Dr. Bing Melody Zhang is board-certified by American Board of Pathology in Clinical Pathology and Molecular Genetic Pathology. She is also a certified and fully credentialed HLA laboratory director by American Society for Histocompatibility & Immunogenetics (ASHI) for the following areas--Solid Organ Transplantation: Deceased Donor; Solid Organ Transplantation: Live Donor; HSC/BM Transplantation: Related Donor; HSC/BM Transplantation: Unrelated Donor; Histocompatibility Testing for Other Clinical Purposes; Transfusion Support. Dr. Zhang completed Clinical Pathology residency, Molecular Genetic Pathology as well as Clinical Genomics fellowships, and Histocompatibility/Immunogetics training at Stanford. She is an attending pathologist at the molecular pathology service and the assistant director of the HLA lab. Her main research interests include genetic/genomic testing for malignant and non-malignant hematologic disorders, NGS-based TCR/Ig clonality/MRD diagnostic testing, molecular testing for BMT/solid organ transplantation, and HLA-related disease association and pharmacogenetic testing.
- Molecular Genetic Pathology
- Histocompatibility and Immunogenetics
- Clinical Pathology
Clinical Associate Professor, Pathology
Co-Director of Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center (2022 - Present)
Attending molecular pathologist, Stanford Health Care and Stanford Children's Health (2017 - Present)
Boards, Advisory Committees, Professional Organizations
Co-Chair, ASHI Science and Technology Initiatives Committee (2021 - Present)
Member, CAP/ACMG Biochemical and Molecular Genetics Committee (2020 - Present)
Member, American Society for Histocompatibility and Immunogenetics CPT code subcommittee (2020 - Present)
Member, ClinGen--Platelet Disorders Variant Curation Expert Panel (2018 - Present)
ASHI Certified HLA Lab Director, American Society for Histocompatibility and Immunogenetics, HLA
Board Certification, American Board of Pathology, Clinical Pathology (2017)
Board Certification, American Board of Pathology and American Board of Medical Genetics and Genomics, Molecular Genetic Pathology (2017)
Residency, Stanford University Department of Pathology, Clinical Pathology (2017)
Fellowship, Stanford University Department of Pathology, Clinical Genomics (2017)
Fellowship, Stanford University Department of Pathology, Molecular Genetic Pathology (2016)
Medical education, Shandong University School of Medicine, Medicine
MS, Shandong University School of Medicine, Medical Genetics
Current Research and Scholarly Interests
My main research interests lie in the following areas:
1) Using genetic/genomic approaches to study the genotype-phenotype correlation of inherited non-malignant hematologic disorders, especially platelet disorders.
2) Development and application of molecular assays for clinical testing to support hematopoietic stem cell transplantation and solid organ transplantation.
3) NGS-based TCR/Ig clonality/MRD diagnostic testing.
4) HLA-related disease association and pharmacogenetic testing.
Graduate and Fellowship Programs
Molecular and Genetic Medicine (Fellowship Program)
An Overview of Characteristics of Clinical Next-Generation Sequencing-Based Testing for Hematologic Malignancies.
Archives of pathology & laboratory medicine
With the increasing integration of molecular alterations into the evaluation of hematologic malignancies (HM), somatic mutation profiling by next-generation sequencing (NGS) has become a common clinical testing strategy. Limited data are available about the characteristics of these assays.To describe assay characteristics, specimen requirements, and reporting practices for NGS-based HM testing using College of American Pathologists proficiency testing survey data.The College of American Pathologists NGS Hematologic Malignancies Survey (NGSHM) results from 78 laboratories were used to determine laboratory practices in NGS-based HM testing.The majority of laboratories performed tumor-only (88.5% [69 of 78]), targeted sequencing of cancer genes or mutation hotspots (98.7% [77 of 78]); greater than 90% performed testing on fresh bone marrow and peripheral blood. The majority of laboratories reported a 5% lower limit of detection for single-nucleotide variants (73.1% [57 of 78]) and small insertions and deletions (50.6% [39 of 77]). A majority of laboratories used benchtop sequencers and custom enrichment approaches.This manuscript summarizes the characteristics of clinical NGS-based testing for the detection of somatic variants in HM. These data may be broadly useful to inform laboratory practice and quality management systems, regulation, and oversight of NGS testing, and precision medicine efforts using a data-driven approach.
View details for DOI 10.5858/arpa.2019-0661-CP
View details for PubMedID 33450747
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
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
Identification of a pathogenic TUBB1 variant in a Chinese family with congenital macrothrombocytopenia through whole genome sequencing.
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
Specifications of the variant curation guidelines for ITGA2B/ITGB3: ClinGen Platelet Disorder Variant Curation Panel.
2021; 5 (2): 414–31
Accurate and consistent sequence variant interpretation is critical to the correct diagnosis and appropriate clinical management and counseling of patients with inherited genetic disorders. To minimize discrepancies in variant curation and classification among different clinical laboratories, the American College of Medical Genetics and Genomics (ACMG), along with the Association for Molecular Pathology (AMP), published standards and guidelines for the interpretation of sequence variants in 2015. Because the rules are not universally applicable to different genes or disorders, the Clinical Genome Resource (ClinGen) Platelet Disorder Expert Panel (PD-EP) has been tasked to make ACMG/AMP rule specifications for inherited platelet disorders. ITGA2B and ITGB3, the genes underlying autosomal recessive Glanzmann thrombasthenia (GT), were selected as the pilot genes for specification. Eight types of evidence covering clinical phenotype, functional data, and computational/population data were evaluated in the context of GT by the ClinGen PD-EP. The preliminary specifications were validated with 70 pilot ITGA2B/ITGB3 variants and further refined. In the final adapted criteria, gene- or disease-based specifications were made to 16 rules, including 7 with adjustable strength; no modification was made to 5 rules; and 7 rules were deemed not applicable to GT. Employing the GT-specific ACMG/AMP criteria to the pilot variants resulted in a reduction of variants classified with unknown significance from 29% to 20%. The overall concordance with the initial expert assertions was 71%. These adapted criteria will serve as guidelines for GT-related variant interpretation to increase specificity and consistency across laboratories and allow for better clinical integration of genetic knowledge into patient care.
View details for DOI 10.1182/bloodadvances.2020003712
View details for PubMedID 33496739
- HLA-haplotype loss after TCRalphabeta/CD19-depleted haploidentical HSCT. Bone marrow transplantation 2020
- IDH2 Mutation in a Patient with Metastatic Colon Cancer NEW ENGLAND JOURNAL OF MEDICINE 2017; 376 (20): 1991-1992
- 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
The role of vanin-1 and oxidative stress-related pathways in distinguishing acute and chronic pediatric ITP
2011; 117 (17): 4569-4579
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
Longitudinal study of 2 patients with cyclic thrombocytopenia, STAT3, and MPL mutations.
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
Complement-Binding Donor-Specific Anti-HLA Antibodies: Biomarker for Immunologic Risk Stratification in Pediatric Kidney Transplantation Recipients.
Transplant international : official journal of the European Society for Organ Transplantation
2022; 35: 10158
Antibody-mediated rejection is a common cause of early kidney allograft loss but the specifics of antibody measurement, therapies and endpoints have not been universally defined. In this retrospective study, we assessed the performance of risk stratification using systematic donor-specific antibody (DSA) monitoring. Included in the study were children who underwent kidney transplantation between January 1, 2010 and March 1, 2018 at Stanford, with at least 12-months follow-up. A total of 233 patients were included with a mean follow-up time of 45 (range, 9-108) months. Median age at transplant was 12.3 years, 46.8% were female, and 76% had a deceased donor transplant. Fifty-two (22%) formed C1q-binding de novo donor-specific antibodies (C1q-dnDSA). After a standardized augmented immunosuppressive protocol was implemented, C1q-dnDSA disappeared in 31 (58.5%). Graft failure occurred in 16 patients at a median of 54 (range, 5-83) months, of whom 14 formed dnDSA. The 14 patients who lost their graft due to rejection, all had persistent C1q-dnDSA. C1q-binding status improved the individual risk assessment, with persistent; C1q binding yielding the strongest independent association of graft failure (hazard ratio, 45.5; 95% confidence interval, 11.7-177.4). C1q-dnDSA is more useful than standard dnDSA as a noninvasive biomarker for identifying patients at the highest risk of graft failure.
View details for DOI 10.3389/ti.2021.10158
View details for PubMedID 35992747
View details for PubMedCentralID PMC9386741
Next generation sequencing confirms T-cell clonality in a subset of pediatric pityriasis lichenoides.
Journal of cutaneous pathology
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
The Role of Donor KIR Genotyping in Pediatric Hematopoietic Stem Cell Transplantation For Non-Malignant Disorders
SPRINGERNATURE. 2020: 640
View details for Web of Science ID 000600556202248
Chimerism Monitoring with Highly Sensitive and Precise Next-Generation Sequencing Assay in Patients Post-Allogeneic Hematopoietic Stem Cell Transplantation
ELSEVIER SCIENCE INC. 2020: S310
View details for Web of Science ID 000516887900473
- Next Generation Sequencing-Based Characterization of T Cell Receptor Repertoire of Patients with Immune Thrombocytopenia AMER SOC HEMATOLOGY. 2019
Non-HLA Antibody-Mediated Rejection of Lung Transplant Masquerading Transfusion-Related Acute Lung Injury
WILEY. 2019: 199A
View details for Web of Science ID 000502826600470
Detection of Circulating Tumor DNA with a Single-Molecule Sequencing Analysis Validated for Targeted and Immunotherapy Selection.
Molecular diagnosis & therapy
INTRODUCTION: Comprehensive genetic cancer profiling using circulating tumor DNA has enabled the detection of National Comprehensive Cancer Network (NCCN) guideline-recommended somatic alterations from a single, non-invasive blood draw. However, reliably detecting somatic variants at low variant allele fractions (VAFs) remains a challenge for next-generation sequencing (NGS)-based tests. We have developed the single-molecule sequencing (SMSEQ) platform to address these challenges.METHODS: The OncoLBx assay utilizes the SMSEQ platform to optimize cell-free DNA extraction and library preparation with variant type-specific calling algorithms to improve sensitivity and specificity. OncoLBx is a pan-cancer panel for solid tumors targeting 75 genes and five microsatellite sites analyzing five classes of NCCN-recommended somatic variants: single-nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), fusions and microsatellite instability (MSI). Circulating DNA was extracted from plasma, followed by library preparation using SMSEQ. Analytical validation was performed according to recently published American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines and established the limit of detection (LOD), sensitivity, specificity, accuracy and reproducibility using 126 gold-standard reference samples, healthy donor samples verified by whole-exome sequencing by an external College of American Pathologists (CAP) reference lab and cell lines with known variants. Results were analyzed using a locus-specific modeling algorithm.RESULTS: We have demonstrated that OncoLBx detects VAFs of≥0.1% for SNVs and indels,≥0.5% for fusions,≥4.5 copies for CNVs and≥2% for MSI, with all variant types having specificity≥99.999%. Diagnostic performance of paired samples displays 80% sensitivity and>99.999% clinical specificity. Clinical utility and performance were assessed in 416 solid tumor samples. Variants were detected in 79% of samples, for which 87.34% of positive samples had available targeted therapy.
View details for DOI 10.1007/s40291-019-00406-0
View details for PubMedID 31209714
- Case series of MET exon 14 skipping mutation-positive non-small-cell lung cancers with response to crizotinib and cabozantinib ANTI-CANCER DRUGS 2019; 30 (5): 537–41
De novo complement-activating donor-specific antibodies in pediatric renal transplant recipients are highly responsive to therapy
View details for Web of Science ID 000485482200137
Chimerism Analysis in Pediatric Hematopoietic Stem Cell Transplantation for Non-Malignant Disorders
ELSEVIER SCIENCE INC. 2019
View details for Web of Science ID 000540655500467
Case series of MET exon 14 skipping mutation-positive non-small-cell lung cancers with response to crizotinib and cabozantinib.
The mesenchymal-to-epithelial transition (MET) gene is altered and becomes a driver mutation in up to 5% of non-small-cell lung cancer (NSCLC). We report our institutional experience treating patients with MET exon 14 skipping (METex14) mutations, including responses to the MET inhibitors crizotinib and cabozantinib. We identified cases of NSCLC with METex14 mutations using an institutionally developed or commercial next-generation sequencing assay. We assessed patient and disease characteristics by retrospective chart review. Some patients were treated off-label by the physician with crizotinib or cabozantinib, and tumor responses to these agents were assessed. A total of 15 patients with METex14-mutated NSCLC were identified, predominantly male (n=10) with a smoking history (60%) and a median age of 74.0 years. No other actionable somatic mutations were detected. Stage distribution included 26.7% stage I, 6.7% stage II, 6.7% stage III, and 60.0% stage IV. Among patients treated with crizotinib or cabozantinib (n=6), three patients showed partial response and one patient showed stable disease on the basis of RECIST criteria. Four patients experienced side effects requiring drug holiday, reduction, or cessation. Our findings highlight the diversity in presentation and histology of NSCLC with METex14 mutations, which were found in the absence of other actionable driver mutations. We observed evidence of tumor response to crizotinib and cabozantinib, supporting the previous reports that METex14 mutations in NSCLC are actionable driver events.
View details for PubMedID 30762593
- 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
- Molecular Diagnosis in Hematology Wintrobe’s Clinical Hematology 2019; 14e: 56–66
Assessment by Extended-Coverage Next-Generation Sequencing Typing of DPA1 and DPB1 Mismatches in Siblings Matching at HLA-A, -B, -C, -DRB1, and -DQ Loci.
Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation
Allogeneic hematopoietic stem cell transplant from an HLA matched sibling donor is usually the preferable choice. The use of next-generation sequencing (NGS) for HLA typing in clinical practice provides broader coverage and higher resolution of HLA genes. We evaluated the frequency of DPB1 crossing-over events among patients and potential related donors typed with NGS. From July 2016 to January 2018, 593 patients and 2385 siblings were typed. We evaluated sibling matching status in 546 patients, and 44.8% of these patients had siblings that matched at HLA-A, -B, -C, -DRB1, and -DQB1 loci. In 306 patient-HLA matched sibling pairs, we found 6 pairs (1.96%) with 1 DPB1 mismatch, and 5 of these pairs included an additional mismatch in DPA1. No additional mismatches were observed at the low expression loci. Using the T cell epitope algorithm, 4 of these DP mismatches were classified as permissive, 1 as nonpermissive in the host-versus-graft direction, and 1 as nonpermissive in the graft-versus-host direction. The frequency of DPB1 and DPA1 mismatches is low, and their impact in related donor transplants is not well established. Although DP typing in related transplants goes beyond guidelines, it is especially relevant for sensitized patients. NGS-based HLA typing provides full gene coverage, and its use in clinical practice can enable better donor selection.
View details for DOI 10.1016/j.bbmt.2019.07.033
View details for PubMedID 31381995
- Case Series of MET Exon 14 Skipping Mutation-positive Non-Small Cell Lung Cancers and Response to Crizotinib. International journal of radiation oncology, biology, physics 2017; 98 (1): 239-?
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
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
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
- PS01.67: Case Series of MET Exon 14 Skipping Mutation-Positive Non-Small Cell Lung Cancers and Response to Crizotinib: Topic: Medical Oncology. Journal of thoracic oncology 2016; 11 (11S): S312-S313
- ROS: novel regulators of thrombopoiesis BLOOD 2016; 128 (5): 613-?
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
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
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
Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes.
2013; 98 (11): 1689-1696
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
Minimal residual disease quantification using consensus primers and high- throughput IGH sequencing predicts post-transplant relapse in chronic lymphocytic leukemia
2013; 27 (8): 1659-1665
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
Oxidative stress and immune thrombocytopenia.
Seminars in hematology
2013; 50 (3): e1-4
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
Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations.
American journal of surgical pathology
2013; 37 (6): 796-803
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
Sequential azacitidine plus lenalidomide combination for elderly patients with untreated acute myeloid leukemia.
2013; 98 (4): 591-596
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
- 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
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
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
The Role of Oxidative Stress in Pediatric Immune Thrombocytopenia
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000314049602365
Azacitidine Plus Lenalidomide for Untreated AML Patients Ineligible for Conventional Chemotherapy
AMER SOC HEMATOLOGY. 2012
View details for Web of Science ID 000313838906082
Safety, efficacy and biological predictors of response to sequential azacitidine and lenalidomide for elderly patients with acute myeloid leukemia
2012; 26 (5): 893-901
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
Tailored temozolomide therapy according to MGMT methylation status for elderly patients with acute myeloid leukemia
AMERICAN JOURNAL OF HEMATOLOGY
2012; 87 (1): 45-50
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
- 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-?
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
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
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
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
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
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
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
Large granular lymphocyte leukemia: Clonality reconsidered.
AMER SOC HEMATOLOGY. 2007: 912A
View details for Web of Science ID 000251100804139
- T-cell clonality analysis in biopsy specimens from two different skin sites shows high specificity in the diagnosis of patients with suggested mycosis fungoides J Am Acad Dermatol. 2007; 57 (5)