTASIS
2006; 95 (6): 1031-1032
View details for DOI 10.1160/TH06-03-0177
View details for Web of Science ID 000238557200019
View details for PubMedID 16732384
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Mast cells can promote the development of multiple features of chronic asthma in mice
JOURNAL OF CLINICAL INVESTIGATION
2006; 116 (6): 1633-1641
Abstract
Bronchial asthma, the most prevalent cause of significant respiratory morbidity in the developed world, typically is a chronic disorder associated with long-term changes in the airways. We developed a mouse model of chronic asthma that results in markedly increased numbers of airway mast cells, enhanced airway responses to methacholine or antigen, chronic inflammation including infiltration with eosinophils and lymphocytes, airway epithelial goblet cell hyperplasia, enhanced expression of the mucin genes Muc5ac and Muc5b, and increased levels of lung collagen. Using mast cell-deficient (Kit(W-sh/W-sh) and/or Kit(W/W-v)) mice engrafted with FcRgamma+/+ or FcRgamma-/- mast cells, we found that mast cells were required for the full development of each of these features of the model. However, some features also were expressed, although usually at less than wild-type levels, in mice whose mast cells lacked FcRgamma and therefore could not be activated by either antigen- and IgE-dependent aggregation of Fc epsilonRI or the binding of antigen-IgG1 immune complexes to Fc gammaRIII. These findings demonstrate that mast cells can contribute to the development of multiple features of chronic asthma in mice and identify both Fc Rgamma-dependent and Fc Rgamma-independent pathways of mast cell activation as important for the expression of key features of this asthma model.
View details for DOI 10.1172/JCI25702
View details for Web of Science ID 000237979700025
View details for PubMedID 16710480
View details for PubMedCentralID PMC1462940
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Successful transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response (vol 12, pg 342, 2006)
NATURE MEDICINE
2006; 12 (5): 592-592
View details for Web of Science ID 000238149100046
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The JAK2 V617F mutation occurs in hematopoietic stem cells in polycythemia vera and predisposes toward erythroid differentiation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2006; 103 (16): 6224-6229
Abstract
Although a large proportion of patients with polycythemia vera (PV) harbor a valine-to-phenylalanine mutation at amino acid 617 (V617F) in the JAK2 signaling molecule, the stage of hematopoiesis at which the mutation arises is unknown. Here we isolated and characterized hematopoietic stem cells (HSC) and myeloid progenitors from 16 PV patient samples and 14 normal individuals, testing whether the JAK2 mutation could be found at the level of stem or progenitor cells and whether the JAK2 V617F-positive cells had altered differentiation potential. In all PV samples analyzed, there were increased numbers of cells with a HSC phenotype (CD34+CD38-CD90+Lin-) compared with normal samples. Hematopoietic progenitor assays demonstrated that the differentiation potential of PV was already skewed toward the erythroid lineage at the HSC level. The JAK2 V617F mutation was detectable within HSC and their progeny in PV. Moreover, the aberrant erythroid potential of PV HSC was potently inhibited with a JAK2 inhibitor, AG490.
View details for DOI 10.1073/pnas.0601462103
View details for Web of Science ID 000236999000031
View details for PubMedID 16603627
View details for PubMedCentralID PMC1434515
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Gene expression patterns in human placenta
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2006; 103 (14): 5478-5483
Abstract
The placenta is the principal metabolic, respiratory, excretory, and endocrine organ for the first 9 months of fetal life. Its role in fetal and maternal physiology is remarkably diverse. Because of the central role that the placenta has in fetal and maternal physiology and development, the possibility that variation in placental gene expression patterns might be linked to important abnormalities in maternal or fetal health, or even variations in later life, warrants investigation. As an initial step, we used DNA microarrays to analyze gene expression patterns in 72 samples of amnion, chorion, umbilical cord, and sections of villus parenchyma from 19 human placentas from successful full-term pregnancies. The umbilical cord, chorion, amnion, and villus parenchyma samples were readily distinguished by differences in their global gene-expression patterns, many of which seemed to be related to physiology and histology. Differentially expressed genes have roles that include placental trophoblast secretion, signal transduction, metabolism, immune regulation, cell adhesion, and structure. We found interindividual differences in expression patterns in villus parenchyma and systematic differences between the maternal, fetal, and intermediate layers. A group of genes that was expressed in both the maternal and fetal villus parenchyma sections of placenta included genes that may be associated with preeclampsia. We identified sets of genes whose expression in placenta was significantly correlated with the sex of the fetus. This study provides a rich and diverse picture of the molecular variation in the placenta from healthy pregnancies.
View details for DOI 10.1073/pnas.0508035103
View details for Web of Science ID 000236636400044
View details for PubMedID 16567644
View details for PubMedCentralID PMC1414632
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Successful transduction of liver in hemophilia by AAV-factor IX and limitations imposed by the host immune response
NATURE MEDICINE
2006; 12 (3): 342-347
Abstract
We have previously shown that a single portal vein infusion of a recombinant adeno-associated viral vector (rAAV) expressing canine Factor IX (F.IX) resulted in long-term expression of therapeutic levels of F.IX in dogs with severe hemophilia B. We carried out a phase 1/2 dose-escalation clinical study to extend this approach to humans with severe hemophilia B. rAAV-2 vector expressing human F.IX was infused through the hepatic artery into seven subjects. The data show that: (i) vector infusion at doses up to 2 x 10(12) vg/kg was not associated with acute or long-lasting toxicity; (ii) therapeutic levels of F.IX were achieved at the highest dose tested; (iii) duration of expression at therapeutic levels was limited to a period of approximately 8 weeks; (iv) a gradual decline in F.IX was accompanied by a transient asymptomatic elevation of liver transaminases that resolved without treatment. Further studies suggested that destruction of transduced hepatocytes by cell-mediated immunity targeting antigens of the AAV capsid caused both the decline in F.IX and the transient transaminitis. We conclude that rAAV-2 vectors can transduce human hepatocytes in vivo to result in therapeutically relevant levels of F.IX, but that future studies in humans may require immunomodulation to achieve long-term expression.
View details for DOI 10.1038/nm1358
View details for Web of Science ID 000235802900035
View details for PubMedID 16474400
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Microsatellite instability in ovarian cancer subtypes and in synchronous ovarian and endometrial cancers: The Stanford experience
NATURE PUBLISHING GROUP. 2006: 182A
View details for Web of Science ID 000234207601277
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Microsatellite instability in ovarian cancer subtypes and in synchronous ovarian and endometrial cancers: The Stanford experience
NATURE PUBLISHING GROUP. 2006: 182A
View details for Web of Science ID 000234094501282
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Bioluminescent imaging of human leukemic stem cell engraftment.
47th Annual Meeting of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2005: 205A–205A
View details for Web of Science ID 000233426001165
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Gene expression profiling of multiple patients with cyclic thrombocytopenia reveals consistent profile.
AMER SOC HEMATOLOGY. 2005: 67A
View details for Web of Science ID 000233426000220
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First molecular characterization of a family with combined FV and FVII deficiency.
AMER SOC HEMATOLOGY. 2005: 508A
View details for Web of Science ID 000233426003148
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Molecular progenitor profiling in human myeloproliferative disorders.
47th Annual Meeting of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2005: 38A–39A
View details for Web of Science ID 000233426000119
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Characterization of a novel prothrombin variant, Prothrombin C20209T, as a modifier of thrombotic risk among African-Americans
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
2005; 3 (10): 2357-2359
View details for Web of Science ID 000232443200036
View details for PubMedID 16194213
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A comparison study of different PCR assays in measuring circulating plasma Epstein-Barr virus DNA levels in patients with nasopharyngeal carcinoma
CLINICAL CANCER RESEARCH
2005; 11 (16): 5700-5707
Abstract
To compare the performance of three PCR assays in measuring circulating Epstein-Barr virus (EBV). DNA levels in nasopharyngeal carcinoma patients and to confirm its prognostic significance.Plasma from 58 newly diagnosed nasopharyngeal carcinoma patients were collected before, during, and every 3 to 6 months after radiotherapy. EBV DNA levels were determined by real-time quantitative PCR using primer/probe sets for polymerase-1 (Pol-1), latent membrane protein 2 (Lmp2), and BamHI-W. Pretreatment levels from the three assays were correlated with each other and serial measurements from the Pol-1 assay were correlated with clinical variables.Pol-1 was more accurate than BamHI-W in predicting EBV DNA concentrations in cell lines. Of the three assays, BamHI-W yielded the highest concentrations followed by Pol-1 in plasmas (n = 23). The correlation coefficient was 0.99 (P < 0.0001) for Pol-1 and Lmp2, 0.66 (P < 0.0001) for Pol-1 and BamHI-W, and 0.55 (P < 0.0001) for BamHI-W and Lmp2. Elevated pretreatment DNA levels as detected by Pol-1 were correlated with advanced nodal stage (P = 0.04) and overall stage (P = 0.028). There was no correlation between pretreatment EBV DNA levels and freedom-from-relapse or overall survival; however, there was a significant correlation between posttreatment levels and these variables. The 2-year freedom-from-relapse and overall survival rates were 92% and 94% for patients with undetectable, and 37% and 55% for those with detectable, posttreatment levels (P < 0.0001 and P < 0.002).The three PCR assays yielded similar results in detecting EBV DNA in plasmas. The Pol-1-detected posttreatment EBV DNA level was the strongest predictor for treatment outcomes.
View details for DOI 10.1158/1078-0432.CCR-05-0648
View details for PubMedID 16115906
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Identification of mislabeled specimen by molecular methods: Case report and review
INTERNATIONAL JOURNAL OF SURGICAL PATHOLOGY
2005; 13 (3): 253-258
Abstract
Specimen misidentification is a common cause of errors in surgical pathology. We report a case where bone-marrow biopsies from patients of different genders were mislabeled and molecular methods were applied to resolve the identity. A short tandem repeat (STR)-polymerase chain reaction-based assay, commonly used in paternity testing, was employed in an attempt to assign the correct identity to the specimens. However, the specimens had been processed by decalcification and the DNA yield was poor. One of the markers in the assay is the non-STR amelogenin locus that distinguishes the X and Y chromosomes. This amelogenin marker results in a product of low molecular weight, enabling unequivocal resolution of identity despite a poor DNA yield. The prevalence of errors in pathology due to specimen misidentifications is reviewed.
View details for Web of Science ID 000231185700004
View details for PubMedID 16086080
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Varicella-zoster virus infection of human dorsal root ganglia in vivo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2005; 102 (18): 6490-6495
Abstract
Varicella-zoster virus (VZV) causes varicella and establishes latency in sensory ganglia. VZV reactivation results in herpes zoster. We developed a model using human dorsal root ganglion (DRG) xenografts in severe combined immunodeficient (SCID) mice to investigate VZV infection of differentiated neurons and satellite cells in vivo. DRG engrafted under the kidney capsule and contained neurons and satellite cells within a typical DRG architecture. VZV clinical isolates infected the neurons within DRG. At 14 days postinfection, VZ virions were detected by electron microscopy in neuronal cell nuclei and cytoplasm but not in satellite cells. The VZV genome copy number was 7.1 x 10(7) to 8.0 x 10(8) copies per 10(5) cells, and infectious virus was recovered. This initial phase of viral replication was followed within 4-8 weeks by a transition to VZV latency, characterized by the absence of infectious virus release, the cessation of virion assembly, and a reduction in VZV genome copies to 3.7 x 10(5) to 4.7 x 10(6) per 10(5) cells. VZV persistence in DRG was achieved without any requirement for VZV-specific adaptive immunity and was associated with continued transcription of the ORF63 regulatory gene. The live attenuated varicella vaccine virus exhibited the same pattern of short-term replication, persistence of viral DNA, and prominent ORF63 transcription as the clinical isolates. VZV-infected T cells transferred virus from the circulation into DRG, suggesting that VZV lymphotropism facilitates its neurotropism. DRG xenografts may be useful for investigating neuropathogenic mechanisms of other human viruses.
View details for DOI 10.1073/pnas.0501045102
View details for Web of Science ID 000228918400045
View details for PubMedID 15851670
View details for PubMedCentralID PMC1088374
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High frequency of premature termination mutations in the factor V gene: Three factor V deficiency case reports and a mutation review
THROMBOSIS AND HAEMOSTASIS
2005; 93 (3): 610-611
View details for Web of Science ID 000227808200034
View details for PubMedID 15735818
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Identification of a novel factor V A2 domain tyrosine deletion mutation in a patient with Factor V deficiency and bleeding.
AMER SOC HEMATOLOGY. 2004: 94B
View details for Web of Science ID 000225127700362
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Gene expression patterns in placenta from normal and preeclamptic pregnancies
W B SAUNDERS CO LTD. 2004: A21
View details for Web of Science ID 000223898300085
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Granulocyte-macrophage progenitors as candidate leukemic stem cells in blast-crisis CML
NEW ENGLAND JOURNAL OF MEDICINE
2004; 351 (7): 657-667
Abstract
The progression of chronic myelogenous leukemia (CML) to blast crisis is supported by self-renewing leukemic stem cells. In normal mouse hematopoietic stem cells, the process of self-renewal involves the beta-catenin-signaling pathway. We investigated whether leukemic stem cells in CML also use the beta-catenin pathway for self-renewal.We used fluorescence-activated cell sorting to isolate hematopoietic stem cells, common myeloid progenitors, granulocyte-macrophage progenitors, and megakaryocyte-erythroid progenitors from marrow during several phases of CML and from normal marrow. BCR-ABL, beta-catenin, and LEF-1 transcripts were compared by means of a quantitative reverse-transcriptase-polymerase-chain-reaction assay in normal and CML hematopoietic stem cells and granulocyte-macrophage progenitors. Confocal fluorescence microscopy and a lymphoid enhancer factor/T-cell factor reporter assay were used to detect nuclear beta-catenin in these cells. In vitro replating assays were used to identify self-renewing cells as candidate leukemic stem cells, and the dependence of self-renewal on beta-catenin activation was tested by lentiviral transduction of hematopoietic progenitors with axin, an inhibitor of the beta-catenin pathway.The granulocyte-macrophage progenitor pool from patients with CML in blast crisis and imatinib-resistant CML was expanded, expressed BCR-ABL, and had elevated levels of nuclear beta-catenin as compared with the levels in progenitors from normal marrow. Unlike normal granulocyte-macrophage progenitors, CML granulocyte-macrophage progenitors formed self-renewing, replatable myeloid colonies, and in vitro self-renewal capacity was reduced by enforced expression of axin.Activation of beta-catenin in CML granulocyte-macrophage progenitors appears to enhance the self-renewal activity and leukemic potential of these cells.
View details for PubMedID 15306667
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Rapid combined genotyping assay for four achondroplasia and hypochondroplasia mutations by real-time PCR with multiple detection probes
GENETIC TESTING
2004; 8 (2): 185-189
Abstract
Achondroplasia (ACH) and hypochondroplasia (HYCH) are the most prevalent genetic short-stature syndromes. Whereas the diagnosis of ACH can be established on clinical and radiologic grounds alone in the majority of cases, HYCH is more difficult to confirm. Molecular genetic analysis of both skeletal dysplasias can be especially helpful for the purpose of prenatal diagnosis, in early childhood to differentiate definitively between the largely overlapping phenotypes, and in atypical presentations. The two most prevalent mutations for each syndrome cause substitution of a single respective nucleotide. These mutations can be identified by a variety of molecular methods, including PCR with restriction enzyme digestion or direct DNA sequencing. We have developed a single-step, real-time PCR assay in which two detection probes are applied in combination with a single anchor probe at each mutation position. Because the two most prevalent mutations for each syndrome cause substitution of a single respective nucleotide, this approach guarantees optimal differentiation during probe dissociation analysis after amplification. This assay, which is performed on the LightCycler thermocycler, enables the rapid and reliable detection of the two most common FGFR3 mutations associated with ACH (1138G --> A and 1138G --> C; G380R) and HYCH (1620C --> A and 1620 C --> G; N540K) in a single test.
View details for Web of Science ID 000223513900019
View details for PubMedID 15345118
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CyclinD1/CyclinD3 ratio by real-time PCR improves specificity for the diagnosis of mantle cell lymphoma
JOURNAL OF MOLECULAR DIAGNOSTICS
2004; 6 (2): 84-89
Abstract
We developed a real-time, quantitative, reverse transcription PCR assay for cyclin D1 (CCND1) expression to aid in the diagnosis of mantle cell lymphoma (MCL). The diagnosis of MCL can be problematic, and existing CCND1 expression assays show a lack of specificity, with elevated expression also detected in other lymphoproliferative disorders. We postulated that evaluating CCND1 expression relative to CCND3 expression by quantitative PCR could offer an improved specificity over an evaluation of CCND1 alone. This method quantitates both CCND1 and CCND3, each normalized to a housekeeping gene (GADPH), using the 5'-exonuclease technique. We analyzed 107 clinical specimens: MCL (17), chronic lymphocytic leukemias (CLL) (10), other non-MCL hematolymphoid disorders (41), non-malignant tissues with an epithelial component (7) and other normal samples (32). This method correctly identified 16 of 17 MCLs, and there were no false positives among any of the other diagnostic groups tested including CLL. CLL presents the major diagnostic dilemma at this institution when diagnosing MCL. Sensitivity studies showed that this method could detect an elevated CCND1/CCND3 ratio when the tumor infiltrate is at least 10% of the cells. We compared the specificity of CCND1 expression alone against the CCND1/CCND3 ratio to demonstrate the increased specificity for the latter. We conclude that the CCND1/CCND3 ratio is a sensitive and specific test for the diagnosis of MCL.
View details for Web of Science ID 000221002500002
View details for PubMedID 15096562
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Molecular diagnosis of hypercoagulable states
LABORATORY MEDICINE
2004; 35 (4): 214-221
View details for Web of Science ID 000220469400016
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Randomized trial of folic acid for prevention of cardiovascular events in end-stage renal disease
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
2004; 15 (2): 420-426
Abstract
High serum total homocysteine (tHcy) is gaining scrutiny as a risk factor for cardiovascular disease in the general population. The relationship between tHcy and mortality and cardiovascular events in patients with end-stage renal disease (ESRD) is unsettled. This randomized trial evaluates the efficacy of high-dose folic acid in preventing events in ESRD. A total of 510 patients on chronic dialysis were randomized to 1, 5, or 15 mg of folic acid contained in a renal multivitamin with a median follow-up of 24 mo. Mortality, cardiovascular events, and homocysteine levels were assessed. There were 189 deaths, and 121 patients experienced at least one cardiovascular event. Composite rates of mortality and cardiovascular events among the folic acid groups did not differ (at 24 mo: 43.7% in 1 mg group, 38.6% in 5 mg group, 47.1% in 15 mg group; log-rank P = 0.47). Unexpectedly, high baseline tHcy was associated with lower event rates. From lowest to highest quartile, event rates at 24 mo were 54.5% for Q1, 41.8% for Q2, 41.2% for Q3, and 34.7% for Q4 (log-rank P = 0.033). In contrast to some studies describing tHcy as a risk factor for mortality and cardiovascular events, this study found a reverse relationship between tHcy and events in ESRD patients. Administration of high-dose folic acid did not affect event rates.
View details for DOI 10.1097/01.ASN.0000110181.64655.6C
View details for Web of Science ID 000188604600020
View details for PubMedID 14747389
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Lymphomatoid papulosis associated with mycosis fungoides: A study of 21 patients including analyses for clonality. (vol 49, pg 620, 2003)
JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY
2004; 50 (2): 202
View details for Web of Science ID 000188710100004
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Congenital and acquired thrombocytopenia.
Hematology / the Education Program of the American Society of Hematology. American Society of Hematology. Education Program
2004: 390-406
Abstract
The diagnosis and management of thrombocytopenia is a growing component in the practice of hematology. The frequency with which hematologists are called in consultation for thrombocytopenia continues to increase with the advent of routine automated platelet determinations and the introduction of new medications. For most patients, such as those with inherited and auto-immune thrombocytopenia, emphasis is focused on efforts to treat or forestall bleeding without excess drug-induced toxicity or burden to the patient. However, in disorders such as heparin-induced thrombocytopenia (HIT), avoidance of thrombotic complications is the key to management. In this chapter, we provide the pediatric and adult hematologist with new insights into the pathogenesis and recognition of congenital inherited thrombocytopenias (CTP), a hitherto difficult to comprehend constellation of clinical entities. We also highlight new approaches to the diagnosis and treatment of two of the more common thrombocytopenic conditions encountered in practice, autoimmune or idiopathic thrombocytopenic purpura (ITP) and HIT. In Section I, Dr. James Bussel discusses CTPs and their distinction from childhood ITP. He emphasizes the clinical features that enable the pediatrician and hematologist to suspect the diagnosis of CTP and those that are of use to subcategorize the various entities, where possible. He also emphasizes newer molecular markers that afford definitive diagnosis in some cases and provide insight into platelet production. This section highlights the characteristic associated findings and differences in the natural history and approaches to management of the various entities. In Section II, Dr. Robert McMillan discusses adult chronic ITP. He revisits the utility of platelet antibody determination in diagnosis and review new insights into pathogenesis. The role of Helicobacter pylori infection and the timing of splenectomy in the management of acute and emergent ITP are examined. New insights into the natural history of ITP post-splenectomy and management strategies for patients with severe, chronic, refractory ITP are discussed. In Section III, Dr. James Zehnder updates us on HIT. He emphasizes new insights into the clinical presentation and pathogenesis of this condition. He critically reviews the utility of laboratory testing for heparin-dependent antibodies. Recent studies on the use of direct thrombin inhibitors are examined and the management of cardiopulmonary bypass surgery in patients with HIT is discussed.
View details for PubMedID 15561694
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BCR/ABL expression by highly purified chronic myelogenous leukemic hematopoietic stem cells and myeloid progenitors pre and post-imatinib therapy.
45th Annual Meeting and Exhibition of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2003: 418A–418A
View details for Web of Science ID 000186536701519
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Gene expression profiling of cyclical thrombocytopenia.
AMER SOC HEMATOLOGY. 2003: 789A
View details for Web of Science ID 000186536702916
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The role of beta-catenin in chronic myelogenous leukemic progenitor expansion.
45th Annual Meeting and Exhibition of the American-Society-of-Hematology
AMER SOC HEMATOLOGY. 2003: 570A–570A
View details for Web of Science ID 000186536702096
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Prothrombin gene variants in non-Caucasians with fetal loss and intrauterine growth retardation
JOURNAL OF MOLECULAR DIAGNOSTICS
2003; 5 (4): 250-253
Abstract
Thrombotic predisposition may affect pregnancy outcome, but in non-Caucasians the contributing genetic factors are poorly characterized. Two recently identified prothrombin gene mutations (20209C>T and 20221C>T) have been observed in non-Caucasian patients with thrombosis. The mutations are located near the commonly identified variant 20210G>A and have not been reported in Caucasian patients. The authors report a novel connection with pregnancy complications. The identification of sequence variants other than 20210G>A in the 3'-untranslated region of the prothrombin gene suggests that additional nucleotide substitutions may contribute to the development of thrombotic events and adverse pregnancy outcomes, especially in less well-characterized populations.
View details for Web of Science ID 000186292700009
View details for PubMedID 14573785
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Lymphomatoid papulosis associated with mycosis fungoides: A study of 21 patients including analyses for clonality
JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY
2003; 49 (4): 620-623
Abstract
Although an association of lymphomatoid papulosis (LyP) with mycosis fungoides (MF) is recognized, our understanding of this relation is limited.We sought to document the clinical experience at the University of California, San Francisco, in 21 patients who had both LyP and MF and to do clonality studies in 7 of those patients in whom this was possible.We conducted chart review of the 21 patients and analysis for T-cell receptor-gamma gene rearrangements by the polymerase chain reaction.Of 54 patients, 21 (39%) with LyP had associated MF. LyP preceded MF in 14 (67%), MF preceded LyP in 4 (19%), and there was concurrent appearance in 3 (14%). Of the 21 patients, 20 (95%) were type A and only 1 (5%) was type B. An identical clone was found in lesions of both LyP and MF in all 7 patients in whom analysis was possible.Findings of this study strengthen the idea that LyP and MF are related T-cell lymphoproliferative disorders.
View details for DOI 10.1067/S0190-9622(03)01577-9
View details for Web of Science ID 000185606500006
View details for PubMedID 14512906
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Heterozygous prothrombin G20210A gene mutation in a patient with livedoid vasculitis
ARCHIVES OF DERMATOLOGY
2003; 139 (8): 1081-1083
View details for Web of Science ID 000184692700021
View details for PubMedID 12925402
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Comprehensive validation of a real-time quantitative bcr-abl assay for clinical laboratory use
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
2003; 120 (1): 42-48
Abstract
We developed and extensively validated a real-time PCR assay for the quantitation of bcr-abl to determine residual disease in patients with chronic myelogenous leukemia. This method quantitates the p210 and the p190 bcr-abl RNA fusion transcripts with results normalized to a housekeeping gene, using the 5'-exonuclease technique and the ABI PRISM 7700 Sequence Detection System (Applied Biosystems, Foster City, CA). We parallel tested 372 clinical specimens and 50 peripheral blood samples from patients not known to have any myeloproliferative disorders. The results were 100% specific. Sensitivity studies showed that this method can detect bcr-abl in cell lines diluted to 0.0001% and can detect a single bcr-abl plasmid spiked into negative RNA. The between-run reproducibility showed a coefficient of variance (CV) of 12.3%, and within-run reproducibility showed a CV of 13.8%. This method can be used to reliably monitor the disease load in patients with bcr-abl-positive diseases.
View details for DOI 10.1309/60A9C8WGEGHRNXEE
View details for Web of Science ID 000183730300005
View details for PubMedID 12866371
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Diagnostic single nucleotide polymorphism analysis of factor V Leiden and prothrombin 20210G > A - A comparison of the nanogen electronic microarray with restriction enzyme digestion and the Roche LightCycler
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
2003; 119 (4): 490-496
Abstract
Genetic thrombosis risk factors include a sequence variant in the prothrombin gene (20210G > A) and factor V Leiden (1691G > A). These single nucleotide polymorphisms can be diagnosed with restriction fragment length polymorphism (RFLP) analysis, fluorescent genotyping on the LightCycler (Roche Diagnostics, Indianapolis, IN), and microarray-based testing on the novel NanoChip electronic microarray (NanoChip Molecular Biology Workstation, Nanogen, San Diego, CA). We compared these methods for accuracy, time to results, throughput, and interpretation. Results from 789 of 800 individual amplicons analyzed on the NanoChip were in complete agreement with the other assays. Eleven were "no calls" (uninterpreted by the NanoChip system) resulting from failed polymerase chain reaction amplifications. Although the NanoChip System, when used in a low-throughput setting, requires more overall time than the LightCycler, it is nearly equivalent per genotyping call. Owing to minimal sample handling, assay results are more reliable on the NanoChip platform and on the LightCycler than with RFLP. The NanoChip assay is reliable and may be especially valuable to laboratories with a large volume of thrombophilia test requests.
View details for DOI 10.1309/3VTR7TL2X7TXL0XY
View details for Web of Science ID 000181872500002
View details for PubMedID 12710121
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Lack of human herpesvirus 8 and Epstein-Barr virus in Kikuchi's histiocytic necrotizing lymphadenitis
HUMAN PATHOLOGY
2003; 34 (2): 130-135
Abstract
Kikuchi's histiocytic necrotizing lymphadenitis is a self-limited disorder that typically involves the cervical lymph nodes of young women. Although a viral etiology has been postulated, a definitive viral agent has not been identified. Recent reports have suggested that human herpesvirus 8 (HHV 8) or Epstein-Barr virus (EBV) may play an etiologic role. We investigated the presence of HHV 8 and EBV in archival tissue from 34 cases of Kikuchi's histiocytic necrotizing lymphadenitis. We examined 29 cases for HHV 8 using a nested polymerase chain reaction (PCR) on paraffin-embedded or frozen tissue, and 24 cases for EBV RNA using in situ hybridization (ISH) for EBER1. Controls included reactive lymph nodes from 8 adult women presenting with cervical or axillary lymphadenopathy. The study patients included 7 men and 27 women with a mean age of 28 years. All patients were previously healthy without evidence of immunocompromise and presented with cervical, axillary, or inguinal lymphadenopathy. Two cases exhibited EBV RNA by ISH; this was confirmed by PCR for EBV DNA. HHV 8 DNA was not amplified by nested PCR in any of the cases of Kikuchi's histiocytic necrotizing lymphadenitis or reactive lymph nodes; control PCR demonstrated the presence of amplifiable DNA in all cases. These findings suggest that HHV 8 and EBV do not play causative roles in Kikuchi's histiocytic necrotizing lymphadenitis.
View details for DOI 10.1053/hupa.2003.11
View details for PubMedID 12612880
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Psoriasiform mycosis fungoides with fatal outcome after treatment with cyclosporine
JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY
2002; 47 (1): 155-157
View details for DOI 10.1067/mjd.2002.120571
View details for Web of Science ID 000176560400023
View details for PubMedID 12077599
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Homozygous factor V splice site mutation associated with severe factor V deficiency
BLOOD
2002; 99 (8): 3063-3065
Abstract
We investigated a family whose proband has a severe bleeding disorder and factor V antigenic and functional levels of 8% and less than 1% of control values, respectively. Molecular analysis of the factor V gene revealed a novel homozygous mutation in the last nucleotide of exon 10. 1701G>T causes activation of a cryptic exonic splice site in exon 10, which encodes part of the factor V heavy chain (A2 domain). This leads to the deletion of 35 nucleotides and results in a frameshift with a premature stop codon at amino acid position 498. The G1701 and corresponding Gln509 are conserved in murine, bovine, and porcine factor V and in human factor VIII. Few factor V deficiency mutations have been identified as yet. Several are present in the heterozygous form in combination with factor V Leiden (Arg506Gln). This is the first reported homozygous splice site mutation in a patient with factor V deficiency.
View details for Web of Science ID 000174866500055
View details for PubMedID 11929802
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Randomized trial of folic acid for homocysteine reduction in end-stage renal disease.
W B SAUNDERS CO. 2002: A34
View details for Web of Science ID 000174835000126
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The effect of a supplement containing Ginkgo biloba (Gb), fish oil (DHA) and Gotu kola (Gk) on platelet function in older healthy adults
FEDERATION AMER SOC EXP BIOL. 2002: A646
View details for Web of Science ID 000174533603589
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Novel factor VC2-domain mutation (R2074H) in two families with factor V deficiency and bleeding
THROMBOSIS AND HAEMOSTASIS
2002; 87 (2): 294-299
Abstract
The molecular basis of Factor V deficiency has been defined in few patients only. We report a homozygous nucleotide change (G6395A) in two Tunisian probands with Factor V deficiency and bleeding episodes. This substitution results in the replacement of an arginine (R) by a histidine (H) in amino acid position 2074, located in the Factor V C2-domain. Mutations in this protein domain have not previously been described. Several lines of evidence support that this sequence variant is indeed disease causing: 1) Crystal structures of Factor V and molecular C2-domain modeling studies of H2074 suggest that the conserved R2074 is required for correct folding; 2) Structure-function studies of selective Factor V mutants (R2074A) demonstrate the importance of R2074 for structural stability of the Factor V C2-domain and for cofactor activity (1); 3) In Factor VIII, point mutations in codon 2209, which corresponds to position 2074 in Factor V, cause hemophilia A.
View details for Web of Science ID 000173869300020
View details for PubMedID 11858490
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Immunological consequences of topical bovine thrombin
AMERICAN JOURNAL OF PATHOLOGY
2001; 159 (6): 2371-2371
View details for Web of Science ID 000172457400040
View details for PubMedID 11733385
View details for PubMedCentralID PMC1850577
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Real-time PCR assay for quantitation of BCR-ABL mRNA in patients with chronic phase CML treated with the tyrosine kinase inhibitor GLEEVEC (TM) (STI-571).
AMER SOC HEMATOLOGY. 2001: 258B–259B
View details for Web of Science ID 000172134201177
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A polymorphism in the BCL-6 gene is associated with follicle center lymphoma
LEUKEMIA & LYMPHOMA
2001; 42 (6): 1343-1350
Abstract
Follicle center lymphoma (FCL) accounts for approximately 40% of all non-Hodgkin's lymphomas (NHL). The genetic-environmental interactions involved in the etiology and pathogenesis of this disease are unknown. In our previous study a single nucleotide polymorphism (SNP) (397C) in the regulatory untranslated first intron region of the BCL-6 gene was found in four of the eight FCL patients but in none of the 10 healthy controls. To further evaluate the potential association between the 397C allele of the BCL-6 gene and FCL, we performed a case-control study. Genomic DNA was isolated from 85 FCL patients, from 98 control cases without a previous history of malignancy, treated at Stanford University Medical Center for non-malignant disorders and from 90 samples from the DNA Polymorphism Discovery Resource. The 397G and the 397C polymorphic alleles were identified by a PCR-RFLP method. To evaluate the possible effect of this polymorphism on gene expression, BCL-6 mRNA levels in nine FCL tumors with the 397G-G genotype and in nine FCL tumors with the 397G-C genotype were measured by quantitative real-time RT-PCR. The 397C polymorphic allele was found in 32 FCL cases (37.6%), in 20 controls (20.4%) and in 17 (18.9%) samples from the DNA Polymorphism Discovery Resource. The prevalence of the 397G-C and 397C-C genotypes was significantly higher in FCL cases than in control group (p = 0.01). No difference in BCL-6 gene expression was observed between FCL cases with 397G-G and 397G-C genotypes. The present study demonstrates a possible association between the 397C allele of the BCL-6 proto-oncogene and FCL. The similar levels of BCL-6 mRNA expression in 397G-G and in 397G-C FCL cases suggests that any possible oncogenic effect of the polymorphic allele would not simply be related to a direct effect on BCL-6 gene expression and suggests the existence of other FCL susceptibility genes that are in linkage disequilibrium with the 397C allele of the BCL-6 gene.
View details for Web of Science ID 000173558700022
View details for PubMedID 11911418
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An MTHFR variant, homocysteine, and cardiovascular comorbidity in renal disease
32nd Annual Meeting of the American-Society-of-Nephrology
NATURE PUBLISHING GROUP. 2001: 1106–13
Abstract
It is unclear whether total serum homocysteine (tHcy) and the C677T mutation of methylenetetrahydrofolate reductase (MTHFR) are associated with cardiovascular disease (CVD) in patients with end-stage renal disease (ESRD).A cross-sectional sample of 459 patients with ESRD on chronic dialysis was assessed to determine whether tHcy and the C677T mutation are associated with CVD prevalence in multiple logistic regression. As CVD mortality is high, we examined the relationship between homozygosity and duration of dialysis.Mean tHcy was higher in patients without a history of CVD (35.2 micromol/L vs. 30.4 micromol/L, P = 0.02). In multivariate models, CVD was negatively associated with tHcy and positively associated with TT genotype, male gender, and body mass index. Mean tHcy levels were higher among those with the TT genotype compared with those with the CC genotype when adjusted for age, folate, creatinine, and albumin (37.9 micromol/L vs. 31.9 micromol/L, P = 0.005). Among whites, the prevalence of the TT genotype was higher in those having undergone less than one year of dialysis (P = 0.002).The C677T genotype of MTHFR is associated with CVD in ESRD and may be a more meaningful marker than tHcy for abnormal homocysteine metabolism in ESRD. Prospective data from ongoing clinical trials are needed to improve our understanding of these findings. Screening for this polymorphism may help guide prevention measures.
View details for Web of Science ID 000170668100029
View details for PubMedID 11532106
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Expression of a single gene, BCL-6, strongly predicts survival in patients with diffuse large B-cell lymphoma
BLOOD
2001; 98 (4): 945-951
Abstract
Diffuse large B-cell lymphoma (DLBCL) is characterized by a marked degree of morphologic and clinical heterogeneity. Establishment of parameters that can predict outcome could help to identify patients who may benefit from risk-adjusted therapies. BCL-6 is a proto-oncogene commonly implicated in DLBCL pathogenesis. A real-time reverse transcription-polymerase chain reaction assay was established for accurate and reproducible determination of BCL-6 mRNA expression. The method was applied to evaluate the prognostic significance of BCL-6 expression in DLBCL. BCL-6 mRNA expression was assessed in tumor specimens obtained at the time of diagnosis from 22 patients with primary DLBCL. All patients were subsequently treated with anthracycline-based chemotherapy regimens. These patients could be divided into 2 DLBCL subgroups, one with high BCL-6 gene expression whose median overall survival (OS) time was 171 months and the other with low BCL-6 gene expression whose median OS was 24 months (P =.007). BCL-6 gene expression also predicted OS in an independent validation set of 39 patients with primary DLBCL (P =.01). BCL-6 protein expression, assessed by immunohistochemistry, also predicted longer OS in patients with DLBCL. BCL-6 gene expression was an independent survival predicting factor in multivariate analysis together with the elements of the International Prognostic Index (IPI) (P =.038). By contrast, the aggregate IPI score did not add further prognostic information to the patients' stratification by BCL-6 gene expression. High BCL-6 mRNA expression should be considered a new favorable prognostic factor in DLBCL and should be used in the stratification and the design of risk-adjusted therapies for patients with DLBCL. (Blood. 2001;98:945-951)
View details for Web of Science ID 000170364100008
View details for PubMedID 11493437
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The transcriptional program in human mast cells stimulated via the Fc[epsilon]RI: New insights into the immunological functions of mast cells in allergic inflammation.epsilon
FEDERATION AMER SOC EXP BIOL. 2001: A1020–A1020
View details for Web of Science ID 000167454201772
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CD31 mismatching affects marrow transplantation outcome
BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION
2001; 7 (9): 503-512
Abstract
Graft-versus-host disease (GVHD) complicating allogeneic bone marrow transplantation (BMT) is often attributed to mismatched minor histocompatibility antigens (mHags), which are poorly defined in humans. CD31 is a candidate human mHag relevant to acute GVHD, but reports disagree about its level of significance, the role of HLA restriction, and the relative importance of different polymorphic codons within the molecule. We therefore examined in greater detail the impact of CD31-matching on BMT outcome in a prospective study from a single institution. Samples of recipient and donor DNA were collected pretransplantation for all patients receiving unmanipulated bone marrow from an HLA-identical sibling over a 45-month period at our institution. CD31 DNA typing of alleles at the 3 polymorphic codons 125 (L or V), 563 (N or S), and 670 (R or G) was performed for 118 patient-donor pairs plus 2 additional pairs who had codon 125 typing only. Donor-recipient CD31 nonidentity was tested for correlation with BMT clinical outcome measures of severe acute GVHD, chronic GVHD, relapse, and survival. Gene frequencies of approximately 0.5 for each allele at all 3 codons were comparable to previous reports. Because complete association was seen for 563N with 670G and for 563S with 670R, nonidentity for those codons was analyzed as a single genetic marker designated codon 563/670. Donor-recipient CD31 nonidentity was a significant risk factor for overall survival, both at codon 563/670 (hazard ratio [hr] = 2.58, P = .005) and at codon 125 (hr = 1.07, P = .036). Similar results held for disease-free survival. Nonidentity at codon 563/670 was also a significant risk factor (odds ratio [OR] = 11.15, P = .011) for severe (grades III, IV) versus no (grade 0) acute GVHD. Nonidentity at codon 125 posed less but still significant risk (OR = 9.30, P = .030). When the comparison group without severe acute GVHD was expanded to include grade I as well as grade 0 patients, the risk from CD31 nonidentity increased for both codon 563/670 (OR = 12.31, P = .010) and codon 125 (OR = 11.24, P = .011). CD31 nonidentity remained a significant independent risk factor for survival and for severe acute GVHD when tested in multivariate analysis with the covariates of adulthood, recipient-donor sex difference, ethnic group, disease, pretransplantation risk category, HLA-A2 type, B44-like types, and GVHD prophylactic regimen. CD31 nonidentity showed a trend but failed to achieve statistical significance as a risk factor for relapse and for chronic GVHD. In conclusion, donor-recipient CD31 nonidentity is a significant risk factor for survival and for severe acute GVHD in HLA-identical sibling BMT. The stronger associations with codon 563/670 suggest that polymorphism may be more important than the linked polymorphism at codon 125.
View details for Web of Science ID 000171449200004
View details for PubMedID 11669217
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Lack of human herpesvirus 8 & Epstein-Barr virus in Kikuchi's histiocytic necrotizing lymphadenitis
NATURE PUBLISHING GROUP. 2001: 164A
View details for Web of Science ID 000166634900973
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CD10 and BCL-6 expression in high-grade marginal zone B-cell lymphoma
NATURE PUBLISHING GROUP. 2001: 166A
View details for Web of Science ID 000166634900987
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Lack of human herpesvirus 8 & Epstein-Barr virus in Kikuchi's histiocytic necrotizing lymphadenitis
NATURE PUBLISHING GROUP. 2001: 164A
View details for Web of Science ID 000166622400969
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Sensitive detection of clonal immunoglobulin rearrangements in frozen and paraffin embedded tissues by polymerase chain reaction heteroduplex analysis
DIAGNOSTIC MOLECULAR PATHOLOGY
2000; 9 (4): 177-183
Abstract
Molecular detection of a clonal population of B or T cells through analysis of rearranged antigen receptor genes is an essential adjunct to the morphologic, flow cytometric, and immunohistochemical evaluation of tissue specimens for the presence of leukemia or lymphoma. Combining polymerase chain reaction (PCR) with heteroduplex annealing and polyacrylamide gel electrophoresis (PAGE) has been used to detect clonal T-cell receptor rearrangements, particularly in skin biopsy specimens. The authors have developed a similar PCR heteroduplex assay for detection of clonal VDJ immunoglobulin gene rearrangements using two sets of primers based on relatively conserved consensus regions in the J(H) and framework I and 2 regions of the immunoglobulin heavy chain V region gene. This method is able to detect a clonal rearrangement when the clone comprises as little as 1% of the population in a polyclonal B-cell background. It may be used on fresh, frozen, or paraffin-embedded tissue and detects a clonal population in a majority of lymphoma subtypes. Compared with conventional PCR analysis, this method requires only a short additional cycle of denaturation and slow renaturation before PAGE. Interpretation is simplified as the clonal PCR product migrates away from the polyclonal background products.
View details for Web of Science ID 000165556700001
View details for PubMedID 11129440
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BCL-6 proto-oncogene polymorphism and susceptibility to follicle center lymphoma (FCL).
AMER SOC HEMATOLOGY. 2000: 574A–575A
View details for Web of Science ID 000165256102468
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Search for ATM gene mutations in patients with follicle center lymphoma (FCL), in the FCL tumors and in tumors following transformation to a higher-grade.
AMER SOC HEMATOLOGY. 2000: 574A-+
View details for Web of Science ID 000165256102466
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Real-time PCR assay for quantitation of BCL-6 mRNA.
AMER SOC HEMATOLOGY. 2000: 166B
View details for Web of Science ID 000165256200763
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Identification of a novel factor VC2-domain mutation (R2074H) in two separate families with factor V deficiency and bleeding.
AMER SOC HEMATOLOGY. 2000: 533A
View details for Web of Science ID 000165256102292
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Argatroban reexposure in patients with heparin-induced thrombocytopenia (HIT).
AMER SOC HEMATOLOGY. 2000: 52A–52A
View details for Web of Science ID 000165256100217
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Peripheral T-cell lymphoma complicated by a proliferation of large B cells
88th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology
AMER SOC CLINICAL PATHOLOGY. 2000: 236–47
Abstract
We studied 14 cases that showed a morphologic appearance of peripheral T-cell lymphoma and contained substantial numbers of CD20+ large B cells. In all but 2 cases, the CD20+ large cells showed a mix of kappa and lambda light chain expression. Two cases showed a focal predominance of kappa expression. In situ hybridization using the EBER1 probe for detection of Epstein-Barr virus (EBV) RNA was performed on every case. EBV RNA was present in 10 cases. Of 8 cases with EBV RNA stained by immunohistochemistry for the latent membrane protein of EBV, 6 were positive. Double-labeling immunohistochemistry and in situ hybridization confirmed that EBV was present in the large B cells. Polymerase chain reaction (PCR) analysis showed a clonal rearrangement of the T-cell receptor (TCR)-gamma chain gene in 12 of 13 cases tested. One additional case showed a clonal rearrangement of the TCR-beta chain gene by Southern blot hybridization. PCR analysis showed a clonal immunoglobulin gene rearrangement in 5 cases, a suggestion of a clonal rearrangement in 1, an oligoclonal pattern in 4, and a polyclonal pattern in 4. The finding of large B and T cells may result in a misdiagnosis of a reactive process or of T-cell-rich B-cell lymphoma. The presence of EBV in some cases could cause further confusion with the reactive T- and B-immunoblastic proliferation of infectious mononucleosis.
View details for Web of Science ID 000088460700010
View details for PubMedID 10941339
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PCR-heteroduplex analysis of T-cell receptor gamma gene rearrangement in paraffin-embedded skin biopsies
AMERICAN JOURNAL OF DERMATOPATHOLOGY
2000; 22 (4): 321-327
Abstract
We developed a rapid, simple, and sensitive method for the detection of T-cell receptor-gamma (TCRgamma) gene rearrangements in paraffin-embedded skin biopsies. Available techniques often require either fresh tissue, several primer pairs, nested amplifications, or specialized electrophoresis steps such as denaturing gradient gel electrophoresis. Our method is based on heteroduplex analysis of polymerase chain reaction (PCR) products of the TCRgamma in a nondenaturing modified polyacrylamide gel using a single pair of primers and is adapted for paraffin-embedded tissue. When tested against Southern blot analysis, the PCR results correlated in 8 of 9 cases. Six mature cutaneous B-cell lymphomas and 29 inflammatory skin disorders all resulted in a polyclonal amplification pattern. When analyzing 3-mm or 4-mm punch biopsies of 51 cases of cutaneous T-cell lymphoma, 37 (72.5%) showed a clonal rearrangement with this technique. For 7 cases of patch stage mycosis fungoides, frozen tissue and formalin-fixed and paraffin-embedded tissue was available, and in 5 of 7 cases (71%), the results in frozen and paraffin-embedded tissue were concordant. One case showed a clonal pattern in frozen tissue but not in paraffin-embedded tissue, and one case was polyclonal in frozen tissue but monoclonal in paraffin-embedded tissue. Using serial dilutions of DNA from a T-cell ALL in a polyclonal background (tonsil), we established a sensitivity of 0.5%. Heteroduplex PCR of the TCRgamma is a rapid, sensitive, and inexpensive screening procedure as well as a useful adjunct to histologic analysis and immunophenotyping of cutaneous T-cell proliferations.
View details for Web of Science ID 000088565400005
View details for PubMedID 10949457
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Blastic/blastoid transformation of follicular lymphoma - Immunohistologic and molecular analyses of five cases
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
2000; 24 (4): 525-534
Abstract
Progression of follicular lymphoma to a higher-grade malignancy frequently heralds a poor prognosis. Clinical transformation is variably accompanied by a spectrum of histologic changes characterized by alteration in growth and cytology. Although several cytogenetic events and potential oncogenes have been documented in this progression, the underlying molecular mechanisms are largely unknown. We present five patients with an unusual histologic transformation of follicular lymphoma manifested by blastic/blastoid morphology. This transformation is histologically distinct from other types of transformation of follicular lymphoma. All five cases exhibited the t(14;18) translocation and expressed the BCL-2 protein. In addition, two of the five patients showed increased levels of the p53 protein within neoplastic cells implicating a possible role for this oncogene in blastic/blastoid transformation. The lack of BCL-1 and myeloid antigens by immunohistochemistry and flow cytometry studies served to distinguish blastic/blastoid transformation of follicular lymphoma from its morphologic mimics. This distinction is clinically important because lymphoblastic and myeloid leukemias require significantly different therapeutic modalities and show better prognosis. Moreover, the lack of Epstein-Barr virus-specific mRNA suggests that this virus is unlikely to participate in blastic/blastoid transformation of follicular lymphoma.
View details for Web of Science ID 000086211700006
View details for PubMedID 10757399
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Antibodies against the first Ig-like domain of human platelet endothelial cell adhesion molecule-1 (PECAM-1) that inhibit PECAM-1-dependent homophilic adhesion block in vivo neutrophil recruitment
JOURNAL OF IMMUNOLOGY
2000; 164 (1): 452-462
Abstract
Platelet endothelial cell adhesion molecule (PECAM-1), a member of the Ig superfamily, is found on endothelial cells and neutrophils and has been shown to be involved in the migration of leukocytes across the endothelium. Adhesion is mediated, at least in part, through binding interactions involving its first N-terminal Ig-like domain, but it is still unclear which sequences in this domain are required for in vivo function. Therefore, to identify functionally important regions of the first Ig-like domain of PECAM-1 that are required for the participation of PECAM-1 in in vivo neutrophil recruitment, a panel of mAbs against this region of PECAM-1 was generated and characterized in in vitro adhesion assays and in an in vivo model of cutaneous inflammation. It was observed that mAbs that disrupted PECAM-1-dependent homophilic adhesion in an L cell aggregation assay also blocked TNF-alpha-induced intradermal accumulation of neutrophils in a transmigration model using human skin transplanted onto SCID mice. Localization of the epitopes of these Abs indicated that these function-blocking Abs mapped to specific regions on either face of domain 1. This suggests that these regions of the first Ig-like domain may contain or be close to binding sites involved in PECAM-1-dependent homophilic adhesion, and thus may represent potential targets for the development of antiinflammatory reagents.
View details for Web of Science ID 000084321200060
View details for PubMedID 10605042
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Blastic/blastoid transformation of follicular lymphoma: Clinicopathologic, immunophenotypic cytogenetic and molecular analyses of five cases.
AMER SOC HEMATOLOGY. 1999: 251B
View details for Web of Science ID 000083790701168
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Familial coagulation factor V deficiency due to multiple discrete base pair substitutions.
AMER SOC HEMATOLOGY. 1999: 232A–233A
View details for Web of Science ID 000083790301077
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Kikuchi's necrotizing lymphadenitis and Kaposi's sarcoma-associated herpes virus.
AMER SOC HEMATOLOGY. 1999: 52B
View details for Web of Science ID 000083790700230
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Real-time t(11;14) and t(14;18) PCR assays provide sensitive and quantitative assessments of minimal residual disease (MRD)
LEUKEMIA
1999; 13 (11): 1833-1842
Abstract
Non-Hodgkin's lymphoma (NHL) arises as a clonal transformation of normal B and T cell differentiation and is often characterized by a higher incidence of specific chromosomal translocations. We have developed real-time TaqMan PCR assays directed toward two of these tumor-associated DNA markers, the t(14;18)(q32;q21.3) at the major breakpoint region of the bcl-2 gene and the t(11;14)(q13;q32) at the bcl-1 major translocation cluster. During analysis of serial dilutions of t(14;18)-positive DNA, the t(14;18) real-time PCR was at least as sensitive as nested PCR and demonstrated enhanced quantitative potential. Moreover, in a blinded comparison of the t(14;18) real-time PCR and a clinically validated nested PCR protocol using 134 cell line and patient DNA samples, the real-time PCR detected the translocation in 30.0% more cases than nested PCR. Both the t(14;18) and t(11;14) real-time PCR assays were used to quantitate minimal residual disease (MRD) in an NHL clinical trial assessing the safety and efficacy of a tumor-purging protocol in autologous stem cell transplantation. The assays were also used to evaluate disease depletion in an ex vivo tumor spiking model in which normal peripheral blood was spiked with tumor cell lines and processed according to the clinical purging method. PCR data from both the clinical trial and the ex vivo model demonstrated a 4 to 6 log reduction in tumor cells during CD34+ and CD34+ Thy-1+ enrichment. Because the t(14;18) and t(11;14) real-time PCR assays are very sensitive, quantitative, rapid, and require no post-PCR manipulation, they may serve as practical alternatives to nested PCR.
View details for Web of Science ID 000083664000023
View details for PubMedID 10557059
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Familial coagulation factor V deficiency caused by a novel 4 base pair insertion in the factor V gene: factor V Stanford [erratum].
Thrombosis and haemostasis
1999; 82 (5): XII-?
View details for PubMedID 10681265
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Variability of polymerase chain reaction detection of the bcl-2-IgH translocation in an international multicentre study
ANNALS OF ONCOLOGY
1999; 10 (11): 1349-1354
Abstract
The capacity of the polymerase chain reaction (PCR) to detect very low numbers of cells bearing a t(14;18) translocation has led to its application in assessment of the results of treatment for follicular lymphoma, and suggestions that therapy might be guided by molecular studies. To test the reliability of PCR a collaborative study was undertaken to compare results from different laboratories in Europe and North America.Twenty laboratories with records of publication in molecular diagnostics were sent blood from normal donors with varying numbers of t(14;18)-bearing cells added from a cell line with a translocation in the major breakpoint region (MBR) of the bcl-2 gene. Samples contained 1000, 100, 10, 1 or 0 cells per ml of whole blood and were sent blinded in duplicate. PCR methodology varied widely, with the total number of amplification cycles between 30 and 70, and 13 different primers used for the MBR region. Twelve laboratories used nested PCR and eight single round amplification.The sensitivity of nested and single round PCR was similar at 100 cells/ml but below this the nested method proved significantly more sensitive. The false positive rate was 28%, with 11 samples from 9 laboratories reported as positive when no t(14;18) cells were added. PCR product size and sequence analysis showed that false positives were due to contamination from cell-line DNA rather than background translocations in the donors. There was no significant difference in false positive rates between nested and single round techniques.The polymerase chain reaction to detect bcl-2-IgH rearrangements is presently carried out with widely disparate results. Further effort is required to bring forward a standard PCR protocol which can be re-tested in different laboratories to improve accuracy and reproducibility. The application of quantitative techniques such as real-time PCR may resolve many of the problems presently encountered.
View details for Web of Science ID 000084979300018
View details for PubMedID 10631464
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Familial coagulation factor V deficiency caused by a novel 4 base pair insertion in the factor V gene: Factor v Stanford
THROMBOSIS AND HAEMOSTASIS
1999; 82 (3): 1097-1099
Abstract
An index patient with pseudohomozygosity for factor V Leiden was identified. Each of his two children inherited a different paternal factor V allele; a daughter was heterozygous for factor V Leiden, with 100% factor V activity, and a son was heterozygous for factor V deficiency, with 50% factor V activity. Genomic DNA was obtained from family members, and the 25 factor V exons and flanking intronic regions were sequenced in the proband and confirmed in the children. Within exon 13 of factor V, a 4 base insertion was found at NT 2856 in the proband and son. but not the daughter. This mutation, here designated factor V Stanford, results in a frameshift with loss of a thrombin activation site (R1545V) and premature termination of translation at amino acid 1560.
View details for Web of Science ID 000082421100018
View details for PubMedID 10494770
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Mast-cell heparin demystified.
Nature
1999; 400 (6746): 714-715
View details for PubMedID 10466718
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Use of the polymerase chain reaction in the evaluation of cutaneous T-cell infiltrates
DERMATOLOGIC CLINICS
1999; 17 (3): 657-?
Abstract
Histologic evaluation of suspected cutaneous T-cell neoplasia is challenging. There is significant overlap with features of benign condition, and neoplastic cells often occur in a reactive background. Recently, molecular techniques using paraffin-embedded tissue have been applied to the diagnosis of cutaneous T-cell infiltrates. These methods are useful for determining whether a clonal population of T-cells is present. The advantages and limitation of molecular diagnostic methods in the diagnosis of cutaneous T-cell infiltrates are discussed.
View details for Web of Science ID 000081318700015
View details for PubMedID 10410865
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Aggressive natural killer-like T-cell malignancy with leukemic presentation following solid organ transplantation
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
1999; 111 (5): 663-671
Abstract
NK-like T-cell malignancies are part of a spectrum of lymphoproliferative diseases that complicate immunosuppression associated with solid organ transplantation. We describe 2 patients with long-standing immunosuppression following solid organ transplantation. Both patients had systemic symptoms that included fever, myalgia, and weight loss. Organ involvement and lymphadenopathy were not initially observed. Unique to these 2 cases are the initial leukemic symptoms, which led to further characterization and identification of NK-like T-cell malignancies. Both patients exhibited an anomalous T/NK phenotype, CD56 positivity, and atypical blastic architecture of the large granular lymphocytes. Clonal rearrangement of T-cell receptor genes was detected in both patients. In 1 patient, a cytogenetic abnormality involving 8q24 was demonstrated. The disease course in both patients was aggressive, with involvement of multiple sites and rapid demise. This study emphasizes the importance of including NK-like T-cell malignancies in the differential diagnosis of lymphoproliferative disorders associated with immunosuppression and recognizing that an aggressive clinical course may follow leukemic presentation of disease.
View details for Web of Science ID 000079920500011
View details for PubMedID 10230357
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Aggressive cutaneous NK and NK-like T-cell lymphomas - Clinicopathologic, immunohistochemical, and molecular analyses of 12 cases
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
1999; 23 (5): 571-581
Abstract
Natural killer (NK) and NK-like T-cell lymphomas are rare hematolymphoid malignancies that predominate in the upper aerodigestive system. They also involve other extranodal sites, including the skin. Primary cutaneous manifestations of NK and NK-like T-cell lymphomas are uncommon, and the clinicopathologic features are poorly understood. We have studied 12 patients of varied ethnic backgrounds with CD56-positive lymphomas in the skin. Six patients subsequently progressed to disseminated disease. These lymphomas showed the following immunophenotype: CD56+, CD43+, TCRb-, CD3-/+, CD20-, CD30-/+, CD4-, and CD8-. Two cases exhibited T-cell receptor gene rearrangements supporting a T-cell origin for these lymphomas, whereas the remaining 10 cases were likely derived from NK cells. Our results show inconsistent association of these lymphomas with Epstein-Barr virus (EBV), the multidrug resistance phenotype, and expression of P53. In addition, we found a previously unreported correlation between lymphomas harboring EBV mRNA and the expression of the multidrug resistance phenotype. These lymphomas were aggressive and were associated with rapid clinical progression, treatment failure, multiple relapses, and an average survival of 15 months from the time of diagnosis. Our results indicate the importance of recognizing this disease as a distinct subset of aggressive cutaneous lymphomas that may be diagnosed on the basis of morphology, immunophenotype, and gene rearrangement studies.
View details for Web of Science ID 000080178200012
View details for PubMedID 10328090
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The international normalized ratio during concurrent warfarin and argatroban anticoagulation: Differential contributions of each agent and effects of the choice of thromboplastin used
CLINICAL CHEMISTRY
1999; 45 (3): 409-412
View details for Web of Science ID 000078979100015
View details for PubMedID 10053045
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Blinded comparison demonstrates that BCL-2 real-time PCR assay provides more sensitive and quantitative assessment of residual disease than nested PCR.
W B SAUNDERS CO. 1998: 238A
View details for Web of Science ID 000077121300966
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Performance of the Avocet(PT) prothrombin time (PT)/INR system.
AMER SOC HEMATOLOGY. 1998: 112B–112B
View details for Web of Science ID 000077121400477
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Familial coagulation factor V deficiency caused by a novel 4 base pair insertion in the factor V gene.
W B SAUNDERS CO. 1998: 354A–355A
View details for Web of Science ID 000077121301451
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Sensitive detection of clonal immunoglobulin rearrangements in frozen and paraffin embedded tissues by PCR heteroduplex analysis.
W B SAUNDERS CO. 1998: 229A
View details for Web of Science ID 000077121300936
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Mesenteric artery thrombosis: A case report of combined protein S and protein C deficiency
AMERICAN JOURNAL OF HEMATOLOGY
1998; 58 (3): 246-247
Abstract
Individuals with more than one defect in natural coagulant/anticoagulant systems have been postulated to be at an increased risk for thrombotic events. We report a case of combined protein S and C deficiency in a young woman, which resulted in fatal arterial mesenteric thrombosis. The role of coagulation defects in arterial thrombosis is discussed.
View details for Web of Science ID 000074510000017
View details for PubMedID 9662280
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Factor V Leiden and the risk of proximal venous thrombosis after total hip arthroplasty
JOURNAL OF ARTHROPLASTY
1998; 13 (2): 207-210
Abstract
Deep vein thrombosis (DVT) remains a major cause of morbidity in patients undergoing total hip arthroplasty (THA). Despite postoperative DVT prophylaxis, 20-50% of THA patients still develop DVT. Currently, there is no accurate way of predicting which patients will develop DVT despite standard prophylaxis. The presence of factor V Leiden is the most common cause of inherited DVT risk. It has been postulated that patients who have factor V Leiden and are subjected to thrombogenic stressors such as THA would have an increased risk of thrombosis. The factor V Leiden genotype of 36 patients who developed proximal DVT after surgery and 45 control patients who had THA but did not develop DVT was determined. All patients had had prophylaxis against thrombosis using intermittent pneumatic compression alone or in combination with warfarin or aspirin. Surveillance for proximal DVT was performed on all patients prior to discharge by duplex ultrasound. The 2 groups were similar in age, sex, and type of operation. Three of 36 study patients who had developed DVT (8%) and 2 of 45 control patients who had not developed DVT (4%) were heterozygotes for factor V Leiden; these prevalences were not statistically different. Heterozygosity for factor V Leiden is not associated with DVT prophylaxis failure in patients undergoing THA.
View details for Web of Science ID 000072498700014
View details for PubMedID 9526216
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A microplate allele-specific oligonucleotide hybridization assay for detection of factor V Leiden
DIAGNOSTIC MOLECULAR PATHOLOGY
1997; 6 (6): 347-352
Abstract
Factor V Leiden is the most common genetic risk factor for thrombosis. Currently, the determination of factor V Leiden genotype is limited to laboratories with expertise in molecular methods to develop "home brew" assays using polymerase chain reaction (PCR) to amplify genomic DNA, followed by analysis of Mnl I restriction fragments. These methods are not standardized, are labor intensive, and have low throughput. We describe a method for determination of factor V Leiden genotype using allele-specific oligonucleotide capture probes coated onto 96 well plates, requiring only a thermal cycler and a microplate spectrophotometer to perform. With an automated strip washer and plate reader, genotypes could be determined in 80 min from completion of PCR. Within-run and between-run coefficients of variation for the assay were < 10%. In all 160 cases studied, the microplate assay correctly identified the factor V genotype. The microplate oligonucleotide hybridization assay is a simple and reliable system for determination of factor V Leiden genotype. The assay offers an automatable, high-throughput alternative to current testing methodologies.
View details for Web of Science ID 000072819400007
View details for PubMedID 9559295
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Cross-linking hybridization assay for direct detection of factor V Leiden mutation
29th Annual Oak Ridge Conference
AMER ASSOC CLINICAL CHEMISTRY. 1997: 1703–8
Abstract
A nucleic acid photocross-linking technology was used in the development of a direct assay for factor V Leiden, a point mutation in the factor V gene (G1691A) that is the most common inherited risk factor for thrombosis. This cross-linking hybridization assay included two allele-specific capture probes and six signal-generating reporter probes; all were modified with a photoactivated cross-linking compound. By using two different capture probes complementary to a 16-base sequence at the factor V Leiden mutation site, but differing in the nucleotide opposite the mutation site (C vs T), wild-type and factor V Leiden alleles were differentiated in purified DNA specimens. The assay was also successfully applied to genomic DNA in leukocytes isolated from whole blood; the factor V status of 122 patients as determined by this method was in complete concordance with a standard PCR-based assay and clearly discriminated between healthy individuals and factor V Leiden heterozygotes.
View details for Web of Science ID A1997XV89700033
View details for PubMedID 9299963
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Heparin-induced platelet aggregation vs platelet factor 4 enzyme-linked immunosorbent assay in the diagnosis of heparin-induced thrombocytopenia-thrombosis
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
1997; 108 (1): 78-82
Abstract
Thrombosis occurs in an unpredictable subset of patients with heparin-induced thrombocytopenia (HIT). The diagnosis of HIT requires clinical suspicion and laboratory confirmation. Although the "gold-standard" diagnostic test is considered to be the serotonin release assay (SRA), most laboratories use heparin-induced platelet aggregation (HIPA), which is highly specific but reported to be less sensitive than the SRA. Recently, the heparin-platelet factor 4 (PF4) enzyme-linked immunosorbent assay (ELISA) has been reported to have comparable sensitivity to the SRA. We compared the HIPA and PF4 ELISA in serum samples from 146 patients examined for HIT and assessed whether either test predicted thrombotic risk. Results for 81 patients were positive for HIPA, PF4 ELISA, or both. Of these, 91% were HIPA-positive, while only 60% were PF4 ELISA-positive. Clinical information was available on 63 patients, 17 of whom had thrombotic events (10 venous, 6 arterial, and 1 both). Neither the HIPA nor the PF4 ELISA predicted thrombotic risk, but the HIPA proved to be a more sensitive test for laboratory confirmation.
View details for Web of Science ID A1997XG01600013
View details for PubMedID 9208982
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Administration of a CD31-derived peptide delays the onset and significantly increases survival from lethal graft-versus-host disease
BLOOD
1997; 89 (4): 1452-1459
Abstract
The CD31 monoclonal antibody, LYP21, binds to the CD31 domain 6 and inhibits the human mixed-lymphocyte reaction (MLR) in a specific and dose-dependent fashion. A synthetic CD31 peptide based on human CD31 epitope (amino acids 551 to 574) recognized by LYP21 is equally effective in inhibiting the MLR. In this study, we used the murine homolog of CD31 peptide 551 to 574 and a control peptide to study the role of CD31 molecule on T-cell activation. In vitro, CD31 peptide inhibited the MLR across several major and minor histocompatibility differences in a specific and dose-dependent fashion, similar to the results observed in the human system. Maximal inhibition was achieved at a dose of 200 microg/mL. In the cytotoxic T-lymphocyte (CTL) assay, CD31 peptide inhibited CTL responses by 97%. To study the in vivo effect of this peptide, graft-versus-host disease (GVHD) across minor histocompatibility barriers was induced in the B10.D2 (H-2d) --> BALB/c (H-2d) model. BALB/c recipients received CD31 peptide (100 microg/d), or phosphate-buffered saline (PBS), or control peptide (100 microg/d) intraperitoneally (IP) for the first 5 weeks. CD31 peptide delayed onset of graft-versus-host disease and significantly increased long-term survival. Twelve of 14 mice receiving CD31 peptide survived more than 100 days after transplantation, as compared with none of 10 mice receiving PBS and none of five mice receiving control peptide (P = .0001). Long-term engraftment of allogeneic bone marrow was documented in all transplanted mice by polymerase chain reaction (PCR) analysis of microsatellite region in the interleukin (IL)-1beta gene. Our data suggest that the CD31 molecule has an important functional role in T-cell activation in vitro and in vivo.
View details for Web of Science ID A1997WG79700038
View details for PubMedID 9028970
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Sensitivity and specificity of the APC resistance assay in detection of individuals with factor V Leiden
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
1996; 106 (1): 107-111
Abstract
Resistance to activated protein C (APC) is the most common cause of familial thrombophilia. The partial thromboplastin time (PTT)-based test for resistance to APC has been widely employed as a screening test for this disorder. However, the utility of this test for screening is not well characterized. More than 90% of patients with resistance to APC have the G1691A mutation in factor V (factor V Leiden). The authors studied the ability of a commercial APC resistance assay to correctly identify the factor V Leiden genotype in 130 individuals. At the recommended assay cut-off value of 2, the sensitivity of the APC resistance assay was 50%, with a specificity of 98%. Increasing the cut-off value increased the sensitivity but decreased the specificity of the test. Receiver operating characteristic (ROC) curve analysis indicated that the test was of intermediate utility. There was considerable overlap in APC ratios in the range of 2 to 3 between subjects with a normal factor V genotype and heterozygotes for factor V Leiden. The authors conclude that the APC resistance assay in its present form is not a useful screening test for factor V Leiden heterozygotes. Until the performance of this assay is improved, patients should have molecular diagnostic testing performed to determine their factor V Leiden status.
View details for Web of Science ID A1996UW50500018
View details for PubMedID 8701918
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Recurrent thrombosis due to compound heterozygosity for factor V Leiden and factor V deficiency
BLOOD COAGULATION & FIBRINOLYSIS
1996; 7 (3): 361-362
Abstract
A point mutation in the factor V gene (factor V Leiden) is the most common cause of familial thrombophilia. Patients with factor V Leiden have an increased risk of thrombosis, particularly those homozygous for the mutation. However, the phenotype in individuals with the mutation is variable, suggesting that other factors influence thrombotic risk. We describe for the first time a family in which two independent defects in factor V co-exist: heterozygosity for factor V Leiden and factor V deficiency. Compound heterozygosity for these two defects results in a phenotype similar to a homozygous factor V Leiden state with profound resistance to APC and recurrent thrombosis.
View details for Web of Science ID A1996UL37900012
View details for PubMedID 8735145
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Polymorphism of adhesion molecule CD31 and its role in acute graft-versus-host disease
NEW ENGLAND JOURNAL OF MEDICINE
1996; 334 (5): 286-291
Abstract
Graft-versus-host disease (GVHD) caused by poorly defined minor (i.e., other than HLA) histocompatibility antigens remains a serious problem in recipients of bone marrow transplants. We sought to determine whether the CD31 adhesion molecule is a minor alloantigen.We directly sequenced samples of complementary DNA (cDNA) encoding CD31 molecules from 21 unrelated normal subjects. Sequence-specific primers were then designed to amplify alleles by the polymerase chain reaction, thereby permitting CD31 typing of genomic DNA from additional normal subjects. To assess the relevance of CD31 matching to bone marrow transplantation, we performed CD31 typing of 46 recipients of bone marrow (32 without GVHD and 14 with severe [grade III or IV] acute GVHD) and their HLA-identical sibling donors. The immunoreactivity of CD31 phenotypes with anti-CD31 monoclonal antibodies was compared by flow cytometry.Direct sequencing of cDNA for CD31 from the 21 normal subjects identified a single polymorphism, CTG-->GTG (Leu-->Val), at codon 125; we designated the resulting alleles CD31.L and CD31.V, respectively. The CD31 genotypes of these and 142 other unrelated subjects were of the expected frequencies. Among the transplant recipients, 71 percent of those with acute GVHD had CD31 genotypes that were not identical to the donor's genotype, as compared with 22 percent of the recipients without GVHD (P = 0.004). The binding of anti-CD31 monoclonal antibodies as measured by fluorescence-activated cell sorting correlated with the CD31 types of homozygous cell lines.The adhesion molecule CD31 is polymorphic. When donor and recipient genotypes are not identical, the risk of GVHD increases. Prospective CD31 typing may reduce the risk of acute GVHD.
View details for Web of Science ID A1996TV69500002
View details for PubMedID 8532023
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Administration of a CD31-derived peptide reduces lethal graft-versus-host disease across the minor histocompatibility complex barrier in mice
AMER SOC HEMATOLOGY. 1995: 2286–86
View details for Web of Science ID A1995TH91002287
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PECAM-1 (CD31) is a minor histocompatibility determinant in acute GVHD.
W B SAUNDERS CO. 1995: 2475
View details for Web of Science ID A1995TH91002476
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HISTIDINE-RICH GLYCOPROTEIN - IS THERE A ROLE IN HEMOSTASIS OR IMMUNE FUNCTION
JOURNAL OF LABORATORY AND CLINICAL MEDICINE
1995; 125 (6): 682-683
View details for Web of Science ID A1995RB44500004
View details for PubMedID 7769360
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LAMININ MEDIATES AGGREGATION OF CD31-TRANSFECTED CELLS
SCHATTAUER GMBH-VERLAG MEDIZIN NATURWISSENSCHAFTEN. 1995: 1153–53
View details for Web of Science ID A1995RP38500966
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INVOLVEMENT OF CD31 IN LYMPHOCYTE-MEDIATED IMMUNE-RESPONSES - IMPORTANCE OF THE MEMBRANE-PROXIMAL IMMUNOGLOBULIN DOMAIN AND IDENTIFICATION OF AN INHIBITING CD31 PEPTIDE
BLOOD
1995; 85 (5): 1282-1288
Abstract
CD31 (PECAM-1) is an immunoglobulin gene superfamily cell adhesion molecule found on vascular endothelium, platelets, and leukocytes. Lymphocyte expression of CD31 is most closely associated with the CD45RA+CD8+ naive T phenotype. CD31 has recently been shown to play a role in leukocyte egress to inflammatory sites. The mechanism of CD31 adhesion remains under investigation. Several investigators have reported evidence for a heterotypic ligand. We have previously shown that CD31 is phosphorylated with cell activation, which suggests a possible role for CD31 in cell activation events. We therefore studied the effects of CD31 antibodies on in vitro assays of lymphocyte activation. One CD31 antibody, LYP21, inhibited the mixed lymphocyte reaction (MLR) in a specific and dose-dependent fashion. An LYP21 epitope was localized to the sixth Ig domain of CD31. This peptide and a scrambled control peptide were synthesized and used to study effects of this epitope on lymphocyte activation. The CD31 peptide strongly inhibited the MLR. Because CD31 is expressed on both stimulator and responder populations, stimulator peripheral blood leukocytes and responder lymphocyte populations were separately incubated with CD31 peptide or control peptide and then washed before mixing. The CD31 peptide inhibited the MLR equally when either stimulator or responder cells were preincubated with the CD31 peptide. We further sorted responder cells into CD31-high and CD31-low populations and separately incubated these subsets with peptides. The CD31 peptide strongly inhibited MLRs, regardless of level of responder-cell CD31 expression. Examination of MLR reactions involving the CD31 peptide showed dispersed small aggregates of cells, rather than the single large aggregate observed in control MLRs. The CD31 peptide did not affect activation of lymphocytes by phorbol myristate acetate (PMA) and ionomycin. These results suggest that a surface CD31-ligand interaction may have a functional role in alloimmune lymphocyte activation and identify a functionally important domain of CD31.
View details for Web of Science ID A1995QJ43500018
View details for PubMedID 7858258
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ACQUIRED ACTIVATED PROTEIN-C RESISTANCE CAUSED BY FACTOR-VA ANTIBODY - A POSSIBLE MECHANISM OF INCREASED THROMBOSIS IN THE ANTIPHOSPHOLIPID ANTIBODY SYNDROME
W B SAUNDERS CO. 1994: A83
View details for Web of Science ID A1994PR75400319
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ADHESION MECHANISM OF CD31 (PECAM-1)
SLACK INC. 1994: A129
View details for Web of Science ID A1994NF02000103
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THE CELL-ADHESION MOLECULE CD31 IS PHOSPHORYLATED AFTER CELL ACTIVATION - DOWN-REGULATION OF CD31 IN ACTIVATED LYMPHOCYTES-T
JOURNAL OF BIOLOGICAL CHEMISTRY
1992; 267 (8): 5243-5249
Abstract
We report the independent cloning of the cDNA for CD31, a recently described cell adhesion molecule of the immunoglobulin gene superfamily present on platelets, granulocytes, monocytes, lymphocytes, and endothelial cells. Northern analysis revealed three major mRNA transcripts in Jurkat (a human T cell line) and K562 and HEL (leukemia cell lines) cells with an additional 5.3-kilobase transcript seen in cultured human umbilical vein endothelial cells. Following T cell activation, CD31 mRNA was down-regulated by Northern analysis, and decreased CD31 protein expression was confirmed by immunoblots. The down-regulation of CD31 was partially mediated by decreased transcription as demonstrated by nuclear run-on studies. CD31 became rapidly phosphorylated in platelets, Jurkat cells, and endothelial cells after cell activation. We were unable to demonstrate the presence of a phosphotyrosine in CD31 using monoclonal and polyclonal phosphotyrosine antibodies. In addition, CD31 phosphorylation in platelets was induced by phorbol ester and was blocked by staurosporin, a protein kinase C inhibitor, suggesting that CD31 phosphorylation is mediated by protein kinase C and involves serine and/or threonine residues. The phosphorylation of CD31 following cell activation may modulate its cellular adhesiveness, and the down-regulation of its expression may serve to impart target specificity and to localize effector lymphocytes to areas of inflammation.
View details for Web of Science ID A1992HH74700040
View details for PubMedID 1544907
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DEVELOPMENT OF ANTIBODIES TO THROMBIN AND FACTOR-V WITH RECURRENT BLEEDING IN A PATIENT EXPOSED TO TOPICAL BOVINE THROMBIN
BLOOD
1990; 76 (10): 2011-2016
Abstract
A 65 year old patient who was exposed to topical bovine thrombin during cardiac surgery developed markedly prolonged clotting times and a severe bleeding diathesis. Mixing studies with normal plasma failed to correct the clotting times. Platelet transfusions, immunosuppressive and immunomodulatory therapies were ineffective, but plasmapheresis was effective in decreasing clotting times and in the resolution of clinical bleeding events. The patient's purified IgG reacted with bovine thrombin by immunoblotting and enzyme-linked immunosorbent assay (ELISA). However, the IgG reacted minimally with human thrombin. In view of the severe bleeding, a coexisting inhibitor was sought. The patient's factor V activity was 1% of normal and was not corrected by mixing with normal plasma, demonstrating the presence of an inhibitor against factor V. The patient's IgG reacted with both bovine and human factor V. Immunoblotting localized the site of antibody binding to the light chain of activated bovine factor V. Detectable amounts of bovine factor V were found in commercial bovine thrombin preparations by ELISA. The data suggest that patients exposed to topical bovine thrombin may develop antibodies to thrombin and factor V. Anti-thrombin antibodies may mask coexisting factor V inhibitors responsible for clinical bleeding.
View details for Web of Science ID A1990EJ39100016
View details for PubMedID 2242423
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DEVELOPMENT OF ANTIBODIES TO THROMBIN AND FACTOR-V WITH RECURRENT BLEEDING IN A PATIENT EXPOSED TO TOPICAL BOVINE THROMBIN
SLACK INC. 1990: A427–A427
View details for Web of Science ID A1990CZ24401154
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A PLATELET MEMBRANE GLYCOPROTEIN, GP128, IS SYNTHESIZED BY HUMAN VASCULAR ENDOTHELIAL-CELLS AND SECRETED INTO THE MEDIA
SCHATTAUER GMBH-VERLAG MEDIZIN NATURWISSENSCHAFTEN. 1989: 44–44
View details for Web of Science ID A1989AR58400138
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TORSADES-DE-POINTES PRECIPITATED BY A CHINESE HERBAL REMEDY
AMERICAN JOURNAL OF CARDIOLOGY
1987; 60 (14): 1186-1187
View details for Web of Science ID A1987K936300016
View details for PubMedID 3687752
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REINVESTIGATION OF THE REACTION OF CHYMOTRYPSIN WITH N-FURYLACRYLOYLTRYPTOPHAN DERIVATIVES AT ACIDIC PH
BIOCHEMICAL JOURNAL
1979; 181 (3): 733-736
Abstract
The reaction of alpha-chymotrypsin with N alpha-3-(2-furyl)acryloyl-L-tryptophan methyl ester (FA-Trp-OMe) and amide has been investigated in aqueous and dimethylsulphoxide cryosolvent solutions from pH2 to 7 and over a wide temperature range. Previous reports have suggested that an intermediate preceding the acyl-enzyme can be detected spectrophotometrically in the reaction with methyl esters of FA-Trp and FA-Tyr at low pH [Yu & Viswanatha (1969) Eur. J. Biochem. 11, 347--352), and that this intermediate is an oxazolinone [Coletti-Previero et al. (1970) FEBS Lett. 11, 213--217]. We show that the previous interpretations of the time-dependent spectral changes were incorrect, and that the only detected intermediate is the acyl-enzyme. This may be isolated by gel filtration at pH less than 2.5, 1 degree C, owing to its relative stability. The pH-dependence of the rates of acylation and deacylation from pH 8.5 to 2.0 are consistent with a single ionization of pK congruent to 7.0 in both aqueous and cryosolvent solutions.
View details for Web of Science ID A1979HL98500027
View details for PubMedID 42387
View details for PubMedCentralID PMC1161214