Jon Bernstein

All Publications

• Aortic Root Dilation and Genotype Associations in Phelan-McDermid Syndrome. American journal of medical genetics. Part A Gluckman, J., Levy, T., Friedman, K., Garces, F., Filip-Dhima, R., Quinlan, A., Iannotti, I., Pekar, M., Hernandez, A. L., Nava, M. T., Kravets, E., Siegel, A., Bernstein, J. A., Berry-Kravis, E., Powell, C. M., Soorya, L. V., Thurm, A., Srivastava, S., Buxbaum, J. D., Sahin, M., Kolevzon, A., Gelb, B. D. 2024: e63872

  Abstract

  Phelan-McDermid syndrome (PMS) is a rare genetic neurodevelopmental disorder that results from the loss of one functional copy of the SHANK3 gene. While many clinical features of PMS are well-understood, there is currently limited literature on cardiovascular abnormalities in PMS. This report aims to evaluate the prevalence of aortic root dilation (ARD) among individuals with PMS and to understand if underlying genetic variation relates to risk for ARD. We present findings from 59 participants collected from a multisite observational study evaluating the phenotype and natural history of PMS. Individual echocardiographic and genetic reports were analyzed for aortic root measurements and genetic variant data, respectively. Our a priori hypothesis was that participants with chromosome 22 deletions with hg19 start coordinates on or before 49,900,000 (larger deletions) would have more instances of ARD than participants with deletion start coordinates after 49,900,000 (smaller deletions). Eight participants (14%) had ARD, and its presence was statistically significantly associated with large deletions (p = 0.047). Relatedly, participants with ARD had significantly more genes deleted on chromosome 22 than participants without ARD (p = 0.013). These results could aid in the identification of individuals with PMS who are at higher risk for ARD.

  View details for DOI 10.1002/ajmg.a.63872

  View details for PubMedID 39257296

• Large-scale mutational analysis identifies UNC93B1 variants that drive TLR-mediated autoimmunity in mice and humans. The Journal of experimental medicine Rael, V. E., Yano, J. A., Huizar, J. P., Slayden, L. C., Weiss, M. A., Turcotte, E. A., Terry, J. M., Zuo, W., Thiffault, I., Pastinen, T., Farrow, E. G., Jenkins, J. L., Becker, M. L., Wong, S. C., Stevens, A. M., Otten, C., Allenspach, E. J., Bonner, D. E., Bernstein, J. A., Wheeler, M. T., Saxton, R. A., Undiagnosed Diseases Network, Liu, B., Majer, O., Barton, G. M., Acosta, M. T., Adams, D. R., Alvarez, R. L., Alvey, J., Allworth, A., Andrews, A., Ashley, E. A., Afzali, B., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Cassini, T., Chanprasert, S., Chao, H., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Delgado, M., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Fu, J., Gahl, W. A., Glass, I., Goddard, P. C., Godfrey, R. A., Gropman, A., Halley, M. C., Hamid, R., Hanchard, N., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Hutchison, S., Introne, W., Izumi, K., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Kaitryn, E., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Lewis, R. A., Liu, P., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A., Mahoney, R., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McConkie-Rosell, A., McCray, A. T., McGee, E., Might, M., Mikati, M., Miller, D., Mirzaa, G., Morava, E., Moretti, P., Morimoto, M., Mulvihill, J. J., Nakano-Okuno, M., Nelson, S. F., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Papp, J. C., Parker, N. H., Petcharet, L., Phillips, J. A., Posey, J. E., Potocki, L., Pusey Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenthal, E., Rossignol, F., Ruzhnikov, M., Sabaii, M., Sampson, J. B., Schedl, T., Schoch, K., Scott, D. A., Seto, E., Sharma, P., Shashi, V., Shelkowitz, E., Sheppeard, S., Shin, J., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, K. S., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stergachis, A., Stoler, J. M., Sullivan, K., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, Q. K., Tan, A. L., Tarakad, A., Taylor, H., Tekin, M., Thorson, W., Tifft, C. J., Toro, C., Tran, A. A., Ungar, R. A., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Walley, N. M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Hubshman, M. W., Wener, M., Wenger, T., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Worley, K., Yamamoto, S., Zhang, Z., Zuchner, S. 2024; 221 (8)

  Abstract

  Nucleic acid-sensing Toll-like receptors (TLR) 3, 7/8, and 9 are key innate immune sensors whose activities must be tightly regulated to prevent systemic autoimmune or autoinflammatory disease or virus-associated immunopathology. Here, we report a systematic scanning-alanine mutagenesis screen of all cytosolic and luminal residues of the TLR chaperone protein UNC93B1, which identified both negative and positive regulatory regions affecting TLR3, TLR7, and TLR9 responses. We subsequently identified two families harboring heterozygous coding mutations in UNC93B1, UNC93B1+/T93I and UNC93B1+/R336C, both in key negative regulatory regions identified in our screen. These patients presented with cutaneous tumid lupus and juvenile idiopathic arthritis plus neuroinflammatory disease, respectively. Disruption of UNC93B1-mediated regulation by these mutations led to enhanced TLR7/8 responses, and both variants resulted in systemic autoimmune or inflammatory disease when introduced into mice via genome editing. Altogether, our results implicate the UNC93B1-TLR7/8 axis in human monogenic autoimmune diseases and provide a functional resource to assess the impact of yet-to-be-reported UNC93B1 mutations.

  View details for DOI 10.1084/jem.20232005

  View details for PubMedID 38780621

• De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome. Nature Chen, Y., Dawes, R., Kim, H. C., Ljungdahl, A., Stenton, S. L., Walker, S., Lord, J., Lemire, G., Martin-Geary, A. C., Ganesh, V. S., Ma, J., Ellingford, J. M., Delage, E., D'Souza, E. N., Dong, S., Adams, D. R., Allan, K., Bakshi, M., Baldwin, E. E., Berger, S. I., Bernstein, J. A., Bhatnagar, I., Blair, E., Brown, N. J., Burrage, L. C., Chapman, K., Coman, D. J., Compton, A. G., Cunningham, C. A., D'Souza, P., Danecek, P., Délot, E. C., Dias, K. R., Elias, E. R., Elmslie, F., Evans, C. A., Ewans, L., Ezell, K., Fraser, J. L., Gallacher, L., Genetti, C. A., Goriely, A., Grant, C. L., Haack, T., Higgs, J. E., Hinch, A. G., Hurles, M. E., Kuechler, A., Lachlan, K. L., Lalani, S. R., Lecoquierre, F., Leitão, E., Fevre, A. L., Leventer, R. J., Liebelt, J. E., Lindsay, S., Lockhart, P. J., Ma, A. S., Macnamara, E. F., Mansour, S., Maurer, T. M., Mendez, H. R., Metcalfe, K., Montgomery, S. B., Moosajee, M., Nassogne, M. C., Neumann, S., O'Donoghue, M., O'Leary, M., Palmer, E. E., Pattani, N., Phillips, J., Pitsava, G., Pysar, R., Rehm, H. L., Reuter, C. M., Revencu, N., Riess, A., Rius, R., Rodan, L., Roscioli, T., Rosenfeld, J. A., Sachdev, R., Shaw-Smith, C. J., Simons, C., Sisodiya, S. M., Snell, P., St Clair, L., Stark, Z., Stewart, H. S., Tan, T. Y., Tan, N. B., Temple, S. E., Thorburn, D. R., Tifft, C. J., Uebergang, E., VanNoy, G. E., Vasudevan, P., Vilain, E., Viskochil, D. H., Wedd, L., Wheeler, M. T., White, S. M., Wojcik, M., Wolfe, L. A., Wolfenson, Z., Wright, C. F., Xiao, C., Zocche, D., Rubenstein, J. L., Markenscoff-Papadimitriou, E., Fica, S. M., Baralle, D., Depienne, C., MacArthur, D. G., Howson, J. M., Sanders, S. J., O'Donnell-Luria, A., Whiffin, N. 2024

  Abstract

  Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals where it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to RNU4-1 and other U4 homologs. Using RNA-sequencing, we show how 5' splice site usage is systematically disrupted in individuals with RNU4-2 variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 bp region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide.

  View details for DOI 10.1038/s41586-024-07773-7

  View details for PubMedID 38991538

• The Undiagnosed Diseases Network: Characteristics of solvable applicants and diagnostic suggestions for non-accepted ones. Genetics in medicine : official journal of the American College of Medical Genetics Mulvihill, J. J., Findley, L., Ni, W., Sinsheimer, J. S., Cole, F. S., Esteves, C., Bernstein, J. A., Newman, J. H., Wheeler, M. T., Mokry, J. R. 2024: 101203

  Abstract

  Can certain characteristics identify as solvable some undiagnosed patients who seek extensive evaluation and thorough record review, like by the Undiagnosed Diseases Network (UDN)?The UDN is a national research resource to solve medical mysteries through team science. Applicants provide informed consent to access to their medical records. After review, expert panels assess if applicants meet inclusion and exclusion criteria to select participants. When not accepting applicants, UDN experts may offer suggestions for diagnostic efforts. Using minimal information from initial applications, we compare features in applicants not accepted with those accepted and either solved or still not solved by the UDN. The diagnostic suggestions offered to non-accepted applicants and their clinicians were tallied.Non-accepted applicants were more often female, older at first symptoms and application, and longer in review than accepted applicants. The accepted and successfully diagnosed applicants were younger in ages, shorter in review time, more often non-white, of Hispanic ethnicity, and presenting with nervous system features. Half of non-accepted applicants were given suggestions for further local diagnostic evaluation. A few seemed to have two major diagnoses or a provocative environmental exposure history.Comprehensive UDN record review generates possibly helpful advice.

  View details for DOI 10.1016/j.gim.2024.101203

  View details for PubMedID 38967101

• MRI in LARS1 deficiency-Spectrum, patterns, and correlation with acute neurological deterioration. Journal of inherited metabolic disease Hammann, N., Lenz, D., Bianzano, A., Husain, R. A., Forman, E., Bernstein, J. A., Dattner, T., Engelen, M., Hanson-Kahn, A. K., Isidor, B., Kotzaeridou, U., Tietze, A., Trollmann, R., Weiß, C., Wolffenbuttel, B. H., Kölker, S., Hoffmann, G. F., Crushell, E., Staufner, C., Mohr, A., Harting, I. 2024

  Abstract

  Leucine aminoacyl tRNA-synthetase 1 (LARS1)-deficiency (infantile liver failure syndrome type 1 (ILFS1)) has a multisystemic phenotype including fever-associated acute liver failure (ALF), chronic neurologic abnormalities, and encephalopathic episodes. In order to better characterize encephalopathic episodes and MRI changes, 35 cranial MRIs from 13 individuals with LARS1 deficiency were systematically assessed and neurological phenotype was analyzed. All individuals had developmental delay and 10/13 had seizures. Encephalopathic episodes in 8/13 were typically associated with infections, presented with seizures and reduced consciousness, mostly accompanied by hepatic dysfunction, and recovery in 17/19 episodes. Encephalopathy without hepatic dysfunction occurred in one individual after liver transplantation. On MRI, 5/7 individuals with MRI during acute encephalopathy had deep gray matter and brainstem changes. Supratentorial cortex involvement (6/13) and cerebellar watershed injury (4/13) occurred with seizures and/or encephalopathy. Abnormal brainstem contour on sagittal images (8/13), atrophy (8/13), and myelination delay (8/13) were not clearly associated with encephalopathy. The pattern of deep gray matter and brainstem changes are apparently characteristic of encephalopathy in LARS1-deficiency, differing from patterns of hepatic encephalopathy or metabolic stroke in organic acidurias and mitochondrial diseases. While the pathomechanism remains unclear, fever and energy deficit during infections might be causative; thus, sufficient glucose and protein intake along with pro-active fever management is suggested. As severe episodes were observed during influenza infections, we strongly recommend seasonal vaccination.

  View details for DOI 10.1002/jimd.12764

  View details for PubMedID 38951950

• Implications of Provider Specialty, Test Type, and Demographic Factors on Genetic Testing Outcomes for Patients with Autism Spectrum Disorder. Journal of autism and developmental disorders Harrington, C. N., Morales, A., Bernstein, J. A., Calderwood, L. 2024

  Abstract

  A minority of patients with autism spectrum disorder (ASD) are offered genetic testing by their providers or referred for genetics evaluation despite published guidelines and consensus statements supporting genetics-informed care for this population. This study aimed to investigate the ordering habits of providers of different specialties and to additionally assess the diagnostic utility of genetic testing by test type, patient sex, and race and ethnicity. We retrospectively analyzed data associated with orders for the indication of ASD from a large clinical laboratory over 6 years (2017-2022). Geneticists and neurologists were more likely than other specialists to order exome sequencing and neurodevelopmental (NDD) panel testing while other providers were more likely to order chromosomal microarray (CMA) and Fragile X testing. Exome had the highest diagnostic yield (24.5%), followed by NDD panel (6.4%), CMA (6.2%), and Fragile X testing (0.4%). Females were 1.4x (95% CI: 1.2-1.7) more likely than males to receive a genetic diagnosis. However, for Fragile X, males had a higher diagnostic yield than females (0.4% vs 0.2%). Our findings highlight the need to enable non-genetics providers to order comprehensive genetic testing or promote referral to genetics following negative CMA and/or Fragile X testing. Our data supports that ASD testing should include exome, CMA, and other clinically indicated tests, as first-tier tests, with the consideration of panel testing, in cases where exome sequencing is not an option. Lastly, our study helps to inform expectations for genetic testing yield by test type and patient presentation.

  View details for DOI 10.1007/s10803-024-06423-1

  View details for PubMedID 38858309

  View details for PubMedCentralID 8068856

• Impact of genome build on RNA-seq interpretation and diagnostics. American journal of human genetics Ungar, R. A., Goddard, P. C., Jensen, T. D., Degalez, F., Smith, K. S., Jin, C. A., Bonner, D. E., Bernstein, J. A., Wheeler, M. T., Montgomery, S. B. 2024

  Abstract

  Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.

  View details for DOI 10.1016/j.ajhg.2024.05.005

  View details for PubMedID 38834072

• Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Genetics in medicine : official journal of the American College of Medical Genetics Kohler, J. N., Legro, N. R., Baldridge, D., Shin, J., Bowman, A., Ugur, B., Jackstadt, M. M., Shriver, L. P., Patti, G. J., Zhang, B., Feng, W., McAdow, A. R., Goddard, P., Ungar, R. A., Jensen, T., Smith, K. S., Fresard, L., Alvarez, R., Bonner, D., Reuter, C. M., McCormack, C., Kravets, E., Marwaha, S., Holt, J. M., Worthey, E., Ashley, E. A., Montgomery, S. B., Fisher, P., Postlethwait, J., De Camilli, P., Solnica-Krezel, L., Bernstein, J. A., Wheeler, M. T. 2024: 101166

  Abstract

  The function of FAM177A1 and its relationship to human disease is largely unknown. Recent studies have demonstrated FAM177A1 to be a critical immune-associated gene. One previous case study has linked FAM177A1 to a neurodevelopmental disorder in four siblings.We identified five individuals from three unrelated families with biallelic variants in FAM177A1. The physiological function of FAM177A1 was studied in a zebrafish model organism and human cell lines with loss-of-function variants similar to the affected cohort.These individuals share a characteristic phenotype defined by macrocephaly, global developmental delay, intellectual disability, seizures, behavioral abnormalities, hypotonia, and gait disturbance. We show that FAM177A1 localizes to the Golgi complex in mammalian and zebrafish cells. Intersection of the RNA-seq and metabolomic datasets from FAM177A1-deficient human fibroblasts and whole zebrafish larvae demonstrated dysregulation of pathways associated with apoptosis, inflammation, and negative regulation of cell proliferation.Our data sheds light on the emerging function of FAM177A1 and defines FAM177A1-related neurodevelopmental disorder as a new clinical entity.

  View details for DOI 10.1016/j.gim.2024.101166

  View details for PubMedID 38767059

• Clinical, genetic, and cognitive correlates of seizure occurrences in Phelan-McDermid syndrome. Journal of neurodevelopmental disorders Levy, T., Gluckman, J., Siper, P. M., Halpern, D., Zweifach, J., Filip-Dhima, R., Holder, J. L., Trelles, M. P., Johnson, K., Bernstein, J. A., Berry-Kravis, E., Powell, C. M., Soorya, L. V., Thurm, A., Buxbaum, J. D., Sahin, M., Kolevzon, A., Srivastava, S., Developmental Synaptopathies Consortium 2024; 16 (1): 25

  Abstract

  BACKGROUND: Phelan-McDermid syndrome (PMS) is a genetic neurodevelopmental disorder caused by SHANK3 haploinsufficiency and is associated with an increased risk for seizures. Previous literature indicates that around one third of individuals with PMS also have epilepsy or seizures, with a wide range of types and ages of onset. Investigating the impact of seizures on intellectual and adaptive functioning for PMS is a primary concern for caregivers and is important to understanding the natural history of this syndrome.METHODS: We report on results from 98 individuals enrolled in a prospective, longitudinal study. We detailed seizure frequency, type, and age of onset, and we analyzed seizure occurrence with best estimate IQ, adaptive functioning, clinical features, and genotype. We conducted multiple linear regression analyses to assess the relationship between the presence of seizures and the Vineland Adaptive Behavior Scale, Second Edition (VABS-II) Adaptive Behavior Composite score and the best estimate full-scale IQ. We also performed Chi-square tests to explore associations between seizure prevalence and genetic groupings. Finally, we performed Chi-square tests and t-tests to explore the relationship between seizures and demographic features, features that manifest in infancy, and medical features.RESULTS: Seizures were present in 41% of the cohort, and age of onset was widely variable. The presence of seizures was associated with significantly lower adaptive and intellectual functioning. Genotype-phenotype analyses were discrepant, with no differences in seizure prevalence across genetic classes, but with more genes included in deletions of participants with 22q13 deletions and seizures compared to those with 22q13 deletions and no seizures. No clinical associations were found between the presence of seizures and sex, history of pre- or neonatal complications, early infancy, or medical features. In this cohort, generalized seizures were associated with developmental regression, which is a top concern for PMS caregivers.CONCLUSIONS: These results begin to eludicate correlates of seizures in individuals with PMS and highlight the importance of early seizure management. Importantly, presence of seizures was associated with adaptive and cognitive functioning. A larger cohort might be able to identify additional associations with medical features. Genetic findings suggest an increased capability to realize genotype-phenotype relationships when deletion size is taken into account.

  View details for DOI 10.1186/s11689-024-09541-0

  View details for PubMedID 38730350

• Immunological and hematological findings as major features in a patient with a new germline pathogenic CBL variant. American journal of medical genetics. Part A Stellacci, E., Carter, J. N., Pannone, L., Stevenson, D., Moslehi, D., Venanzi, S., Bernstein, J. A., Tartaglia, M., Martinelli, S. 2024: e63627

  Abstract

  Casitas B-lineage lymphoma (CBL) encodes an adaptor protein with E3-ligase activity negatively controlling intracellular signaling downstream of receptor tyrosine kinases. Somatic CBL mutations play a driver role in a variety of cancers, particularly myeloid malignancies, whereas germline defects in the same gene underlie a RASopathy having clinical overlap with Noonan syndrome (NS) and predisposing to juvenile myelomonocytic leukemia and vasculitis. Other features of the disorder include cardiac defects, postnatal growth delay, cryptorchidism, facial dysmorphisms, and predisposition to develop autoimmune disorders. Here we report a novel CBL variant (c.1202G>T; p.Cys401Phe) occurring de novo in a subject with café-au-lait macules, feeding difficulties, mild dysmorphic features, psychomotor delay, autism spectrum disorder, thrombocytopenia, hepatosplenomegaly, and recurrent hypertransaminasemia. The identified variant affects an evolutionarily conserved residue located in the RING finger domain, a known mutational hot spot of both germline and somatic mutations. Functional studies documented enhanced EGF-induced ERK phosphorylation in transiently transfected COS1 cells. The present findings further support the association of pathogenic CBL variants with immunological and hematological manifestations in the context of a presentation with only minor findings reminiscent of NS or a clinically related RASopathy.

  View details for DOI 10.1002/ajmg.a.63627

  View details for PubMedID 38613168

• Filamin A heart valve disease as a genetic cause of inherited bicuspid and tricuspid aortic valve disease. Heart (British Cardiac Society) Delwarde, C., Toquet, C., Boureau, A. S., Le Ruz, R., Le Scouarnec, S., Mérot, J., Kyndt, F., Bernstein, D., Bernstein, J. A., Aalberts, J. J., Le Marec, H., Schott, J. J., Roussel, J. C., Le Tourneau, T., Capoulade, R. 2023

  Abstract

  Variants in the FLNA gene have been associated with mitral valve dystrophy (MVD), and even polyvalvular disease has been reported. This study aimed to analyse the aortic valve and root involvement in FLNA-MVD families and its impact on outcomes.262 subjects (37 (18-53) years, 140 male, 79 carriers: FLNA+) from 4 FLNA-MVD families were included. Echocardiography was performed in 185 patients and histological analysis in 3 explanted aortic valves. The outcomes were defined as aortic valve surgery or all-cause mortality.Aortic valve alterations were found in 58% of FLNA+ compared with 6% of FLNA- (p<0.001). 9 (13.4%) FLNA+ had bicuspid aortic valve compared with 4 (3.4%) FLNA- (p=0.03). Overall, the transvalvular mean gradient was slightly increased in FLNA+ (4.8 (4.1-6.1) vs 4.0 (2.9-4.9) mm Hg, p=0.02). The sinuses of Valsalva and sinotubular junction diameters were enlarged in FLNA+ subjects (all p<0.05). 8 FLNA+ patients underwent aortic valve surgery (0 in relatives; p<0.001). Myxomatous remodelling with an infiltration of immune cells was observed. Overall survival was similar between FLNA+ versus FLNA- subjects (86±5% vs 85±6%, p=0.36). There was no statistical evidence for an interaction between genetic status and sex (p=0.15), but the survival tended to be impaired in FLNA+ men (p=0.06) whereas not in women (p=0.71).The patients with FLNA variants present frequent aortic valve disease and worse outcomes. Bicuspid aortic valve is more frequent in patients carrying the FLNA-MVD variants. These unique features should be factored into the management of patients with dystrophic and/or bicuspid aortic valve.

  View details for DOI 10.1136/heartjnl-2023-323491

  View details for PubMedID 38148157

• Updated consensus guidelines on the management of Phelan-McDermid syndrome. American journal of medical genetics. Part A Srivastava, S., Sahin, M., Buxbaum, J. D., Berry-Kravis, E., Soorya, L. V., Thurm, A., Bernstein, J. A., Asante-Otoo, A., Bennett, W. E., Betancur, C., Brickhouse, T. H., Passos Bueno, M. R., Chopra, M., Christensen, C. K., Cully, J. L., Dies, K., Friedman, K., Gummere, B., Holder, J. L., Jimenez-Gomez, A., Kerins, C. A., Khan, O., Kohlenberg, T., Lacro, R. V., Levi, L. A., Levy, T., Linnehan, D., Eva, L., Moshiree, B., Neumeyer, A., Paul, S. M., Phelan, K., Persico, A., Rapaport, R., Rogers, C., Saland, J., Sethuram, S., Shapiro, J., Tarr, P. I., White, K. M., Wickstrom, J., Williams, K. M., Winrow, D., Wishart, B., Kolevzon, A. 2023

  Abstract

  Phelan-McDermid syndrome (PMS) is a genetic condition caused by SHANK3 haploinsufficiency and characterized by a wide range of neurodevelopmental and systemic manifestations. The first practice parameters for assessment and monitoring in individuals with PMS were published in 2014; recently, knowledge about PMS has grown significantly based on data from longitudinal phenotyping studies and large-scale genotype-phenotype investigations. The objective of these updated clinical management guidelines was to: (1) reflect the latest in knowledge in PMS and (2) provide guidance for clinicians, researchers, and the general community. A taskforce was established with clinical experts in PMS and representatives from the parent community. Experts joined subgroups based on their areas of specialty, including genetics, neurology, neurodevelopment, gastroenterology, primary care, physiatry, nephrology, endocrinology, cardiology, gynecology, and dentistry. Taskforce members convened regularly between 2021 and 2022 and produced specialty-specific guidelines based on iterative feedback and discussion. Taskforce leaders then established consensus within their respective specialty group and harmonized the guidelines. The knowledge gained over the past decade allows for improved guidelines to assess and monitor individuals with PMS. Since there is limited evidence specific to PMS, intervention mostly follows general guidelines for treating individuals with developmental disorders. Significant evidence has been amassed to guide the management of comorbid neuropsychiatric conditions in PMS, albeit mainly from caregiver report and the experience of clinical experts. These updated consensus guidelines on the management of PMS represent an advance for the field and will improve care in the community. Several areas for future research are also highlighted and will contribute to subsequent updates with more refined and specific recommendations as new knowledge accumulates.

  View details for DOI 10.1002/ajmg.a.63312

  View details for PubMedID 37392087

• Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites. Science advances de Prisco, N., Ford, C., Elrod, N. D., Lee, W., Tang, L. C., Huang, K., Lin, A., Ji, P., Jonnakuti, V. S., Boyle, L., Cabaj, M., Botta, S., Ounap, K., Reinson, K., Wojcik, M. H., Rosenfeld, J. A., Bi, W., Tveten, K., Prescott, T., Gerstner, T., Schroeder, A., Fong, C., George-Abraham, J. K., Buchanan, C. A., Hanson-Khan, A., Bernstein, J. A., Nella, A. A., Chung, W. K., Brandt, V., Jovanovic, M., Targoff, K. L., Yalamanchili, H. K., Wagner, E. J., Gennarino, V. A. 2023; 9 (7): eade4814

  Abstract

  Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' untranslated region (3'UTR), introns, or exons. Most studies focus on APA within the 3'UTR; however, here, we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function mostly undergo 3'UTR APA and are up-regulated. This suggests that, under healthy conditions, cells toggle between internal and 3'UTR APA to modulate protein expression.

  View details for DOI 10.1126/sciadv.ade4814

  View details for PubMedID 36800428

• Large 22q13.3 deletions perturb peripheral transcriptomic and metabolomic profiles in Phelan-McDermid syndrome. HGG advances Breen, M. S., Fan, X., Levy, T., Pollak, R. M., Collins, B., Osman, A., Tocheva, A. S., Sahin, M., Berry-Kravis, E., Soorya, L., Thurm, A., Powell, C. M., Bernstein, J. A., Kolevzon, A., Buxbaum, J. D., Developmental Synaptopathies Consortium, Warfield, S. K., Scherrer, B., Filip-Dhima, R., Dies, K., Siper, P., Hanson, E., Phillips, J. M. 2023; 4 (1): 100145

  Abstract

  Phelan-McDermid syndrome (PMS) is a rare neurodevelopmental disorder caused at least in part by haploinsufficiency of the SHANK3 gene, due to sequence variants in SHANK3 or subtelomeric 22q13.3 deletions. Phenotypic differences have been reported between PMS participants carrying small "class I" mutations and large "class II" mutations; however, the molecular perturbations underlying these divergent phenotypes remain obscure. Using peripheral blood transcriptome and serum metabolome profiling, we examined the molecular perturbations in the peripheral circulation associated with a full spectrum of PMS genotypes spanning class I (n= 37) and class II mutations (n= 39). Transcriptomic data revealed 52 genes with blood expression profiles that tightly scale with 22q.13.3 deletion size. Furthermore, we uncover 208 underexpressed genes in PMS participants with class II mutations, which were unchanged in class I mutations. These genes were not linked to 22q13.3 and were strongly enriched for glycosphingolipid metabolism, NCAM1 interactions, and cytotoxic natural killer (NK) immune cell signatures. In silico predictions estimated a reduction in CD56+ CD16- NK cell proportions in class II mutations, which was validated by mass cytometry time of flight. Global metabolomics profiling identified 24 metabolites that were significantly altered in PMS participants with class II mutations and confirmed a general reduction in sphingolipid metabolism. Collectively, these results provide new evidence linking PMS participants carrying class II mutations with decreased expression of cytotoxic cell signatures, reduced relative proportions of NK cells, and lower sphingolipid metabolism. These findings highlight alternative avenues for therapeutic development and offer new mechanistic insights supporting genotype-to-phenotype associations in PMS.

  View details for DOI 10.1016/j.xhgg.2022.100145

  View details for PubMedID 36276299

• A concurrent dual analysis of genomic data augments diagnoses: experiences of two clinical sites in the Undiagnosed Diseases Network. Genetics in medicine : official journal of the American College of Medical Genetics Spillmann, R. C., Tan, Q. K., Reuter, C., Schoch, K., Kohler, J., Bonner, D., Zastrow, D., Alkelai, A., Baugh, E., Cope, H., Marwaha, S., Wheeler, M. T., Bernstein, J. A., Shashi, V. 2022

  Abstract

  Next generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultra-rare conditions. However, diagnosis rates differ between analytical pipelines. In the NIH-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice.A retrospective review was performed at two UDN clinical sites, to compare variants, and diagnoses/candidate genes identified with the dual analyses of the NGS data.Ninety-five individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, while the clinical sites prioritized more research variants/candidate genes (p <0.001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the two pipelines were more often due to variant prioritization disparities, than variant detection.The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provides a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.

  View details for DOI 10.1016/j.gim.2022.12.001

  View details for PubMedID 36481303

• TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. American journal of human genetics Hijazi, H., Reis, L. M., Pehlivan, D., Bernstein, J. A., Muriello, M., Syverson, E., Bonner, D., Estiar, M. A., Gan-Or, Z., Rouleau, G. A., Lyulcheva, E., Greenhalgh, L., Tessarech, M., Colin, E., Guichet, A., Bonneau, D., van Jaarsveld, R. H., Lachmeijer, A. M., Ruaud, L., Levy, J., Tabet, A., Ploski, R., Rydzanicz, M., Kepczynski, L., Polatynska, K., Li, Y., Fatih, J. M., Marafi, D., Rosenfeld, J. A., Coban-Akdemir, Z., Bi, W., Gibbs, R. A., Hobson, G. M., Hunter, J. V., Carvalho, C. M., Posey, J. E., Semina, E. V., Lupski, J. R. 2022

  Abstract

  An Xq22.2 region upstream of PLP1 has been proposed to underly a neurological disease trait when deleted in 46,XX females. Deletion mapping revealed that heterozygous deletions encompassing the smallest region of overlap (SRO) spanning six Xq22.2 genes (BEX3, RAB40A, TCEAL4, TCEAL3, TCEAL1, and MORF4L2) associate with an early-onset neurological disease trait (EONDT) consisting of hypotonia, intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. None of the genes within the SRO have been associated with monogenic disease in OMIM. Through local and international collaborations facilitated by GeneMatcher and Matchmaker Exchange, we have identified and herein report seven de novo variants involving TCEAL1 in seven unrelated families: three hemizygous truncating alleles; one hemizygous missense allele; one heterozygous TCEAL1 full gene deletion; one heterozygous contiguous deletion of TCEAL1, TCEAL3, and TCEAL4; and one heterozygous frameshift variant allele. Variants were identified through exome or genome sequencing with trio analysis or through chromosomal microarray. Comparison with previously reported Xq22 deletions encompassing TCEAL1 identified a more-defined syndrome consisting of hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features include strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies. An additional maternally inherited hemizygous missense allele of uncertain significance was identified in a male with hypertonia and spasticity without syndromic features. These data provide evidence that TCEAL1 loss of function causes a neurological rare disease trait involving significant neurological impairment with features overlapping the EONDT phenotype in females with the Xq22 deletion.

  View details for DOI 10.1016/j.ajhg.2022.10.007

  View details for PubMedID 36368327

• A Cross-Sectional Study of the Neuropsychiatric Phenotype of CACNA1C-Related Disorder. Pediatric neurology Levy, R. J., Timothy, K. W., Underwood, J. F., Hall, J., Bernstein, J. A., Pașca, S. P. 2022; 138: 101-106

  Abstract

  BACKGROUND: CACNA1C encodes the voltage-gated L-type calcium channel CaV1.2. A specific gain-of-function pathogenic variant in CACNA1C causes Timothy syndrome type 1 (TS1) with cardiac long QT syndrome, syndactyly, and neuropsychiatric symptoms. Our previous work found that the TS1 mutation alters neuronal activity-dependent signaling and interneuron migration. Recent case series highlighted a broader spectrum of CACNA1C-related disorder (CRD) that includes isolated cardiac disease, isolated neurologic deficits, and TS, but it is unknown how the clinical presentation of other CRD variants relates to neural defects. We surveyed individuals with CRD to define the neuropsychiatric and developmental phenotype in an effort to guide future research into the role of calcium channels in neural development.METHODS: Caregivers of and individuals with CRD completed an online survey of pre- and perinatal events, cardiac events, developmental milestones, neuropsychiatric symptoms, and neuropsychiatric diagnoses. Multiple Mann-Whitney tests were used for comparison of categorical values and Fisher exact test for comparison of categorical variables between participants with and without cardiac arrhythmia.RESULTS: Twenty-four participants with germline CACNA1C variants including TS1 completed the survey. The most common neuropsychiatric symptoms and/or diagnoses were developmental delay in 92%, incoordination in 71%, hypotonia in 67%, autism spectrum disorder in 50% (autistic features in 92%), seizures in 37.5%, and attention-deficit/hyperactivity disorder in 21% of participants. There were no significant differences in symptoms between participants with and without arrhythmia.CONCLUSIONS: In our CRD cohort, there was an increased prevalence of multiple neuropsychiatric symptoms compared with the general population. These findings indicate the key role of CaV1.2 in brain development and the clinical importance of screening and therapeutically addressing neuropsychiatric symptoms in all individuals with CRD. Future directions include deep phenotyping of neuropsychiatric symptoms and efforts to relate these symptoms to cellular defects.

  View details for DOI 10.1016/j.pediatrneurol.2022.10.013

  View details for PubMedID 36436328

• DPP9 deficiency: An inflammasomopathy that can be rescued by lowering NLRP1/IL-1 signaling. Science immunology Harapas, C. R., Robinson, K. S., Lay, K., Wong, J., Moreno Traspas, R., Nabavizadeh, N., Rass-Rothschild, A., Boisson, B., Drutman, S. B., Laohamonthonkul, P., Bonner, D., Xiong, J. R., Gorrell, M. D., Davidson, S., Yu, C. H., Fleming, M. D., Gudera, J., Stein, J., Ben-Harosh, M., Groopman, E., Shimamura, A., Tamary, H., Kayserili, H., Hatipoğlu, N., Casanova, J. L., Bernstein, J. A., Zhong, F. L., Masters, S. L., Reversade, B. 2022; 7 (75): eabi4611

  Abstract

  Dipeptidyl peptidase 9 (DPP9) is a direct inhibitor of NLRP1, but how it affects inflammasome regulation in vivo is not yet established. Here, we report three families with immune-associated defects, poor growth, pancytopenia, and skin pigmentation abnormalities that segregate with biallelic DPP9 rare variants. Using patient-derived primary cells and biochemical assays, these variants were shown to behave as hypomorphic or knockout alleles that failed to repress NLRP1. The removal of a single copy of Nlrp1a/b/c, Asc, Gsdmd, or Il-1r, but not Il-18, was sufficient to rescue the lethality of Dpp9 mutant neonates in mice. Similarly, dpp9 deficiency was partially rescued by the inactivation of asc, an obligate downstream adapter of the NLRP1 inflammasome, in zebrafish. These experiments suggest that the deleterious consequences of DPP9 deficiency were mostly driven by the aberrant activation of the canonical NLRP1 inflammasome and IL-1β signaling. Collectively, our results delineate a Mendelian disorder of DPP9 deficiency driven by increased NLRP1 activity as demonstrated in patient cells and in two animal models of the disease.

  View details for DOI 10.1126/sciimmunol.abi4611

  View details for PubMedID 36112693

• 2022 Association of Professors of Human and Medical Genetics (APHMG) consensus-based update of the core competencies for undergraduate medical education in genetics and genomics. Genetics in medicine : official journal of the American College of Medical Genetics Massingham, L. J., Nunez, S., Bernstein, J. A., Gardner, D. P., Parikh, A. S., Strovel, E. T., Quintero-Rivera, F., Association of Professors of Human and Medical Genetics Course Directors Special Interest Group Medical Education Core Curriculum Workgroup, Anderson, H., Ashfaq, M., Bernstein, J., Burke, L., Cross, C., Dhar, S., Garber, K., Gardner, D., Gold, J., Hudder, A., Hyland, K., Larsen, N., Massingham, L., Nunez, S., Parikh, A., Penney, L., Philp, A. R., Popejoy, A. B., Quintero-Rivera, F., Sobering, A. K., Starr, L., Strovel, E., Toriello, H. V., Weiler, T., Yatsenko, S. 2022

  Abstract

  PURPOSE: The field of genetics and genomics continues to expand at an unprecedented pace. As scientific knowledge is translated to clinical practice, genomic information is routinely being used in preventive, diagnostic, and therapeutic decision-making across a variety of clinical practice areas. As adoption of genomic medicine further evolves, health professionals will be required to stay abreast of new genetic discoveries and technologies and implementation of these advances within their scope of practice will be indicated.METHODS: The Association of Professors of Human and Medical Genetics previously developed medical school genetics core competencies, last updated in 2013. The competencies were reviewed and updated through a structured approach incorporating a modified Delphi method.RESULTS: The updated Association of Professors of Human and Medical Genetics core competencies are presented. Current revisions include competencies that are concise, specific, and assessable. In addition, they incorporate recent advances in clinical practice and promote equity and inclusion in clinical care.CONCLUSION: The 2022 competencies will serve as a guide for medical school leadership and educators involved in curriculum development, implementation, and assessment. Use of these competencies across the undergraduate medical curricula will foster knowledge, skills, and behaviors required in medical practice across a wide range of specialties.

  View details for DOI 10.1016/j.gim.2022.07.014

  View details for PubMedID 36040446

• Discovering monogenic patients with a confirmed molecular diagnosis in millions of clinical notes with MonoMiner. Genetics in medicine : official journal of the American College of Medical Genetics Wu, D. W., Bernstein, J. A., Bejerano, G. 2022

  Abstract

  PURPOSE: Cohort building is a powerful foundation for improving clinical care, performing biomedical research, recruiting for clinical trials, and many other applications. We set out to build a cohort of all monogenic patients with a definitive causal gene diagnosis in a 3-million patient hospital system.METHODS: We define a subset (4461) of OMIM diseases that have at least 1 known monogenic causal gene. We then introduce MonoMiner, a natural language processing framework to identify molecularly confirmed monogenic patients from free-text clinical notes.RESULTS: We show that ICD-10-CM codes cover only a fraction of monogenic diseases and that even where available, ICD-10-CM code‒based patient retrieval offers 0.14 precision. Searching by causal gene symbol offers great recall but has an even worse 0.07 precision. MonoMiner achieves 6 to 11 times higher precision (0.80), with 0.87 precision on disease diagnosis alone, tagging 4259 patients with 560 monogenic diseases and 534 causal genes, at 0.48 recall.CONCLUSION: MonoMiner enables the discovery of a large, high-precision cohort of patients with monogenic diseases with an established molecular diagnosis, empowering numerous downstream uses. Because it relies solely on clinical notes, MonoMiner is highly portable, and its approach is adaptable to other domains and languages.

  View details for DOI 10.1016/j.gim.2022.07.008

  View details for PubMedID 35976265

• Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature biotechnology Goenka, S. D., Gorzynski, J. E., Shafin, K., Fisk, D. G., Pesout, T., Jensen, T. D., Monlong, J., Chang, P. C., Baid, G., Bernstein, J. A., Christle, J. W., Dalton, K. P., Garalde, D. R., Grove, M. E., Guillory, J., Kolesnikov, A., Nattestad, M., Ruzhnikov, M. R., Samadi, M., Sethia, A., Spiteri, E., Wright, C. J., Xiong, K., Zhu, T., Jain, M., Sedlazeck, F. J., Carroll, A., Paten, B., Ashley, E. A. 2022

  Abstract

  Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nanopore WGS that combines an optimized sample preparation protocol, distributing sequencing over 48 flow cells, near real-time base calling and alignment, accelerated variant calling and fast variant filtration for efficient manual review. Application to two example clinical cases identified a candidate variant in <8 h from sample preparation to variant identification. We show that this framework provides accurate variant calls and efficient prioritization, and accelerates diagnostic clinical genome sequencing twofold compared with previous approaches.

  View details for DOI 10.1038/s41587-022-01221-5

  View details for PubMedID 35347328

• Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock. Circulation. Genomic and precision medicine Gorzynski, J. E., Goenka, S. D., Shafin, K., Jensen, T. D., Fisk, D. G., Grove, M. E., Spiteri, E., Pesout, T., Monlong, J., Bernstein, J. A., Ceresnak, S., Chang, P., Christle, J. W., Chubb, H., Dunn, K., Garalde, D. R., Guillory, J., Ruzhnikov, M. R., Wright, C., Wusthoff, C. J., Xiong, K., Hollander, S. A., Berry, G. J., Jain, M., Sedlazeck, F. J., Carroll, A., Paten, B., Ashley, E. A. 2022: CIRCGEN121003591

  View details for DOI 10.1161/CIRCGEN.121.003591

  View details for PubMedID 35133172

• Perceived utility and disutility of genomic sequencing for pediatric patients: Perspectives from parents with diverse sociodemographic characteristics. American journal of medical genetics. Part A Halley, M. C., Young, J. L., Fernandez, L., Kohler, J. N., Undiagnosed Diseases Network, Bernstein, J. A., Wheeler, M. T., Tabor, H. K. 1800

  Abstract

  Given the limited therapeutic options for most rare diseases diagnosed through genomic sequencing (GS) and the proportion of patients who remain undiagnosed even after GS, it is important to characterize a broader range of benefits and potential harms of GS from the perspectives of families with diverse sociodemographic characteristics. We recruited parents of children enrolled in the Undiagnosed Diseases Network. Parents completed an in-depth interview, and we conducted a comparative content analysis of the data. Parents (n=30) were demographically diverse, with 43.3% identifying as Hispanic, 33.3% primarily Spanish-speaking, and widely variable household income and education. Parents reported minimal changes in their child's health status following GS but did report a range of other forms of perceived utility, including improvements in their child's healthcare management and access, in their own psychological well-being, and in disease-specific social connections and research opportunities. Parents who received a diagnosis more frequently perceived utility across all domains; however, disutility also was reported by both those with and without a diagnosis. Impacts depended on multiple mediating factors, including parents' underlying expectations and beliefs, family sociodemographic characteristics, individual disease characteristics, and prior healthcare access. Our study suggests that the perceived utility of GS varies widely among parents and may depend on multiple individual, sociodemographic, and contextual factors that are relevant for pre- and post-GS counseling, for value assessment of GS, and for policymaking related to access to new genomic technologies.

  View details for DOI 10.1002/ajmg.a.62619

  View details for PubMedID 34981646

• NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Human molecular genetics Brennan, K., Zheng, H., Fahrner, J. A., Shin, J. H., Gentles, A. J., Schaefer, B., Sunwoo, J. B., Bernstein, J. A., Gevaert, O. 2022

  Abstract

  Sotos syndrome (SS), the most common overgrowth with intellectual disability (OGID) disorder, is caused by inactivating germline mutations of NSD1, which encodes a histone H3 lysine 36 methyltransferase. To understand how NSD1 inactivation deregulates transcription and DNA methylation (DNAm), and to explore how these abnormalities affect human development, we profiled transcription and DNAm in SS patients and healthy control individuals. We identified a transcriptional signature that distinguishes individuals with SS from controls and was also deregulated in NSD1 mutated cancers. Most abnormally expressed genes displayed reduced expression in SS; these downregulated genes consisted mostly of bivalent genes and were enriched for regulators of development and neural synapse function. DNA hypomethylation was strongly enriched within promoters of transcriptionally deregulated genes: Overexpressed genes displayed hypomethylation at their transcription start sites (TSSs) while underexpressed genes featured hypomethylation at polycomb binding sites within their promoter CpG island shores. SS patients featured accelerated molecular aging at the levels of both transcription and DNAm. Overall, these findings indicate that NSD1-deposited H3K36 methylation regulates transcription by directing promoter DNA methylation, partially by repressing polycomb repressive complex 2 (PRC2) activity. These findings could explain the phenotypic similarity of SS to OGID disorders that are caused by mutations in PRC2 complex-encoding genes.

  View details for DOI 10.1093/hmg/ddac026

  View details for PubMedID 35094088

• TOWARDS TRANSCRIPTOMICS AS A PRIMARY TOOL FOR RARE DISEASE INVESTIGATION. Cold Spring Harbor molecular case studies Montgomery, S. B., Bernstein, J. A., Wheeler, M. T. 2022

  Abstract

  In the past five years transcriptome or RNA-sequencing (RNA-seq) has steadily emerged as a complementary assay for rare disease diagnosis and discovery. In this perspective, we summarize several recent developments and challenges in use of RNA-seq for rare disease investigation. Using an accessible patient sample, such as blood, skin, or muscle, RNA-seq enables the assay of expressed RNA transcripts. Analysis of RNA-seq allows the identification of aberrant or outlier gene expression and alternative splicing as functional evidence to support rare disease study and diagnosis. Further, many types of variant effects can be profiled beyond coding variants, as the consequences of non-coding variants that impact gene expression and splicing can be directly observed. This is particularly apparent for structural variants which disproportionately underlie outlier gene expression and for splicing variants where RNA-seq can both measure aberrant canonical splicing and detect deep intronic effects. However, a major potential limitation of RNA-seq in rare disease investigation is the developmental and cell type-specificity of gene expression as a pathogenic variant's effect may be limited to a specific spatiotemporal context and access to a patient's tissue sample from the relevant tissue and timing of disease expression may not be possible. We speculate that as advances in computational methods and emerging experimental techniques overcome both developmental and cell type-specificity, there will be broadening use of RNA sequencing and multi-omics in rare disease diagnosis and delivery of precision health.

  View details for DOI 10.1101/mcs.a006198

  View details for PubMedID 35217565

• Beyond race: Recruitment of diverse participants in clinical genomics research for rare disease. Frontiers in genetics Young, J. L., Halley, M. C., Anguiano, B., Fernandez, L., Bernstein, J. A., Wheeler, M. T., Tabor, H. K., Undiagnosed Diseases Network Consortium 2022; 13: 949422

  Abstract

  Purpose: Despite recent attention to increasing diversity in clinical genomics research, researchers still struggle to recruit participants from varied sociodemographic backgrounds. We examined the experiences of parents from diverse backgrounds with enrolling their children in clinical genomics research on rare diseases. We explored the barriers and facilitators parents encountered and possible impacts of sociodemographic factors on their access to research. Methods: We utilized semi-structured interviews with parents of children participating in the Undiagnosed Diseases Network. Interview data were analyzed using comparative content analysis. Results: We interviewed 13 Hispanic, 11 non-Hispanic White, four Asian, and two biracial parents. Participants discussed different pathways to clinical genomics research for rare disease as well as how sociodemographic factors shaped families' access. Themes focused on variation in: 1) reliance on providers to access research; 2) cultural norms around health communication; 3) the role of social capital in streamlining access; and 4) the importance of language-concordant research engagement. Conclusion: Our findings suggest that variables beyond race/ethnicity may influence access in clinical genomics research. Future efforts to diversify research participation should consider utilizing varied recruitment strategies to reach participants with diverse sociodemographic characteristics.

  View details for DOI 10.3389/fgene.2022.949422

  View details for PubMedID 36072659

• Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder. American journal of human genetics Küry, S., Ebstein, F., Mollé, A., Besnard, T., Lee, M. K., Vignard, V., Hery, T., Nizon, M., Mancini, G. M., Giltay, J. C., Cogné, B., McWalter, K., Deb, W., Mor-Shaked, H., Li, H., Schnur, R. E., Wentzensen, I. M., Denommé-Pichon, A. S., Fourgeux, C., Verheijen, F. W., Faurie, E., Schot, R., Stevens, C. A., Smits, D. J., Barr, E., Sheffer, R., Bernstein, J. A., Stimach, C. L., Kovitch, E., Shashi, V., Schoch, K., Smith, W., van Jaarsveld, R. H., Hurst, A. C., Smith, K., Baugh, E. H., Bohm, S. G., Vyhnálková, E., Ryba, L., Delnatte, C., Neira, J., Bonneau, D., Toutain, A., Rosenfeld, J. A., Audebert-Bellanger, S., Gilbert-Dussardier, B., Odent, S., Laumonnier, F., Berger, S. I., Smith, A. C., Bourdeaut, F., Stern, M. H., Redon, R., Krüger, E., Margueron, R., Bézieau, S., Poschmann, J., Isidor, B. 2022

  Abstract

  Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.

  View details for DOI 10.1016/j.ajhg.2021.12.011

  View details for PubMedID 35051358

• Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. The New England journal of medicine Gorzynski, J. E., Goenka, S. D., Shafin, K., Jensen, T. D., Fisk, D. G., Grove, M. E., Spiteri, E., Pesout, T., Monlong, J., Baid, G., Bernstein, J. A., Ceresnak, S., Chang, P. C., Christle, J. W., Chubb, H., Dalton, K. P., Dunn, K., Garalde, D. R., Guillory, J., Knowles, J. W., Kolesnikov, A., Ma, M., Moscarello, T., Nattestad, M., Perez, M., Ruzhnikov, M. R., Samadi, M., Setia, A., Wright, C., Wusthoff, C. J., Xiong, K., Zhu, T., Jain, M., Sedlazeck, F. J., Carroll, A., Paten, B., Ashley, E. A. 2022

  View details for DOI 10.1056/NEJMc2112090

  View details for PubMedID 35020984

• Parent-reported measure of repetitive behavior in Phelan-McDermid syndrome. Journal of neurodevelopmental disorders Srivastava, S., Condy, E., Carmody, E., Filip-Dhima, R., Kapur, K., Bernstein, J. A., Berry-Kravis, E., Powell, C. M., Soorya, L., Thurm, A., Buxbaum, J. D., Sahin, M., Kolevzon, A. L., Developmental Synaptopathies Consortium, Sahin, M., Kolevzon, A., Buxbaum, J. D., Kravis, E. B., Soorya, L., Thurm, A., Powell, C., Bernstein, J. A., Warfield, S., Dies, K., Siper, P., Hanson, E., Phillips, J. M. 2021; 13 (1): 53

  Abstract

  BACKGROUND: Phelan McDermid syndrome (PMS) is a neurogenetic condition associated with a high prevalence of intellectual disability (ID) and autism spectrum disorder (ASD). This study provides a more comprehensive and quantitative profile of repetitive behaviors within the context of ID seen with the condition.METHODS: Individuals age 3-21 years with a confirmed PMS diagnosis participated in a multicenter observational study evaluating the phenotype and natural history of the disorder. We evaluated data collected from this study pertaining to repetitive behaviors from the Repetitive Behavior Scales-Revised (RBS-R).RESULTS: There were n = 90 participants who were part of this analysis. Forty-seven percent (n = 42/90) were female, and the average age at baseline evaluation was 8.88 ± 4.72 years. The mean best estimate IQ of the cohort was 26.08 ± 17.67 (range = 3.4-88), with n = 8 with mild ID (or no ID), n = 20 with moderate ID, and n = 62 with severe-profound ID. The RBS-R total overall score was 16.46 ± 13.9 (compared to 33.14 ± 20.60 reported in previous studies of ASD) (Lam and Aman, 2007), and the total number of items endorsed was 10.40 ± 6.81 (range = 0-29). After statistical correction for multiple comparisons, IQ correlated with the RBS-R stereotypic behavior subscale score (rs = - 0.33, unadjusted p = 0.0014, adjusted p = 0.01) and RBS-R stereotypic behavior total number of endorsed items (rs = - 0.32, unadjusted p = 0.0019, adjusted p = 0.01). IQ did not correlate with any other RBS-R subscale scores.CONCLUSIONS: The RBS-R total overall score in a PMS cohort appears milder compared to individuals with ASD characterized in previous studies. Stereotypic behavior in PMS may reflect cognitive functioning.

  View details for DOI 10.1186/s11689-021-09398-7

  View details for PubMedID 34740315

• Variable clinical severity in TANGO2 deficiency: Case series and literature review. American journal of medical genetics. Part A Schymick, J., Leahy, P., Cowan, T., Ruzhnikov, M. R., Gates, R., Fernandez, L., Pramanik, G., Undiagnosed Diseases Network, Yarlagadda, V., Wheeler, M., Bernstein, J. A., Enns, G. M., Lee, C. 2021

  Abstract

  Biallelic pathogenic variants in the TANGO2 (transport and Golgi organization 2 homolog) gene have been identified as causing a rare metabolic disorder characterized by susceptibility to recurrent rhabdomyolysis, lactic acidosis, encephalopathy, and life-threatening tachyarrhythmias. Recently published reports suggest variable clinical severity and phenotypes. This study details five new patients from two families with biallelic pathogenic variants in the TANGO2 gene identified by whole exome sequencing and includes the largest number of affected individuals from a single family reported to date. We document significant intrafamilial variability and highlight that milder phenotypes may be underrecognized. We present biochemical and clinical data to help highlight the features that aid in consideration of this condition in the differential with disorders of fatty acid oxidation. We also present a comprehensive literature review summarizing the molecular, clinical, and biochemical findings for 92 individuals across 13 publications. Of the 27 pathogenic variants reported to date, the recurrent exons 3-9 deletion represents the most common variant seen in 42% of individuals with TANGO2 deficiency. Common clinical features seen in >70% of all individuals include acute metabolic crisis, rhabdomyolysis, neurologic abnormalities, developmental delay, and intellectual disability. Findings such as elevated creatine kinase, hypothyroidism, ketotic hypoglycemia, QT prolongation, or abnormalities of long-chain acylcarnitines and urine dicarboxylic acids should raise clinical suspicion for this life-threatening condition.

  View details for DOI 10.1002/ajmg.a.62543

  View details for PubMedID 34668327

• InpherNet accelerates monogenic disease diagnosis using patients' candidate genes' neighbors. Genetics in medicine : official journal of the American College of Medical Genetics Yoo, B., Birgmeier, J., Bernstein, J. A., Bejerano, G. 2021

  Abstract

  PURPOSE: Roughly 70% of suspected Mendelian disease patients remain undiagnosed after genome sequencing, partly because knowledge about pathogenic genes is incomplete and constantly growing. Generating a novel pathogenic gene hypothesis from patient data can be time-consuming especially where cohort-based analysis is not available.METHODS: Each patient genome contains dozens to hundreds of candidate variants. Many sources of indirect evidence about each candidate may be considered. We introduce InpherNet, a network-based machine learning approach leveraging Monarch Initiative data to accelerate this process.RESULTS: InpherNet ranks candidate genes based on orthologs, paralogs, functional pathway members, and colocalized interaction partner gene neighbors. It can propose novel pathogenic genes and reveal known pathogenic genes whose diagnosed patient-based annotation is missing or partial. InpherNet is applied to patient cases where the causative gene is incorrectly ranked low by clinical gene-ranking methods that use only patient-derived evidence. InpherNet correctly ranks the causative gene top 1 or top 1-5 in roughly twice as many cases as seven comparable tools, including in cases where no clinical evidence for the diagnostic gene is in our knowledgebase.CONCLUSION: InpherNet improves the state of the art in considering candidate gene neighbors to accelerate monogenic diagnosis.

  View details for DOI 10.1038/s41436-021-01238-2

  View details for PubMedID 34230641

• Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity. PLoS genetics Besterman, A. D., Althoff, T., Elfferich, P., Gutierrez-Mejia, I., Sadik, J., Bernstein, J. A., van Ierland, Y., Kattentidt-Mouravieva, A. A., Nellist, M., Abramson, J., Martinez-Agosto, J. A. 2021; 17 (7): e1009651

  Abstract

  Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder characterized by macrocephaly/megalencephaly, developmental delay, intellectual disability, hypotonia, and seizures. It is caused by dominant missense mutations in MTOR. The pathogenicity of novel variants in MTOR in patients with neurodevelopmental disorders can be difficult to determine and the mechanism by which variants cause disease remains poorly understood. We report 7 patients with SKS with 4 novel MTOR variants and describe their phenotypes. We perform in vitro functional analyses to confirm MTOR activation and interrogate disease mechanisms. We complete structural analyses to understand the 3D properties of pathogenic variants. We examine the accuracy of relative accessible surface area, a quantitative measure of amino acid side-chain accessibility, as a predictor of MTOR variant pathogenicity. We describe novel clinical features of patients with SKS. We confirm MTOR Complex 1 activation and identify MTOR Complex 2 activation as a new potential mechanism of disease in SKS. We find that pathogenic MTOR variants disproportionately cluster in hotspots in the core of the protein, where they disrupt alpha helix packing due to the insertion of bulky amino acid side chains. We find that relative accessible surface area is significantly lower for SKS-associated variants compared to benign variants. We expand the phenotype of SKS and demonstrate that additional pathways of activation may contribute to disease. Incorporating 3D properties of MTOR variants may help in pathogenicity classification. We hope these findings may contribute to improving the precision of care and therapeutic development for individuals with SKS.

  View details for DOI 10.1371/journal.pgen.1009651

  View details for PubMedID 34197453

• "Doctors can read about it, they can know about it, but they've never lived with it": How parents use social media throughout the diagnostic odyssey. Journal of genetic counseling Deuitch, N. T., Beckman, E., Halley, M. C., Young, J. L., Reuter, C. M., Kohler, J., Bernstein, J. A., Wheeler, M. T., Undiagnosed Diseases Network, Ormond, K. E., Tabor, H. K. 2021

  Abstract

  Parents of children with undiagnosed conditions struggle to obtain information about how to treat and support their children. It can be particularly challenging to find communities and other parents who share their experiences and can provide emotional and informational support. This study sought to characterize how parents use social media, both throughout the diagnostic odyssey and post-diagnosis, to meet their informational, social, and emotional support needs. We conducted qualitative semi-structured interviews with 14 parents from the Stanford site of the Undiagnosed Diseases Network (UDN), including five whose children had received a diagnosis through study participation. Interview recordings were analyzed using inductive, team-based coding and thematic analysis based in grounded theory using Dedoose qualitative analysis software. Through this process, we identified four key themes related to social media use. First, parents struggled to find the "right" community, often seeking out groups of similar patients based on symptoms or similar conditions. Second, though they found much valuable information through social media about caring for their child, they also struggled to interpret the relevance of the information to their own child's condition. Third, the social support and access to other patients' and families' lived experiences were described as both highly valued and emotionally challenging, particularly in the case of poor outcomes for similar families. Finally, parents expressed the need to balance concerns about their child's privacy with the value of transparency and data sharing for diagnosis. Our results suggest that the needs and experiences of undiagnosed patients and families differ from those with diagnosed diseases and highlight the need for support in best utilizing social media resources at different stages of the diagnostic odyssey.

  View details for DOI 10.1002/jgc4.1438

  View details for PubMedID 34096130

• Expanding the genotypic and phenotypic spectrum in a diverse cohort of 104 individuals with Wiedemann-Steiner syndrome. American journal of medical genetics. Part A Sheppard, S. E., Campbell, I. M., Harr, M. H., Gold, N., Li, D., Bjornsson, H. T., Cohen, J. S., Fahrner, J. A., Fatemi, A., Harris, J. R., Nowak, C., Stevens, C. A., Grand, K., Au, M., Graham, J. M., Sanchez-Lara, P. A., Campo, M. D., Jones, M. C., Abdul-Rahman, O., Alkuraya, F. S., Bassetti, J. A., Bergstrom, K., Bhoj, E., Dugan, S., Kaplan, J. D., Derar, N., Gripp, K. W., Hauser, N., Innes, A. M., Keena, B., Kodra, N., Miller, R., Nelson, B., Nowaczyk, M. J., Rahbeeni, Z., Ben-Shachar, S., Shieh, J. T., Slavotinek, A., Sobering, A. K., Abbott, M., Allain, D. C., Amlie-Wolf, L., Au, P. Y., Bedoukian, E., Beek, G., Barry, J., Berg, J., Bernstein, J. A., Cytrynbaum, C., Chung, B. H., Donoghue, S., Dorrani, N., Eaton, A., Flores-Daboub, J. A., Dubbs, H., Felix, C. A., Fong, C., Fung, J. L., Gangaram, B., Goldstein, A., Greenberg, R., Ha, T. K., Hersh, J., Izumi, K., Kallish, S., Kravets, E., Kwok, P., Jobling, R. K., Knight Johnson, A. E., Kushner, J., Lee, B. H., Levin, B., Lindstrom, K., Manickam, K., Mardach, R., McCormick, E., McLeod, D. R., Mentch, F. D., Minks, K., Muraresku, C., Nelson, S. F., Porazzi, P., Pichurin, P. N., Powell-Hamilton, N. N., Powis, Z., Ritter, A., Rogers, C., Rohena, L., Ronspies, C., Schroeder, A., Stark, Z., Starr, L., Stoler, J., Suwannarat, P., Velinov, M., Weksberg, R., Wilnai, Y., Zadeh, N., Zand, D. J., Falk, M. J., Hakonarson, H., Zackai, E. H., Quintero-Rivera, F. 2021

  Abstract

  Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder caused by monoallelic variants in KMT2A and characterized by intellectual disability and hypertrichosis. We performed a retrospective, multicenter, observational study of 104 individuals with WSS from five continents to characterize the clinical and molecular spectrum of WSS in diverse populations, to identify physical features that may be more prevalent in White versus Black Indigenous People of Color individuals, to delineate genotype-phenotype correlations, to define developmental milestones, to describe the syndrome through adulthood, and to examine clinicians' differential diagnoses. Sixty-nine of the 82 variants (84%) observed in the study were not previously reported in the literature. Common clinical features identified in the cohort included: developmental delay or intellectual disability (97%), constipation (63.8%), failure to thrive (67.7%), feeding difficulties (66.3%), hypertrichosis cubiti (57%), short stature (57.8%), and vertebral anomalies (46.9%). The median ages at walking and first words were 20months and 18months, respectively. Hypotonia was associated with loss of function (LoF) variants, and seizures were associated with non-LoF variants. This study identifies genotype-phenotype correlations as well as race-facial feature associations in an ethnically diverse cohort, and accurately defines developmental trajectories, medical comorbidities, and long-term outcomes in individuals with WSS.

  View details for DOI 10.1002/ajmg.a.62124

  View details for PubMedID 33783954

• Functional and structural analysis of cytokine selective IL6ST defects that cause recessive hyper-IgE syndrome. The Journal of allergy and clinical immunology Chen, Y., Zastrow, D. B., Metcalfe, R. D., Gartner, L., Krause, F., Morton, C. J., Marwaha, S., Fresard, L., Huang, Y., Zhao, C., McCormack, C., Bick, D., Worthey, E. A., Eng, C. M., Gold, J., Undiagnosed Diseases Network, Montgomery, S. B., Fisher, P. G., Ashley, E. A., Wheeler, M. T., Parker, M. W., Shanmugasundaram, V., Putoczki, T. L., Schmidt-Arras, D., Laurence, A., Bernstein, J. A., Griffin, M. D., Uhlig, H. H. 2021

  Abstract

  BACKGROUND: Biallelic variants in IL6ST cause a recessive form of hyper-IgE syndrome (HIES) characterized by high IgE, eosinophilia, defective acute phase response, susceptibility to bacterial infections and skeletal abnormalities due to cytokine selective loss-of-function in GP130 with defective IL-6 and IL-11, variable OSM and IL-27 but sparing LIF signaling.OBJECTIVE: To understand the functional and structural impact of recessive HIES-associated IL6ST variants.METHODS: We investigated a patient with HIES using exome, genome and RNA sequencing. Functional assays assessed IL-6, IL-11, IL-27, OSM, LIF, CT-1, CLC, and CNTF signaling. Molecular dynamic simulations and structural modeling of GP130 cytokine receptor complexes were performed.RESULTS: We identify a patient with compound heterozygous novel missense variants in IL6ST (p.Ala517Pro, and exon-skipping null variant p.Gly484_Pro518delinsArg). The p.Ala517Pro variant results in a more profound IL-6 and IL-11 dominated signaling defect compared to the previously identified recessive IL6ST variants p.Asn404Tyr, and p.Pro498Leu. Molecular dynamics simulations suggest that the p.Ala517Pro and p.Asn404Tyr variants result in increased flexibility of the extracellular membrane-proximal domains of GP130. We propose a structural model that explains the cytokine selectivity of pathogenic IL6ST variants that result in recessive HIES. The variants destabilize the hexameric cytokine receptor complexes whereas the trimeric LIF-GP130-LIFR complex remains stable by an additional membrane-proximal interaction. Deletion of this membrane-proximal interaction site in GP130 consequently causes additional defective LIF signaling and Stuve-Wiedemann syndrome.CONCLUSION: Our data provide a structural basis to understand clinical phenotypes in patients with IL6ST variants.

  View details for DOI 10.1016/j.jaci.2021.02.044

  View details for PubMedID 33771552

• Biallelic UBE4A loss-of-function variants cause intellectual disability and global developmental delay. Genetics in medicine : official journal of the American College of Medical Genetics Melo, U. S., Bonner, D. n., Kent Lloyd, K. C., Moshiri, A. n., Willis, B. n., Lanoue, L. n., Bower, L. n., Leonard, B. C., Martins, D. J., Gomes, F. n., de Souza Leite, F. n., Oliveira, D. n., Kitajima, J. P., Monteiro, F. P., Zatz, M. n., Menck, C. F., Wheeler, M. T., Bernstein, J. A., Dumas, K. n., Spiteri, E. n., Di Donato, N. n., Jahn, A. n., Hashem, M. n., Alsaif, H. S., Chedrawi, A. n., Alkuraya, F. S., Kok, F. n., Byers, H. M. 2021

  Abstract

  To identify novel genes associated with intellectual disability (ID) in four unrelated families.Here, through exome sequencing and international collaboration, we report eight individuals from four unrelated families of diverse geographic origin with biallelic loss-of-function variants in UBE4A.Eight evaluated individuals presented with syndromic intellectual disability and global developmental delay. Other clinical features included hypotonia, short stature, seizures, and behavior disorder. Characteristic features were appreciated in some individuals but not all; in some cases, features became more apparent with age. We demonstrated that UBE4A loss-of-function variants reduced RNA expression and protein levels in clinical samples. Mice generated to mimic patient-specific Ube4a loss-of-function variant exhibited muscular and neurological/behavioral abnormalities, some of which are suggestive of the clinical abnormalities seen in the affected individuals.These data indicate that biallelic loss-of-function variants in UBE4A cause a novel intellectual disability syndrome, suggesting that UBE4A enzyme activity is required for normal development and neurological function.

  View details for DOI 10.1038/s41436-020-01047-z

  View details for PubMedID 33420346

• Strong evidence for genotype-phenotype correlations in Phelan-McDermid syndrome: Results from the developmental Synaptopathies consortium. Human molecular genetics Levy, T., Foss-Feig, J. H., Betancur, C., Siper, P. M., Pilar Trelles-Thorne, M., Halpern, D., Frank, Y., Lozano, R., Layton, C., Britvan, B., Bernstein, J. A., Buxbaum, J. D., Berry-Kravis, E., Powell, C. M., Srivastava, S., Sahin, M., Soorya, L., Thurm, A., Kolevzon, A. 2021

  Abstract

  Individuals with Phelan-McDermid syndrome (PMS) present with a wide range of developmental, medical, cognitive, and behavioral abnormalities. Previous literature has begun to elucidate genotype-phenotype associations that may contribute to the wide spectrum of features. Here, we report results of genotype-phenotype associations in a cohort of 170 individuals with PMS. Genotypes were defined as Class I deletions (include SHANK3 only or SHANK3 with ARSA and/or ACR and RABL2B), Class II deletions (all other deletions), or sequence variants. Phenotype data were derived prospectively from direct evaluation, caregiver interview and questionnaires, and medical history. Analyses revealed individuals with Class I deletions or sequence variants had fewer delayed developmental milestones and higher cognitive ability compared to those with Class II deletions but had more skill regressions. Individuals with Class II deletions were more likely to have a variety of medical features, including renal abnormalities, spine abnormalities, and ataxic gait. Those with Class I deletions or sequence variants were more likely to have psychiatric diagnoses including bipolar disorder, depression, and schizophrenia. Autism spectrum disorder diagnoses did not differ between groups. This study represents the largest and most rigorous genotype-phenotype analysis in PMS to date and provides important information for considering clinical functioning, trajectories, and comorbidities as a function of specific genetic alteration.

  View details for DOI 10.1093/hmg/ddab280

  View details for PubMedID 34559195

• "It seems like COVID-19 now is the only disease present on Earth": living with a rare or undiagnosed disease during the COVID-19 pandemic. Genetics in medicine : official journal of the American College of Medical Genetics Halley, M. C., Stanley, T. n., Maturi, J. n., Goldenberg, A. J., Bernstein, J. A., Wheeler, M. T., Tabor, H. K. 2021

  Abstract

  Patients with rare and undiagnosed diseases (RUDs) face significant health challenges, which may be exacerbated during the COVID-19 pandemic. The goal of this study was to identify specific impacts of the pandemic on RUD patients, and targets for improving support and health-care access.We conducted an online survey of RUD patients and their family members from 21 April to 8 June 2020, recruited from 76 Facebook groups for RUDs. Questions assessed patient characteristics and impacts of the pandemic on RUD diagnosis and management.Respondents (n = 413), including 274 RUD patients and 139 family members, were predominantly female and white, though income varied. Impacts of the pandemic included (1) barriers to accessing essential health care, (2) specific impacts of restrictive COVID-19 visitation policies on ability to advocate in health-care settings, (3) uncertainty and fear regarding COVID-19 risk, (4) exacerbated physical and mental health challenges, (5) magnified impacts of reduced educational and therapeutic services, and (6) unexpected positive changes due to the pandemic.There are specific, serious challenges affecting RUD patients and families during the COVID-19 pandemic. There is an urgent need to develop approaches to mitigate these challenges both during and beyond the pandemic.

  View details for DOI 10.1038/s41436-020-01069-7

  View details for PubMedID 33420343

• Predominant and novel de novo variants in 29 individuals with ALG13 deficiency: Clinical description, biomarker status, biochemical analysis and treatment suggestions. Journal of inherited metabolic disease Ng, B. G., Eklund, E. A., Shiryaev, S. A., Dong, Y. Y., Abbott, M., Asteggiano, C., Bamshad, M. J., Barr, E., Bernstein, J. A., Chelakkadan, S., Christodoulou, J., Chung, W. K., Ciliberto, M. A., Cousin, J., Gardiner, F., Ghosh, S., Graf, W. D., Grunewald, S., Hammond, K., Hauser, N. S., Hoganson, G. E., Houck, K. M., Kohler, J. N., Morava, E., Larson, A. A., Liu, P., Madathil, S., McCormack, C., Meeks, N. J., Miller, R., Monaghan, K. G., Nickerson, D. A., Palculict, T. B., Papazoglu, G. M., Pletcher, B. A., Scheffer, I. E., Schenone, A. B., Schnur, R. E., Si, Y., Rowe, L. J., Serrano Russi, A. H., Russo, R. S., Thabet, F., Tuite, A., Villanueva, M. M., Wang, R. Y., Webster, R. I., Wilson, D., Zalan, A., Network, U. D., University of Washington Center for Mendelian Genomics (UW-CMG), Wolfe, L. A., Rosenfeld, J. A., Rhodes, L., Freeze, H. H. 2020

  Abstract

  ALG13 encodes a non-redundant, highly conserved, X-linked UDP-N-Acetylglucosaminyltransferase required for the synthesis of lipid linked oligosaccharide precursor and proper N-linked glycosylation. De novo variants in ALG13 underlie a form of early infantile epileptic encephalopathy known as EIEE36, but given its essential role in glycosylation, it is also considered a congenital disorder of glycosylation, ALG13-CDG. Twenty-four previously reported ALG13-CDG cases had de novo variants, but surprisingly, unlike most forms of CDG, ALG13-CDG did not show the anticipated glycosylation defects, typically detected by altered transferrin glycosylation. Structural homology modeling of two recurrent de novo variants, p.A81T and p.N107S, suggests both are likely to impact the function of ALG13. Using a corresponding ALG13-deficient yeast strain, we show that expressing yeast ALG13 with either of the highly conserved hotspot variants rescues the observed growth defect, but not its glycosylation abnormality. We present molecular and clinical data on 29 previously unreported individuals with de novo variants in ALG13. This more than doubles the number of known cases. A key finding is that a vast majority of the individuals presents with West syndrome, a feature shared with other CDG types. Among these, the initial epileptic spasms best responded to ACTH or prednisolone, while clobazam and felbamate showed promise for continued epilepsy treatment. A ketogenic diet seems to play an important role in the treatment of these individuals. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1002/jimd.12290

  View details for PubMedID 32681751

• Neuronal defects in a human cellular model of 22q11.2 deletion syndrome. Nature medicine Khan, T. A., Revah, O. n., Gordon, A. n., Yoon, S. J., Krawisz, A. K., Goold, C. n., Sun, Y. n., Kim, C. H., Tian, Y. n., Li, M. Y., Schaepe, J. M., Ikeda, K. n., Amin, N. D., Sakai, N. n., Yazawa, M. n., Kushan, L. n., Nishino, S. n., Porteus, M. H., Rapoport, J. L., Bernstein, J. A., O'Hara, R. n., Bearden, C. E., Hallmayer, J. F., Huguenard, J. R., Geschwind, D. H., Dolmetsch, R. E., Paşca, S. P. 2020

  Abstract

  22q11.2 deletion syndrome (22q11DS) is a highly penetrant and common genetic cause of neuropsychiatric disease. Here we generated induced pluripotent stem cells from 15 individuals with 22q11DS and 15 control individuals and differentiated them into three-dimensional (3D) cerebral cortical organoids. Transcriptional profiling across 100 days showed high reliability of differentiation and revealed changes in neuronal excitability-related genes. Using electrophysiology and live imaging, we identified defects in spontaneous neuronal activity and calcium signaling in both organoid- and 2D-derived cortical neurons. The calcium deficit was related to resting membrane potential changes that led to abnormal inactivation of voltage-gated calcium channels. Heterozygous loss of DGCR8 recapitulated the excitability and calcium phenotypes and its overexpression rescued these defects. Moreover, the 22q11DS calcium abnormality could also be restored by application of antipsychotics. Taken together, our study illustrates how stem cell derived models can be used to uncover and rescue cellular phenotypes associated with genetic forms of neuropsychiatric disease.

  View details for DOI 10.1038/s41591-020-1043-9

  View details for PubMedID 32989314

• Candidate variants in TUB are associated with familial tremor. PLoS genetics Sailani, M. R., Jahanbani, F. n., Abbott, C. W., Lee, H. n., Zia, A. n., Rego, S. n., Winkelmann, J. n., Hopfner, F. n., Khan, T. N., Katsanis, N. n., Müller, S. H., Berg, D. n., Lyman, K. M., Mychajliw, C. n., Deuschl, G. n., Bernstein, J. A., Kuhlenbäumer, G. n., Snyder, M. P. 2020; 16 (9): e1009010

  Abstract

  Essential tremor (ET) is the most common adult-onset movement disorder. In the present study, we performed whole exome sequencing of a large ET-affected family (10 affected and 6 un-affected family members) and identified a TUB p.V431I variant (rs75594955) segregating in a manner consistent with autosomal-dominant inheritance. Subsequent targeted re-sequencing of TUB in 820 unrelated individuals with sporadic ET and 630 controls revealed significant enrichment of rare nonsynonymous TUB variants (e.g. rs75594955: p.V431I, rs1241709665: p.Ile20Phe, rs55648406: p.Arg49Gln) in the ET cohort (SKAT-O test p-value = 6.20e-08). TUB encodes a transcription factor predominantly expressed in neuronal cells and has been previously implicated in obesity. ChIP-seq analyses of the TUB transcription factor across different regions of the mouse brain revealed that TUB regulates the pathways responsible for neurotransmitter production as well thyroid hormone signaling. Together, these results support the association of rare variants in TUB with ET.

  View details for DOI 10.1371/journal.pgen.1009010

  View details for PubMedID 32956375

• Genotypic diversity and phenotypic spectrum of infantile liver failure syndrome type 1 due to variants in LARS1. Genetics in medicine : official journal of the American College of Medical Genetics Lenz, D. n., Smith, D. E., Crushell, E. n., Husain, R. A., Salomons, G. S., Alhaddad, B. n., Bernstein, J. A., Bianzano, A. n., Biskup, S. n., Brennenstuhl, H. n., Caldari, D. n., Dikow, N. n., Haack, T. B., Hanson-Kahn, A. n., Harting, I. n., Horn, D. n., Hughes, J. n., Huijberts, M. n., Isidor, B. n., Kathemann, S. n., Kopajtich, R. n., Kotzaeridou, U. n., Küry, S. n., Lainka, E. n., Laugwitz, L. n., Lupski, J. R., Posey, J. E., Reynolds, C. n., Rosenfeld, J. A., Schröter, J. n., Vansenne, F. n., Wagner, M. n., Weiß, C. n., Wolffenbuttel, B. H., Wortmann, S. B., Kölker, S. n., Hoffmann, G. F., Prokisch, H. n., Mendes, M. I., Staufner, C. n. 2020

  Abstract

  Biallelic variants in LARS1, coding for the cytosolic leucyl-tRNA synthetase, cause infantile liver failure syndrome 1 (ILFS1). Since its description in 2012, there has been no systematic analysis of the clinical spectrum and genetic findings.Individuals with biallelic variants in LARS1 were included through an international, multicenter collaboration including novel and previously published patients. Clinical variables were analyzed and functional studies were performed in patient-derived fibroblasts.Twenty-five individuals from 15 families were ascertained including 12 novel patients with eight previously unreported variants. The most prominent clinical findings are recurrent elevation of liver transaminases up to liver failure and encephalopathic episodes, both triggered by febrile illness. Magnetic resonance image (MRI) changes during an encephalopathic episode can be consistent with metabolic stroke. Furthermore, growth retardation, microcytic anemia, neurodevelopmental delay, muscular hypotonia, and infection-related seizures are prevalent. Aminoacylation activity is significantly decreased in all patient cells studied upon temperature elevation in vitro.ILFS1 is characterized by recurrent elevation of liver transaminases up to liver failure in conjunction with abnormalities of growth, blood, nervous system, and musculature. Encephalopathic episodes with seizures can occur independently from liver crises and may present with metabolic stroke.

  View details for DOI 10.1038/s41436-020-0904-4

  View details for PubMedID 32699352

• Combined Genome Sequencing and RNA Analysis Reveals and Characterizes a Deep Intronic Variant in IGHMBP2 in a Patient With Spinal Muscular Atrophy With Respiratory Distress Type 1. Pediatric neurology Bodle, E. E., Zhu, W. n., Velez-Bartolomei, F. n., Tesi-Rocha, A. n., Liu, P. n., Bernstein, J. A. 2020; 114: 16–20

  Abstract

  Pathogenic variants in the IGHMBP2 gene cause recessive spinal motor neuropathies of variable phenotype, including a predominantly distal motor impairment of Charcot-Marie-Tooth type 2S and the more severe condition of spinal muscular atrophy with respiratory distress type 1 in which infantile respiratory failure predominates.We describe the first reported case of spinal muscular atrophy with respiratory distress type 1 caused by a novel deep intronic variant in IGHMBP2 (NM_002180c.712-610A>G).The variant was detected by whole genome sequencing. Reverse transcription-polymerase chain reaction and complimentary DNA sequencing were used to characterize the impact of the novel variant.This report illustrates the utility in clinical practice of genome sequencing and RNA analysis, compared with exome sequencing alone.

  View details for DOI 10.1016/j.pediatrneurol.2020.09.011

  View details for PubMedID 33189025

• Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons. Biological psychiatry Zhang, S. n., Zhang, X. n., Purmann, C. n., Ma, S. n., Shrestha, A. n., Davis, K. N., Ho, M. n., Huang, Y. n., Pattni, R. n., Wong, W. H., Bernstein, J. A., Hallmayer, J. n., Urban, A. E. 2020

  Abstract

  The 15q13.3 microdeletion is associated with several neuropsychiatric disorders, including autism and schizophrenia. Previous association and functional studies have investigated the potential role of several genes within the deletion in neuronal dysfunction, but the molecular effects of the deletion as a whole remain largely unknown.Induced pluripotent stem cells, from 3 patients with the 15q13.3 microdeletion and 3 control subjects, were generated and converted into induced neurons. We analyzed the effects of the 15q13.3 microdeletion on genome-wide gene expression, DNA methylation, chromatin accessibility, and sensitivity to cisplatin-induced DNA damage. Furthermore, we measured gene expression changes in induced neurons with CRISPR (clustered regularly interspaced short palindromic repeats) knockouts of individual 15q13.3 microdeletion genes.In both induced pluripotent stem cells and induced neurons, gene copy number change within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression and no compensatory changes in DNA methylation or chromatin accessibility, supporting the model that haploinsufficiency of genes within the deleted region drives the disorder. Furthermore, we observed global effects of the microdeletion on the transcriptome and epigenome, with disruptions in several neuropsychiatric disorder-associated pathways and gene families, including Wnt signaling, ribosome function, DNA binding, and clustered protocadherins. Individual gene knockouts mirrored many of the observed changes in an overlapping fashion between knockouts.Our multiomics analysis of the 15q13.3 microdeletion revealed downstream effects in pathways previously associated with neuropsychiatric disorders and indications of interactions between genes within the deletion. This molecular systems analysis can be applied to other chromosomal aberrations to further our etiological understanding of neuropsychiatric disorders.

  View details for DOI 10.1016/j.biopsych.2020.06.021

  View details for PubMedID 32919612

• Automated syndrome diagnosis by three-dimensional facial imaging. Genetics in medicine : official journal of the American College of Medical Genetics Hallgrímsson, B. n., Aponte, J. D., Katz, D. C., Bannister, J. J., Riccardi, S. L., Mahasuwan, N. n., McInnes, B. L., Ferrara, T. M., Lipman, D. M., Neves, A. B., Spitzmacher, J. A., Larson, J. R., Bellus, G. A., Pham, A. M., Aboujaoude, E. n., Benke, T. A., Chatfield, K. C., Davis, S. M., Elias, E. R., Enzenauer, R. W., French, B. M., Pickler, L. L., Shieh, J. T., Slavotinek, A. n., Harrop, A. R., Innes, A. M., McCandless, S. E., McCourt, E. A., Meeks, N. J., Tartaglia, N. R., Tsai, A. C., Wyse, J. P., Bernstein, J. A., Sanchez-Lara, P. A., Forkert, N. D., Bernier, F. P., Spritz, R. A., Klein, O. D. 2020

  Abstract

  Deep phenotyping is an emerging trend in precision medicine for genetic disease. The shape of the face is affected in 30-40% of known genetic syndromes. Here, we determine whether syndromes can be diagnosed from 3D images of human faces.We analyzed variation in three-dimensional (3D) facial images of 7057 subjects: 3327 with 396 different syndromes, 727 of their relatives, and 3003 unrelated, unaffected subjects. We developed and tested machine learning and parametric approaches to automated syndrome diagnosis using 3D facial images.Unrelated, unaffected subjects were correctly classified with 96% accuracy. Considering both syndromic and unrelated, unaffected subjects together, balanced accuracy was 73% and mean sensitivity 49%. Excluding unrelated, unaffected subjects substantially improved both balanced accuracy (78.1%) and sensitivity (56.9%) of syndrome diagnosis. The best predictors of classification accuracy were phenotypic severity and facial distinctiveness of syndromes. Surprisingly, unaffected relatives of syndromic subjects were frequently classified as syndromic, often to the syndrome of their affected relative.Deep phenotyping by quantitative 3D facial imaging has considerable potential to facilitate syndrome diagnosis. Furthermore, 3D facial imaging of "unaffected" relatives may identify unrecognized cases or may reveal novel examples of semidominant inheritance.

  View details for DOI 10.1038/s41436-020-0845-y

  View details for PubMedID 32475986

• AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature. Science translational medicine Birgmeier, J. n., Haeussler, M. n., Deisseroth, C. A., Steinberg, E. H., Jagadeesh, K. A., Ratner, A. J., Guturu, H. n., Wenger, A. M., Diekhans, M. E., Stenson, P. D., Cooper, D. N., Ré, C. n., Beggs, A. H., Bernstein, J. A., Bejerano, G. n. 2020; 12 (544)

  Abstract

  The diagnosis of Mendelian disorders requires labor-intensive literature research. Trained clinicians can spend hours looking for the right publication(s) supporting a single gene that best explains a patient's disease. AMELIE (Automatic Mendelian Literature Evaluation) greatly accelerates this process. AMELIE parses all 29 million PubMed abstracts and downloads and further parses hundreds of thousands of full-text articles in search of information supporting the causality and associated phenotypes of most published genetic variants. AMELIE then prioritizes patient candidate variants for their likelihood of explaining any patient's given set of phenotypes. Diagnosis of singleton patients (without relatives' exomes) is the most time-consuming scenario, and AMELIE ranked the causative gene at the very top for 66% of 215 diagnosed singleton Mendelian patients from the Deciphering Developmental Disorders project. Evaluating only the top 11 AMELIE-scored genes of 127 (median) candidate genes per patient resulted in a rapid diagnosis in more than 90% of cases. AMELIE-based evaluation of all cases was 3 to 19 times more efficient than hand-curated database-based approaches. We replicated these results on a retrospective cohort of clinical cases from Stanford Children's Health and the Manton Center for Orphan Disease Research. An analysis web portal with our most recent update, programmatic interface, and code is available at AMELIE.stanford.edu.

  View details for DOI 10.1126/scitranslmed.aau9113

  View details for PubMedID 32434849

• Diffusion Tensor Imaging Abnormalities in the Uncinate Fasciculus and Inferior Longitudinal Fasciculus in Phelan-McDermid Syndrome. Pediatric neurology Bassell, J. n., Srivastava, S. n., Prohl, A. K., Scherrer, B. n., Kapur, K. n., Filip-Dhima, R. n., Berry-Kravis, E. n., Soorya, L. n., Thurm, A. n., Powell, C. M., Bernstein, J. A., Buxbaum, J. D., Kolevzon, A. n., Warfield, S. K., Sahin, M. n. 2020

  Abstract

  This cohort study utilized diffusion tensor imaging tractography to compare the uncinate fasciculus and inferior longitudinal fasciculus in children with Phelan-McDermid syndrome with age-matched controls and investigated trends between autism spectrum diagnosis and the integrity of the uncinate fasciculus and inferior longitudinal fasciculus white matter tracts.This research was conducted under a longitudinal study that aims to map the genotype, phenotype, and natural history of Phelan-McDermid syndrome and identify biomarkers using neuroimaging (ClinicalTrial NCT02461420). Patients were aged three to 21 years and underwent longitudinal neuropsychologic assessment over 24 months. MRI processing and analyses were completed using previously validated image analysis software distributed as the Computational Radiology Kit (http://crl.med.harvard.edu/). Whole-brain connectivity was generated for each subject using a stochastic streamline tractography algorithm, and automatically defined regions of interest were used to map the uncinate fasciculus and inferior longitudinal fasciculus.There were 10 participants (50% male; mean age 11.17 years) with Phelan-McDermid syndrome (n = 8 with autism). Age-matched controls, enrolled in a separate longitudinal study (NIH R01 NS079788), underwent the same neuroimaging protocol. There was a statistically significant decrease in the uncinate fasciculus fractional anisotropy measure and a statistically significant increase in uncinate fasciculus mean diffusivity measure, in the patient group versus controls in both right and left tracts (P ≤ 0.024).Because the uncinate fasciculus plays a critical role in social and emotional interaction, this tract may underlie some deficits seen in the Phelan-McDermid syndrome population. These findings need to be replicated in a larger cohort.

  View details for DOI 10.1016/j.pediatrneurol.2020.01.006

  View details for PubMedID 32107139

• Psychometric Study of the Social Responsiveness Scale in Phelan-McDermid Syndrome. Autism research : official journal of the International Society for Autism Research Gergoudis, K. n., Weinberg, A. n., Templin, J. n., Farmer, C. n., Durkin, A. n., Weissman, J. n., Siper, P. n., Foss-Feig, J. n., Del Pilar Trelles, M. n., Bernstein, J. A., Buxbaum, J. D., Berry-Kravis, E. n., Powell, C. M., Sahin, M. n., Soorya, L. n., Thurm, A. n., Kolevzon, A. n. 2020

  Abstract

  The Social Responsiveness Scale-2 (SRS-2) is a quantitative measure used to characterize symptoms of autism spectrum disorder (ASD). However, research suggests that SRS-2 scores are significantly influenced by language ability and intellectual disability (ID). Efforts to refine the SRS-2 by Sturm, Kuhfeld, Kasari, and Mccracken [Journal of Child Psychology and Psychiatry, 58(9), 1053-1061] yielded a shortened form, yet its psychometric properties in populations with severe ID remain unknown. This study aims to examine the psychometric properties of the SRS-2 in Phelan-McDermid syndrome (PMS), a genetic condition associated with ASD and ID, thereby guiding score interpretation in this population and future development of targeted scales. Analyses, including Item Response Theory (IRT), were conducted on a sample of individuals with PMS (n = 91) recruited at six sites nationally. Psychometric properties evaluated include measures of reliability (internal consistency, test-retest reliability) and validity (structural, construct, content). While both SRS-2 forms are reliable, the shortened SRS-2 shows superior validity to the full SRS-2 for measuring ASD symptoms in PMS. On IRT analysis, the shortened SRS-2 shows excellent discrimination and precisely evaluates respondents across a wide range of ASD symptomatology but interpretation is limited by uncertain content validity and small sample size. The shortened SRS-2 shows some promise for use in PMS, but future refinements and additions are needed to develop items that are tailored to identify ASD in children with severe ID and specifically PMS. LAY SUMMARY: This study determined that a shortened form of the Social Responsiveness Scale, Second Edition (SRS-2) shows both promise and limitations for the characterization of autism symptomatology in individuals with Phelan-McDermid syndrome (PMS), a population characterized by intellectual disability (ID). Caution should be used when interpreting SRS-2 scores in individuals with ID and future research should modify existing items and develop new items to improve the SRS-2's ability to accurately characterize autism symptomatology in PMS.

  View details for DOI 10.1002/aur.2299

  View details for PubMedID 32406614

• Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science. Genetics in medicine : official journal of the American College of Medical Genetics Schoch, K. n., Esteves, C. n., Bican, A. n., Spillmann, R. n., Cope, H. n., McConkie-Rosell, A. n., Walley, N. n., Fernandez, L. n., Kohler, J. N., Bonner, D. n., Reuter, C. n., Stong, N. n., Mulvihill, J. J., Novacic, D. n., Wolfe, L. n., Abdelbaki, A. n., Toro, C. n., Tifft, C. n., Malicdan, M. n., Gahl, W. n., Liu, P. n., Newman, J. n., Goldstein, D. B., Hom, J. n., Sampson, J. n., Wheeler, M. T., Cogan, J. n., Bernstein, J. A., Adams, D. R., McCray, A. T., Shashi, V. n. 2020

  Abstract

  The NIH Undiagnosed Diseases Network (UDN) evaluates participants with disorders that have defied diagnosis, applying personalized clinical and genomic evaluations and innovative research. The clinical sites of the UDN are essential to advancing the UDN mission; this study assesses their contributions relative to standard clinical practices.We analyzed retrospective data from four UDN clinical sites, from July 2015 to September 2019, for diagnoses, new disease gene discoveries and the underlying investigative methods.Of 791 evaluated individuals, 231 received 240 diagnoses and 17 new disease-gene associations were recognized. Straightforward diagnoses on UDN exome and genome sequencing occurred in 35% (84/240). We considered these tractable in standard clinical practice, although genome sequencing is not yet widely available clinically. The majority (156/240, 65%) required additional UDN-driven investigations, including 90 diagnoses that occurred after prior nondiagnostic exome sequencing and 45 diagnoses (19%) that were nongenetic. The UDN-driven investigations included complementary/supplementary phenotyping, innovative analyses of genomic variants, and collaborative science for functional assays and animal modeling.Investigations driven by the clinical sites identified diagnostic and research paradigms that surpass standard diagnostic processes. The new diagnoses, disease gene discoveries, and delineation of novel disorders represent a model for genomic medicine and science.

  View details for DOI 10.1038/s41436-020-00984-z

  View details for PubMedID 33093671

• De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. American journal of human genetics Mao, D. n., Reuter, C. M., Ruzhnikov, M. R., Beck, A. E., Farrow, E. G., Emrick, L. T., Rosenfeld, J. A., Mackenzie, K. M., Robak, L. n., Wheeler, M. T., Burrage, L. C., Jain, M. n., Liu, P. n., Calame, D. n., Küry, S. n., Sillesen, M. n., Schmitz-Abe, K. n., Tonduti, D. n., Spaccini, L. n., Iascone, M. n., Genetti, C. A., Koenig, M. K., Graf, M. n., Tran, A. n., Alejandro, M. n., Lee, B. H., Thiffault, I. n., Agrawal, P. B., Bernstein, J. A., Bellen, H. J., Chao, H. T. 2020

  Abstract

  EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.

  View details for DOI 10.1016/j.ajhg.2020.02.016

  View details for PubMedID 32197074

• De novo and inherited variants in ZNF292 underlie a neurodevelopmental disorder with features of autism spectrum disorder. Genetics in medicine : official journal of the American College of Medical Genetics Mirzaa, G. M., Chong, J. X., Piton, A., Popp, B., Foss, K., Guo, H., Harripaul, R., Xia, K., Scheck, J., Aldinger, K. A., Sajan, S. A., Tang, S., Bonneau, D., Beck, A., White, J., Mahida, S., Harris, J., Smith-Hicks, C., Hoyer, J., Zweier, C., Reis, A., Thiel, C. T., Jamra, R. A., Zeid, N., Yang, A., Farach, L. S., Walsh, L., Payne, K., Rohena, L., Velinov, M., Ziegler, A., Schaefer, E., Gatinois, V., Genevieve, D., Simon, M. E., Kohler, J., Rotenberg, J., Wheeler, P., Larson, A., Ernst, M. E., Akman, C. I., Westman, R., Blanchet, P., Schillaci, L., Vincent-Delorme, C., Gripp, K. W., Mattioli, F., Guyader, G. L., Gerard, B., Mathieu-Dramard, M., Morin, G., Sasanfar, R., Ayub, M., Vasli, N., Yang, S., Person, R., Monaghan, K. G., Nickerson, D. A., van Binsbergen, E., Enns, G. M., Dries, A. M., Rowe, L. J., Tsai, A. C., Svihovec, S., Friedman, J., Agha, Z., Qamar, R., Rodan, L. H., Martinez-Agosto, J., Ockeloen, C. W., Vincent, M., Sunderland, W. J., Bernstein, J. A., Undiagnosed Diseases Network, Eichler, E. E., Vincent, J. B., University of Washington Center for Mendelian Genomics (UW-CMG), Bamshad, M. J. 2019

  Abstract

  PURPOSE: Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous neurodevelopmental disorders. We sought to delineate the clinical, molecular, and neuroimaging spectrum of a novel neurodevelopmental disorder caused by variants in the zinc finger protein 292 gene (ZNF292).METHODS: We ascertained a cohort of 28 families with ID due to putatively pathogenic ZNF292 variants that were identified via targeted and exome sequencing. Available data were analyzed to characterize the canonical phenotype and examine genotype-phenotype relationships.RESULTS: Probands presented with ID as well as a spectrum of neurodevelopmental features including ASD, among others. All ZNF292 variants were de novo, except in one family with dominant inheritance. ZNF292 encodes a highly conserved zinc finger protein that acts as a transcription factor and is highly expressed in the developing human brain supporting its critical role in neurodevelopment.CONCLUSION: De novo and dominantly inherited variants in ZNF292 are associated with a range of neurodevelopmental features including ID and ASD. The clinical spectrum is broad, and most individuals present with mild to moderate ID with or without other syndromic features. Our results suggest that variants in ZNF292 are likely a recurrent cause of a neurodevelopmental disorder manifesting as ID with or without ASD.

  View details for DOI 10.1038/s41436-019-0693-9

  View details for PubMedID 31723249

• Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing. Journal of genetic counseling Reuter, C. M., Kohler, J. N., Bonner, D., Zastrow, D., Fernandez, L., Dries, A., Marwaha, S., Davidson, J., Brokamp, E., Herzog, M., Hong, J., Macnamara, E., Rosenfeld, J. A., Schoch, K., Spillmann, R., Undiagnosed Diseases Network, Loscalzo, J., Krier, J., Stoler, J., Sweetser, D., Palmer, C. G., Phillips, J. A., Shashi, V., Adams, D. A., Yang, Y., Ashley, E. A., Fisher, P. G., Mulvihill, J. J., Bernstein, J. A., Wheeler, M. T. 2019

  Abstract

  BACKGROUND: Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored.METHODS: We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated.RESULTS: Sixty-six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty-two of 66 (64%) received insurance denial for clinician-ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%).CONCLUSIONS: These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.

  View details for DOI 10.1002/jgc4.1161

  View details for PubMedID 31478310

• Extracutaneous manifestations in phacomatosis cesioflammea and cesiomarmorata: Case series and literature review. American journal of medical genetics. Part A Kumar, A., Zastrow, D. B., Kravets, E. J., Beleford, D., Ruzhnikov, M. R., Grove, M. E., Dries, A. M., Kohler, J. N., Waggott, D. M., Yang, Y., Huang, Y., Undiagnosed Diseases Network, Mackenzie, K. M., Eng, C. M., Fisher, P. G., Ashley, E. A., Teng, J. M., Stevenson, D. A., Shieh, J. T., Wheeler, M. T., Bernstein, J. A. 2019

  Abstract

  Phacomatosis pigmentovascularis (PPV) comprises a family of rare conditions that feature vascular abnormalities and melanocytic lesions that can be solely cutaneous or multisystem in nature. Recently published work has demonstrated that both vascular and melanocytic abnormalities in PPV of the cesioflammea and cesiomarmorata subtypes can result from identical somatic mosaic activating mutations in the genes GNAQ and GNA11. Here, we present three new cases of PPV with features of the cesioflammea and/or cesiomarmorata subtypes and mosaic mutations in GNAQ or GNA11. To better understand the risk of potentially occult complications faced by such patients we additionally reviewed 176 cases published in the literature. We report the frequency of clinical findings, their patterns of co-occurrence as well as published recommendations for surveillance after diagnosis. Features assessed include: capillary malformation; dermal and ocular melanocytosis; glaucoma; limb asymmetry; venous malformations; and central nervous system (CNS) anomalies, such as ventriculomegaly and calcifications. We found that ocular findings are common in patients with phacomatosis cesioflammea and cesiomarmorata. Facial vascular involvement correlates with a higher risk of seizures (p=.0066). Our genetic results confirm the role of mosaic somatic mutations in GNAQ and GNA11 in phacomatosis cesioflammea and cesiomarmorata. Their clinical and molecular findings place these conditions on a clinical spectrum encompassing other GNAQ and GNA11 related disorders and inform recommendations for their management.

  View details for PubMedID 30920161

• S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing. Nature genetics Jagadeesh, K. A., Paggi, J. M., Ye, J. S., Stenson, P. D., Cooper, D. N., Bernstein, J. A., Bejerano, G. 2019

  Abstract

  Exome analysis of patients with a likely monogenic disease does not identify a causal variant in over half of cases. Splice-disrupting mutations make up the second largest class of known disease-causing mutations. Each individual (singleton) exome harbors over 500 rare variants of unknown significance (VUS) in the splicing region. The existing relevant pathogenicity prediction tools tackle all non-coding variants as one amorphic class and/or are not calibrated for the high sensitivity required for clinical use. Here we calibrate seven such tools and devise a novel tool called Splicing Clinically Applicable Pathogenicity prediction (S-CAP) that is over twice as powerful as all previous tools, removing 41% of patient VUS at 95% sensitivity. We show that S-CAP does this by using its own features and not via meta-prediction over previous tools, and that splicing pathogenicity prediction is distinct from predicting molecular splicing changes. S-CAP is an important step on the path to deriving non-coding causal diagnoses.

  View details for PubMedID 30804562

• Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students. Journal of genetic counseling Grove, M. E., White, S. n., Fisk, D. G., Rego, S. n., Dagan-Rosenfeld, O. n., Kohler, J. N., Reuter, C. M., Bonner, D. n., Wheeler, M. T., Bernstein, J. A., Ormond, K. E., Hanson-Kahn, A. K. 2019

  Abstract

  With the wide adoption of next-generation sequencing (NGS)-based genetic tests, genetic counselors require increased familiarity with NGS technology, variant interpretation concepts, and variant assessment tools. The use of exome and genome sequencing in clinical care has expanded the reach and diversity of genetic testing. Regardless of the setting where genetic counselors are performing variant interpretation or reporting, most of them have learned these skills from colleagues, while on the job. Though traditional, lecture-based learning around these topics is important, there has been growing need for the inclusion of case-based, experiential training of genomics and variant interpretation for genetic counseling students, with the goal of creating a strong foundation in variant interpretation for new genetic counselors, regardless of what area of practice they enter. To address this need, we established a genomics and variant interpretation rotation for Stanford's genetic counseling training program. In response to changes in the genomics landscape, this has now evolved into three unique rotation experiences, each focused on variant interpretation in the context of various genomic settings, including clinical laboratory, research laboratory, and healthy genomic analysis studies. Here, we describe the goals and learning objectives that we have developed for these variant interpretation rotations, and illustrate how these concepts are applied in practice.

  View details for PubMedID 30706981

• AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature. Genetics in medicine : official journal of the American College of Medical Genetics Birgmeier, J. n., Deisseroth, C. A., Hayward, L. E., Galhardo, L. M., Tierno, A. P., Jagadeesh, K. A., Stenson, P. D., Cooper, D. N., Bernstein, J. A., Haeussler, M. n., Bejerano, G. n. 2019

  Abstract

  Both monogenic pathogenic variant cataloging and clinical patient diagnosis start with variant-level evidence retrieval followed by expert evidence integration in search of diagnostic variants and genes. Here, we try to accelerate pathogenic variant evidence retrieval by an automatic approach.Automatic VAriant evidence DAtabase (AVADA) is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates.AVADA automatically retrieved almost 60% of likely disease-causing variants deposited in the Human Gene Mutation Database (HGMD), a 4.4-fold improvement over the current best open source automated variant extractor. AVADA contains over 60,000 likely disease-causing variants that are in HGMD but not in ClinVar. AVADA also highlights the challenges of automated variant mapping and pathogenicity curation. However, when combined with manual validation, on 245 diagnosed patients, AVADA provides valuable evidence for an additional 18 diagnostic variants, on top of ClinVar's 21, versus only 2 using the best current automated approach.AVADA advances automated retrieval of pathogenic monogenic variant evidence from full-text literature. Far from perfect, but much faster than PubMed/Google Scholar search, careful curation of AVADA-retrieved evidence can aid both database curation and patient diagnosis.

  View details for DOI 10.1038/s41436-019-0643-6

  View details for PubMedID 31467448

• Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases. Acta neuropathologica Perenthaler, E. n., Nikoncuk, A. n., Yousefi, S. n., Berdowski, W. M., Alsagob, M. n., Capo, I. n., van der Linde, H. C., van den Berg, P. n., Jacobs, E. H., Putar, D. n., Ghazvini, M. n., Aronica, E. n., van IJcken, W. F., de Valk, W. G., Medici-van den Herik, E. n., van Slegtenhorst, M. n., Brick, L. n., Kozenko, M. n., Kohler, J. N., Bernstein, J. A., Monaghan, K. G., Begtrup, A. n., Torene, R. n., Al Futaisi, A. n., Al Murshedi, F. n., Mani, R. n., Al Azri, F. n., Kamsteeg, E. J., Mojarrad, M. n., Eslahi, A. n., Khazaei, Z. n., Darmiyan, F. M., Doosti, M. n., Karimiani, E. G., Vandrovcova, J. n., Zafar, F. n., Rana, N. n., Kandaswamy, K. K., Hertecant, J. n., Bauer, P. n., AlMuhaizea, M. A., Salih, M. A., Aldosary, M. n., Almass, R. n., Al-Quait, L. n., Qubbaj, W. n., Coskun, S. n., Alahmadi, K. O., Hamad, M. H., Alwadaee, S. n., Awartani, K. n., Dababo, A. M., Almohanna, F. n., Colak, D. n., Dehghani, M. n., Mehrjardi, M. Y., Gunel, M. n., Ercan-Sencicek, A. G., Passi, G. R., Cheema, H. A., Efthymiou, S. n., Houlden, H. n., Bertoli-Avella, A. M., Brooks, A. S., Retterer, K. n., Maroofian, R. n., Kaya, N. n., van Ham, T. J., Barakat, T. S. 2019

  Abstract

  Developmental and/or epileptic encephalopathies (DEEs) are a group of devastating genetic disorders, resulting in early-onset, therapy-resistant seizures and developmental delay. Here we report on 22 individuals from 15 families presenting with a severe form of intractable epilepsy, severe developmental delay, progressive microcephaly, visual disturbance and similar minor dysmorphisms. Whole exome sequencing identified a recurrent, homozygous variant (chr2:64083454A > G) in the essential UDP-glucose pyrophosphorylase (UGP2) gene in all probands. This rare variant results in a tolerable Met12Val missense change of the longer UGP2 protein isoform but causes a disruption of the start codon of the shorter isoform, which is predominant in brain. We show that the absence of the shorter isoform leads to a reduction of functional UGP2 enzyme in neural stem cells, leading to altered glycogen metabolism, upregulated unfolded protein response and premature neuronal differentiation, as modeled during pluripotent stem cell differentiation in vitro. In contrast, the complete lack of all UGP2 isoforms leads to differentiation defects in multiple lineages in human cells. Reduced expression of Ugp2a/Ugp2b in vivo in zebrafish mimics visual disturbance and mutant animals show a behavioral phenotype. Our study identifies a recurrent start codon mutation in UGP2 as a cause of a novel autosomal recessive DEE syndrome. Importantly, it also shows that isoform-specific start-loss mutations causing expression loss of a tissue-relevant isoform of an essential protein can cause a genetic disease, even when an organism-wide protein absence is incompatible with life. We provide additional examples where a similar disease mechanism applies.

  View details for DOI 10.1007/s00401-019-02109-6

  View details for PubMedID 31820119

• Mutation update for the SATB2 gene. Human mutation Zarate, Y. A., Bosanko, K. A., Caffrey, A. R., Bernstein, J. A., Martin, D. M., Williams, M. S., Berry-Kravis, E. M., Mark, P. R., Manning, M. A., Bhambhani, V. n., Vargas, M. n., Seeley, A. H., Estrada-Veras, J. I., van Dooren, M. F., Schwab, M. n., Vanderver, A. n., Melis, D. n., Alsadah, A. n., Sadler, L. n., Van Esch, H. n., Callewaert, B. n., Oostra, A. n., Maclean, J. n., Dentici, M. L., Orlando, V. n., Lipson, M. n., Sparagana, S. P., Maarup, T. J., Alsters, S. I., Brautbar, A. n., Thropp, E. K., Naidu, S. n., Lees, M. n., Smith, D. M., Turner, L. n., Raggio, V. n., Spangenberg, L. n., Garcia-Miñaúr, S. n., Roeder, E. R., Littlejohn, R. O., Grange, D. n., Pfotenhauer, J. n., Jones, M. C., Balasubramanian, M. n., Martinez-Monseny, A. n., Blok, L. S., Gavrilova, R. n., Fish, J. L. 2019

  Abstract

  SATB2-associated syndrome (SAS) is an autosomal dominant neurodevelopmental disorder caused by alterations in the SATB2 gene. Here we present a review of published pathogenic variants in the SATB2 gene to date and report 38 novel alterations found in 57 additional previously unreported individuals. Overall, we present a compilation of 120 unique variants identified in 155 unrelated families ranging from single nucleotide coding variants to genomic rearrangements distributed throughout the entire coding region of SATB2. Single nucleotide variants predicted to result in the occurrence of a premature stop codon were the most commonly seen (51/120=42.5%) followed by missense variants (31/120=25.8%). We review the rather limited functional characterization of pathogenic variants and discuss current understanding of the consequences of the different molecular alterations. We present an expansive phenotypic review along with novel genotype-phenotype correlations. Lastly, we discuss current knowledge on animal models and present future prospects. This review should help provide better guidance for the care of individuals diagnosed with SAS. This article is protected by copyright. All rights reserved.

  View details for PubMedID 31021519

• Reanalysis of Clinical Exome Sequencing Data. The New England journal of medicine Liu, P., Meng, L., Normand, E. A., Xia, F., Song, X., Ghazi, A., Rosenfeld, J., Magoulas, P. L., Braxton, A., Ward, P., Dai, H., Yuan, B., Bi, W., Xiao, R., Wang, X., Chiang, T., Vetrini, F., He, W., Cheng, H., Dong, J., Gijavanekar, C., Benke, P. J., Bernstein, J. A., Eble, T., Eroglu, Y., Erwin, D., Escobar, L., Gibson, J. B., Gripp, K., Kleppe, S., Koenig, M. K., Lewis, A. M., Natowicz, M., Mancias, P., Minor, L., Scaglia, F., Schaaf, C. P., Streff, H., Vernon, H., Uhles, C. L., Zackai, E. H., Wu, N., Sutton, V. R., Beaudet, A. L., Muzny, D., Gibbs, R. A., Posey, J. E., Lalani, S., Shaw, C., Eng, C. M., Lupski, J. R., Yang, Y. 2019; 380 (25): 2478–80

  View details for DOI 10.1056/NEJMc1812033

  View details for PubMedID 31216405

• Genomics in medicine: a novel elective rotation for internal medicine residents. Postgraduate medical journal Geng, L. N., Kohler, J. N., Levonian, P. n., Bernstein, J. A., Ford, J. M., Ahuja, N. n., Witteles, R. n., Hom, J. n., Wheeler, M. n. 2019

  Abstract

  It is well recognised that medical training globally and at all levels lacks sufficient incorporation of genetics and genomics education to keep up with the rapid advances and growing application of genomics to clinical care. However, the best strategy to implement these desired changes into postgraduate medical training and engage learners is still unclear. We developed a novel elective rotation in 'Genomic Medicine and Undiagnosed Diseases' for categorical Internal Medicine Residents to address this educational gap and serve as an adaptable model for training that can be applied broadly across different specialties and at other institutions. Key curriculum goals achieved include increased understanding about genetic testing modalities and tools available for diagnosis and risk analysis, the role of genetics-trained allied health professionals, and indications and limitations of genetic and genomic testing in both rare and common conditions.

  View details for DOI 10.1136/postgradmedj-2018-136355

  View details for PubMedID 31439813

• A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing. Journal of genetic counseling Zastrow, D. B., Kohler, J. N., Bonner, D. n., Reuter, C. M., Fernandez, L. n., Grove, M. E., Fisk, D. G., Yang, Y. n., Eng, C. M., Ward, P. A., Bick, D. n., Worthey, E. A., Fisher, P. G., Ashley, E. A., Bernstein, J. A., Wheeler, M. T. 2019; 28 (2): 213–28

  Abstract

  There are approximately 7,000 rare diseases affecting 25-30 million Americans, with 80% estimated to have a genetic basis. This presents a challenge for genetics practitioners to determine appropriate testing, make accurate diagnoses, and conduct up-to-date patient management. Exome sequencing (ES) is a comprehensive diagnostic approach, but only 25%-41% of the patients receive a molecular diagnosis. The remaining three-fifths to three-quarters of patients undergoing ES remain undiagnosed. The Stanford Center for Undiagnosed Diseases (CUD), a clinical site of the Undiagnosed Diseases Network, evaluates patients with undiagnosed and rare diseases using a combination of methods including ES. Frequently these patients have non-diagnostic ES results, but strategic follow-up techniques identify diagnoses in a subset. We present techniques used at the CUD that can be adopted by genetics providers in clinical follow-up of cases where ES is non-diagnostic. Solved case examples illustrate different types of non-diagnostic results and the additional techniques that led to a diagnosis. Frequent approaches include segregation analysis, data reanalysis, genome sequencing, additional variant identification, careful phenotype-disease correlation, confirmatory testing, and case matching. We also discuss prioritization of cases for additional analyses.

  View details for PubMedID 30964584

• A Patient with Sjogren's Syndrome and Subsequent Diagnosis of Inclusion Body Myositis and Light-Chain Amyloidosis. Journal of general internal medicine Hom, J. n., Marwaha, S. n., Postolova, A. n., Kittle, J. n., Vasquez, R. n., Davidson, J. n., Kohler, J. n., Dries, A. n., Fernandez-Betancourt, L. n., Majcherska, M. n., Dearlove, J. n., Raghavan, S. n., Vogel, H. n., Bernstein, J. A., Fisher, P. n., Ashley, E. n., Sampson, J. n., Wheeler, M. n. 2019

  Abstract

  We discuss a challenging case of a 58-year-old Vietnamese-American woman who presented to her new primary care provider with an 8-year history of slowly progressive dysphagia, hoarseness, muscle weakness with associated frequent falls, and weight loss. She eventually reported dry eyes and dry mouth, and she was diagnosed with Sjogren's syndrome. Subsequently, she was additionally diagnosed with inclusion body myositis and gastric light-chain (AL) amyloidosis. Although inclusion body myositis has been previously associated with Sjogren's syndrome, inclusion body myositis is rare in non-Caucasians, and the trio of Sjogren's syndrome, inclusion body myositis, and AL amyloidosis has not been previously reported. Sjogren's syndrome is a systemic autoimmune condition characterized by ocular and oral dryness. It is one of the most common rheumatologic disorders in the USA and worldwide. Early diagnosis of Sjogren's is particularly important given the frequency and variety of associated autoimmune diseases and extraglandular manifestations. Furthermore, although inclusion body myositis has a low prevalence, it is the most common inflammatory myopathy in older adults and is unfortunately associated with long delays in diagnosis, so knowledge of this disorder is also crucial for practicing internists.

  View details for PubMedID 30887439

• Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nature medicine Frésard, L. n., Smail, C. n., Ferraro, N. M., Teran, N. A., Li, X. n., Smith, K. S., Bonner, D. n., Kernohan, K. D., Marwaha, S. n., Zappala, Z. n., Balliu, B. n., Davis, J. R., Liu, B. n., Prybol, C. J., Kohler, J. N., Zastrow, D. B., Reuter, C. M., Fisk, D. G., Grove, M. E., Davidson, J. M., Hartley, T. n., Joshi, R. n., Strober, B. J., Utiramerur, S. n., Lind, L. n., Ingelsson, E. n., Battle, A. n., Bejerano, G. n., Bernstein, J. A., Ashley, E. A., Boycott, K. M., Merker, J. D., Wheeler, M. T., Montgomery, S. B. 2019

  Abstract

  It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.

  View details for DOI 10.1038/s41591-019-0457-8

  View details for PubMedID 31160820

• High Frequency Actionable Pathogenic Exome Variants in an Average-Risk Cohort. Cold Spring Harbor molecular case studies Rego, S., Dagan-Rosenfeld, O., Zhou, W., Sailani, M. R., Limcaoco, P., Colbert, E., Avina, M., Wheeler, J., Craig, C., Salins, D., Rost, H. L., Dunn, J., McLaughlin, T., Steinmetz, L. M., Bernstein, J. A., Snyder, M. P. 2018

  Abstract

  Exome sequencing is increasingly utilized in both clinical and non-clinical settings, but little is known about its utility in healthy individuals. Most previous studies on this topic have examined a small subset of genes known to be implicated in human disease and/or have used automated pipelines to assess pathogenicity of known variants. In order to determine the frequency of both medically actionable and non-actionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multi-omics profiling study. We analyzed exomes by identifying rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We then used American College of Medical Genetics (ACMG) guidelines for the classification of rare sequence variants. Additionally, we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes. Five had phenotypes or family histories associated with their genetic variants. The frequency of actionable variants is higher than that reported in most previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 63 participants (90%) had additional non-actionable findings, including 60 who were found to be carriers for recessive diseases and 21 who have increased Alzheimer's disease risk due to heterozygous or homozygous APOE e4 alleles (18 participants had both). Our results suggest that exome sequencing may have considerable more utility for health management in the general population than previously thought.

  View details for PubMedID 30487145

• An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease. European journal of human genetics : EJHG Chen, H. I., Jagadeesh, K. A., Birgmeier, J., Wenger, A. M., Guturu, H., Schelley, S., Bernstein, J. A., Bejerano, G. 2018

  Abstract

  Approximately 2% of the human genome accounts for protein-coding genes, yet most known Mendelian disease-causing variants lie in exons or splice sites. Individuals who symptomatically present with monogenic disorders but do not possess function-altering variants in the protein-coding regions of causative genes may harbor variants in the surrounding gene regulatory domains. We present such a case: a male of Afghani descent was clinically diagnosed with Wilson Disease-a disorder of systemic copper buildup-but was found to have no function-altering coding variants in ATP7B (ENST00000242839.4), the typically causative gene. Our analysis revealed the homozygous variant chr13:g.52,586,149T>C (NC_000013.10, hg19) 676bp into the ATP7B promoter, which disrupts a metal regulatory transcription factor 1 (MTF1) binding site and diminishes expression of ATP7B in response to copper intake, likely resulting in Wilson Disease. Our approach to identify the causative variant can be generalized to systematically discover function-altering non-coding variants underlying disease and motivates evaluation of gene regulatory variants.

  View details for PubMedID 30087448

• Change in Prevalence of Orofacial Clefts in California between 1987 and 2010. American journal of medical genetics. Part A Andrew, T., Yang, W., Bernstein, J. A., Shaw, G. M. 2018

  Abstract

  INTRODUCTION: To extend the knowledge base about possible prevalence declines of specific orofacial cleft phenotypes, here we examine prevalence in a population base from California over a two-decade period among numerous race/ethnic groups.METHODS: This population-based study used vital statistics and birth defects registry data. Its population involved all births (~1.5 million births) in central California counties from 1987 to 2010. Orofacial clefts were defined as cleft lip with or without cleft palate (CLP, n=1766), and cleft palate (CP, n=922) only. The slope of prevalence of each cleft phenotype over the period 1987-2010 was estimated using weighted least squares regression.RESULTS: Birth prevalence of CLP was 121/100,000 live births, and 63/100,000 live births for CP. The slope for CLP decreased by 1.2 (slope: -1.2; 95% CI: -1.9, -0.5), and for CP by 0.7 (slope: -0.7; 95% CI: -1.7, 0.2) for CP. Stratification by race/ethnicity or infant sex did not demonstrate a statistical difference in slopes.CONCLUSIONS: We observed a decline in the prevalence in CLP in all ethnic groups, however did not observe the same amount of decline in CP, perhaps due to antenatal screening.

  View details for PubMedID 30063089

• Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization. Genetics in medicine : official journal of the American College of Medical Genetics Jagadeesh, K. A., Birgmeier, J., Guturu, H., Deisseroth, C. A., Wenger, A. M., Bernstein, J. A., Bejerano, G. 2018

  Abstract

  PURPOSE: Exome sequencing and diagnosis is beginning to spread across the medical establishment. The most time-consuming part of genome-based diagnosis is the manual step of matching the potentially long list of patient candidate genes to patient phenotypes to identify the causative disease.METHODS: We introduce Phrank (for phenotype ranking), an information theory-inspired method that utilizes a Bayesian network to prioritize candidate diseases or genes, as a stand-alone module that can be run with any underlying knowledgebase and any variant filtering scheme.RESULTS: Phrank outperforms existing methods at ranking the causative disease or gene when applied to 169 real patient exomes with Mendelian diagnoses. Phrank's greatest improvement is in disease space, where across all 169 patients it ranks only 3 diseases on average ahead of the true diagnosis, whereas Phenomizer ranks 32 diseases ahead of the causal one.CONCLUSIONS: Using Phrank to rank all patient candidate genes or diseases, as they start working through a new case, will save the busy clinician much time in deriving a genetic diagnosis.

  View details for PubMedID 29997393

• Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder AMERICAN JOURNAL OF HUMAN GENETICS Olahova, M., Yoon, W., Thompson, K., Jangam, S., Fernandez, L., Davidson, J. M., Kyle, J. E., Grove, M. E., Fisk, D. G., Kohler, J. N., Holmes, M., Dries, A. M., Huang, Y., Zhao, C., Contrepois, K., Zappala, Z., Fresard, L., Waggott, D., Zink, E. M., Kim, Y., Heyman, H. M., Stratton, K. G., Webb-Robertson, B. M., Snyder, M., Merker, J. D., Montgomery, S. B., Fisher, P. G., Feichtinger, R. G., Mayr, J. A., Hall, J., Barbosa, I. A., Simpson, M. A., Deshpande, C., Waters, K. M., Koeller, D. M., Metz, T. O., Morris, A. A., Schelley, S., Cowan, T., Friederich, M. W., McFarland, R., Van Hove, J. K., Enns, G. M., Yamamoto, S., Ashley, E. A., Wangler, M. F., Taylor, R. W., Bellen, H. J., Bernstein, J. A., Wheeler, M. T., Undiagnosed Diseases Network 2018; 102 (3): 494–504

  Abstract

  ATP synthase, H+ transporting, mitochondrial F1 complex, δ subunit (ATP5F1D; formerly ATP5D) is a subunit of mitochondrial ATP synthase and plays an important role in coupling proton translocation and ATP production. Here, we describe two individuals, each with homozygous missense variants in ATP5F1D, who presented with episodic lethargy, metabolic acidosis, 3-methylglutaconic aciduria, and hyperammonemia. Subject 1, homozygous for c.245C>T (p.Pro82Leu), presented with recurrent metabolic decompensation starting in the neonatal period, and subject 2, homozygous for c.317T>G (p.Val106Gly), presented with acute encephalopathy in childhood. Cultured skin fibroblasts from these individuals exhibited impaired assembly of F1FO ATP synthase and subsequent reduced complex V activity. Cells from subject 1 also exhibited a significant decrease in mitochondrial cristae. Knockdown of Drosophila ATPsynδ, the ATP5F1D homolog, in developing eyes and brains caused a near complete loss of the fly head, a phenotype that was fully rescued by wild-type human ATP5F1D. In contrast, expression of the ATP5F1D c.245C>T and c.317T>G variants rescued the head-size phenotype but recapitulated the eye and antennae defects seen in other genetic models of mitochondrial oxidative phosphorylation deficiency. Our data establish c.245C>T (p.Pro82Leu) and c.317T>G (p.Val106Gly) in ATP5F1D as pathogenic variants leading to a Mendelian mitochondrial disease featuring episodic metabolic decompensation.

  View details for PubMedID 29478781

• Prenatal treatment of ornithine transcarbamylase deficiency. Molecular genetics and metabolism Wilnai, Y. n., Blumenfeld, Y. J., Cusmano, K. n., Hintz, S. R., Alcorn, D. n., Benitz, W. E., Berquist, W. E., Bernstein, J. A., Castillo, R. O., Concepcion, W. n., Cowan, T. M., Cox, K. L., Lyell, D. J., Esquivel, C. O., Homeyer, M. n., Hudgins, L. n., Hurwitz, M. n., Palma, J. P., Schelley, S. n., Akula, V. P., Summar, M. L., Enns, G. M. 2018

  Abstract

  Patients with neonatal urea cycle defects (UCDs) typically experience severe hyperammonemia during the first days of life, which results in serious neurological injury or death. Long-term prognosis despite optimal pharmacological and dietary therapy is still poor. The combination of intravenous sodium phenylacetate and sodium benzoate (Ammonul®) can eliminate nitrogen waste independent of the urea cycle. We report attempts to improve outcomes for males with severe ornithine transcarbamylase deficiency (OTCD), a severe X-linked condition, via prenatal intravenous administration of Ammonul and arginine to heterozygous carrier females of OTCD during labor.Two heterozygote OTCD mothers carrying male fetuses with a prenatal diagnosis of OTCD received intravenous Ammonul, arginine and dextrose-containing fluids shortly before birth. Maintenance Ammonul and arginine infusions and high-caloric enteral nutrition were started immediately after birth. Ammonul metabolites were measured in umbilical cord blood and the blood of the newborn immediately after delivery. Serial ammonia and biochemical analyses were performed following delivery.Therapeutic concentrations of Ammonul metabolites were detected in umbilical cord and neonatal blood samples. Plasma ammonia and glutamine levels in the postnatal period were within the normal range. Peak ammonia levels in the first 24-48h were 53mcmol/l and 62mcmol/l respectively. The boys did not experience neurological sequelae secondary to hyperammonemia and received liver transplantation at ages 3months and 5months. The patients show normal development at ages 7 and 3years.Prenatal treatment of mothers who harbor severe OTCD mutations and carry affected male fetuses with intravenous Ammonul and arginine, followed by immediate institution of maintenance infusions after delivery, results in therapeutic levels of benzoate and phenylacetate in the newborn at delivery and, in conjunction with high-caloric enteral nutrition, prevents acute hyperammonemia and neurological decompensation. Following initial medical management, early liver transplantation may improve developmental outcome.

  View details for PubMedID 29396029

• MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance. American journal of human genetics Dobyns, W. B., Aldinger, K. A., Ishak, G. E., Mirzaa, G. M., Timms, A. E., Grout, M. E., Dremmen, M. H., Schot, R. n., Vandervore, L. n., van Slegtenhorst, M. A., Wilke, M. n., Kasteleijn, E. n., Lee, A. S., Barry, B. J., Chao, K. R., Szczałuba, K. n., Kobori, J. n., Hanson-Kahn, A. n., Bernstein, J. A., Carr, L. n., D'Arco, F. n., Miyana, K. n., Okazaki, T. n., Saito, Y. n., Sasaki, M. n., Das, S. n., Wheeler, M. M., Bamshad, M. J., Nickerson, D. A., Engle, E. C., Verheijen, F. W., Doherty, D. n., Mancini, G. M. 2018

  Abstract

  To date, mutations in 15 actin- or microtubule-associated genes have been associated with the cortical malformation lissencephaly and variable brainstem hypoplasia. During a multicenter review, we recognized a rare lissencephaly variant with a complex brainstem malformation in three unrelated children. We searched our large brain-malformation databases and found another five children with this malformation (as well as one with a less severe variant), analyzed available whole-exome or -genome sequencing data, and tested ciliogenesis in two affected individuals. The brain malformation comprised posterior predominant lissencephaly and midline crossing defects consisting of absent anterior commissure and a striking W-shaped brainstem malformation caused by small or absent pontine crossing fibers. We discovered heterozygous de novo missense variants or an in-frame deletion involving highly conserved zinc-binding residues within the GAR domain of MACF1 in the first eight subjects. We studied cilium formation and found a higher proportion of mutant cells with short cilia than of control cells with short cilia. A ninth child had similar lissencephaly but only subtle brainstem dysplasia associated with a heterozygous de novo missense variant in the spectrin repeat domain of MACF1. Thus, we report variants of the microtubule-binding GAR domain of MACF1 as the cause of a distinctive and most likely pathognomonic brain malformation. A gain-of-function or dominant-negative mechanism appears likely given that many heterozygous mutations leading to protein truncation are included in the ExAC Browser. However, three de novo variants in MACF1 have been observed in large schizophrenia cohorts.

  View details for DOI 10.1016/j.ajhg.2018.10.019

  View details for PubMedID 30471716

• Mutations in MAST1 Cause Mega-Corpus-Callosum Syndrome with Cerebellar Hypoplasia and Cortical Malformations. Neuron Tripathy, R. n., Leca, I. n., van Dijk, T. n., Weiss, J. n., van Bon, B. W., Sergaki, M. C., Gstrein, T. n., Breuss, M. n., Tian, G. n., Bahi-Buisson, N. n., Paciorkowski, A. R., Pagnamenta, A. T., Wenninger-Weinzierl, A. n., Martinez-Reza, M. F., Landler, L. n., Lise, S. n., Taylor, J. C., Terrone, G. n., Vitiello, G. n., Del Giudice, E. n., Brunetti-Pierri, N. n., D'Amico, A. n., Reymond, A. n., Voisin, N. n., Bernstein, J. A., Farrelly, E. n., Kini, U. n., Leonard, T. A., Valence, S. n., Burglen, L. n., Armstrong, L. n., Hiatt, S. M., Cooper, G. M., Aldinger, K. A., Dobyns, W. B., Mirzaa, G. n., Pierson, T. M., Baas, F. n., Chelly, J. n., Cowan, N. J., Keays, D. A. 2018

  Abstract

  Corpus callosum malformations are associated with a broad range of neurodevelopmental diseases. We report that de novo mutations in MAST1 cause mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations (MCC-CH-CM) in the absence of megalencephaly. We show that MAST1 is a microtubule-associated protein that is predominantly expressed in post-mitotic neurons and is present in both dendritic and axonal compartments. We further show that Mast1 null animals are phenotypically normal, whereas the deletion of a single amino acid (L278del) recapitulates the distinct neurological phenotype observed in patients. In animals harboring Mast1 microdeletions, we find that the PI3K/AKT3/mTOR pathway is unperturbed, whereas Mast2 and Mast3 levels are diminished, indicative of a dominant-negative mode of action. Finally, we report that de novo MAST1 substitutions are present in patients with autism and microcephaly, raising the prospect that mutations in this gene give rise to a spectrum of neurodevelopmental diseases.

  View details for DOI 10.1016/j.neuron.2018.10.044

  View details for PubMedID 30449657

• Ethical Issues in Contemporary Clinical Genetics. Mayo Clinic proceedings. Innovations, quality & outcomes Braverman, G. n., Shapiro, Z. E., Bernstein, J. A. 2018; 2 (2): 81–90

  Abstract

  As genetic sequencing capabilities become more powerful and costs decline, the reach of genomics is expanding beyond research laboratories to the wards, outpatient clinics, and, with the marketing of direct-to-consumer testing services, patients' homes. Increasingly, patients receiving various diagnoses-from cancer to cardiomyopathy-can reasonably expect to have conversations with their providers about indications for genetic testing. In this dynamic context, a grasp of the ethical principles and history underlying clinical genetics will provide clinicians with the tools to guide their practice and help patients navigate complex medical-psychosocial terrain. This article provides an overview of the salient ethical concerns pertaining to clinical genetics. The subject is approached with an emphasis on clinical practice, but consideration is also given to research. The review is organized around the temporal and informational sequence of issues commonly arising during the course of pretesting, testing, and posttesting phases of patient care. Drawing from medical, legal, and historical perspectives, this review covers the following topics: (1) informed consent, (2) return of results, and (3) privacy and confidentiality, and intends to equip readers with an appropriate foundation to apply ethical principles to genetic testing paradigms with an understanding of the contextual landscape against which these situations occur.

  View details for PubMedID 30225437

• Volumetric Analysis of the Basal Ganglia and Cerebellar Structures in Patients with Phelan-McDermid Syndrome. Pediatric neurology Srivastava, S. n., Scherrer, B. n., Prohl, A. K., Filip-Dhima, R. n., Kapur, K. n., Kolevzon, A. n., Buxbaum, J. D., Berry-Kravis, E. n., Soorya, L. n., Thurm, A. n., Powell, C. M., Bernstein, J. A., Warfield, S. K., Sahin, M. n. 2018

  Abstract

  Phelan-McDermid syndrome is caused by haploinsufficiency of SHANK3 on terminal chromosome 22. Knowledge about altered neuroanatomic circuitry in Phelan-McDermid syndrome comes from mouse models showing striatal hypertrophy in the basal ganglia, and from humans with evidence of cerebellar atrophy. To date, no studies have performed volumetric analysis on Phelan-McDermid syndrome patients.We performed volumetric analysis on baseline brain MRIs of Phelan-McDermid syndrome patients (ages three to 21 years) enrolled in a prospective natural history study (ClinicalTrials.gov NCT02461420). Using MRI segmentations carried out with PSTAPLE algorithm, we measured relative volumes (volume of the structure divided by the volume of the brain parenchyma) of basal ganglia and cerebellar structures. We compared these measurements to those of age- and sex-matched healthy controls part of another study. Among the patients, we performed linear regression of each relative volume using Repetitive Behavior Scale-Revised total score and Aberrant Behavior Checklist stereotypy score. Eleven patients with Phelan-McDermid syndrome (six females, five males) and 11 healthy controls were in this analysis.At time of MRI, the mean age of the patients and controls was 9.24 (5.29) years and 9.00 (4.49) years, respectively (P = 0.66). Compared to controls, patients had decreased caudate (P ≤ 0.013), putamen (P ≤ 0.026), and left pallidum (P = 0.033) relative volumes. Relative volume of cerebellar vermal lobules I to V (beta coefficient = -17119, P = 0.017) decreased with increasing Repetitive Behavior Scale-Revised total score.The volumes of the striatum and left pallidum are decreased in individuals with Phelan-McDermid syndrome. Cerebellar vermis volume may predict repetitive behavior severity in Phelan-McDermid syndrome. These findings warrant further investigation in larger samples.

  View details for PubMedID 30396833

• ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis. Genetics in medicine : official journal of the American College of Medical Genetics Deisseroth, C. A., Birgmeier, J. n., Bodle, E. E., Kohler, J. N., Matalon, D. R., Nazarenko, Y. n., Genetti, C. A., Brownstein, C. A., Schmitz-Abe, K. n., Schoch, K. n., Cope, H. n., Signer, R. n., Martinez-Agosto, J. A., Shashi, V. n., Beggs, A. H., Wheeler, M. T., Bernstein, J. A., Bejerano, G. n. 2018

  Abstract

  Diagnosing monogenic diseases facilitates optimal care, but can involve the manual evaluation of hundreds of genetic variants per case. Computational tools like Phrank expedite this process by ranking all candidate genes by their ability to explain the patient's phenotypes. To use these tools, busy clinicians must manually encode patient phenotypes from lengthy clinical notes. With 100 million human genomes estimated to be sequenced by 2025, a fast alternative to manual phenotype extraction from clinical notes will become necessary.We introduce ClinPhen, a fast, high-accuracy tool that automatically converts clinical notes into a prioritized list of patient phenotypes using Human Phenotype Ontology (HPO) terms.ClinPhen shows superior accuracy and 20× speedup over existing phenotype extractors, and its novel phenotype prioritization scheme improves the performance of gene-ranking tools.While a dedicated clinician can process 200 patient records in a 40-hour workweek, ClinPhen does the same in 10 minutes. Compared with manual phenotype extraction, ClinPhen saves an additional 3-5 hours per Mendelian disease diagnosis. Providers can now add ClinPhen's output to each summary note attached to a filled testing laboratory request form. ClinPhen makes a substantial contribution to improvements in efficiency critically needed to meet the surging demand for clinical diagnostic sequencing.

  View details for PubMedID 30514889

• De Novo Missense Variants in TRAF7 Cause Developmental Delay, Congenital Anomalies, and Dysmorphic Features. American journal of human genetics Tokita, M. J., Chen, C. A., Chitayat, D. n., Macnamara, E. n., Rosenfeld, J. A., Hanchard, N. n., Lewis, A. M., Brown, C. W., Marom, R. n., Shao, Y. n., Novacic, D. n., Wolfe, L. n., Wahl, C. n., Tifft, C. J., Toro, C. n., Bernstein, J. A., Hale, C. L., Silver, J. n., Hudgins, L. n., Ananth, A. n., Hanson-Kahn, A. n., Shuster, S. n., Magoulas, P. L., Patel, V. N., Zhu, W. n., Chen, S. M., Jiang, Y. n., Liu, P. n., Eng, C. M., Batkovskyte, D. n., di Ronza, A. n., Sardiello, M. n., Lee, B. H., Schaaf, C. P., Yang, Y. n., Wang, X. n. 2018

  Abstract

  TRAF7 is a multi-functional protein involved in diverse signaling pathways and cellular processes. The phenotypic consequence of germline TRAF7 variants remains unclear. Here we report missense variants in TRAF7 in seven unrelated individuals referred for clinical exome sequencing. The seven individuals share substantial phenotypic overlap, with developmental delay, congenital heart defects, limb and digital anomalies, and dysmorphic features emerging as key unifying features. The identified variants are de novo in six individuals and comprise four distinct missense changes, including a c.1964G>A (p.Arg655Gln) variant that is recurrent in four individuals. These variants affect evolutionarily conserved amino acids and are located in key functional domains. Gene-specific mutation rate analysis showed that the occurrence of the de novo variants in TRAF7 (p = 2.6 × 10-3) and the recurrent de novo c.1964G>A (p.Arg655Gln) variant (p = 1.9 × 10-8) in our exome cohort was unlikely to have occurred by chance. In vitro analyses of the observed TRAF7 mutations showed reduced ERK1/2 phosphorylation. Our findings suggest that missense mutations in TRAF7 are associated with a multisystem disorder and provide evidence of a role for TRAF7 in human development.

  View details for PubMedID 29961569

• Exploring the Medical and Psychosocial Concerns of Adolescents and Young Adults With Craniofacial Microsomia: A Qualitative Study. The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association Hamilton, K. V., Ormond, K. E., Moscarello, T. n., Bruce, J. S., Bereknyei Merrell, S. n., Chang, K. W., Bernstein, J. A. 2018: 1055665618768542

  Abstract

  This study explores the experiences of adolescents and young adults with craniofacial microsomia, including the impact of growing up with this craniofacial condition on daily life and sense of self. The results may guide future research on optimally supporting individuals with craniofacial microsomia during this critical life phase.Participants were recruited through a craniofacial center, online patient support groups, and social media sites. Eleven individual semistructured interviews with participants between 12 and 22 years old were conducted by a single interviewer, transcribed, iteratively coded, and thematically analyzed.Five themes were evident in the data: (1) impact on personal growth and character development, (2) negative psychosocial impact, (3) deciding to hide or reveal the condition, (4) desire to make personal surgical decisions, and (5) struggles with hearing loss.We identified both medical and psychosocial concerns prevalent among adolescents with craniofacial microsomia. Although adolescents with craniofacial microsomia exhibit considerable resilience, the challenges they face impact their sense of self and should be addressed through psychosocial support and counseling. Further research should investigate the potential benefit of the wider use of hearing aids, as well as the involvement of patients in decision-making about reconstructive ear surgery.

  View details for PubMedID 29634364

• Biallelic loss-of-function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome. American journal of medical genetics. Part A Birgmeier, J. n., Esplin, E. D., Jagadeesh, K. A., Guturu, H. n., Wenger, A. M., Chaib, H. n., Buckingham, J. A., Bejerano, G. n., Bernstein, J. A. 2018; 176 (4): 1030–36

  Abstract

  Robinow syndrome (RS) is a well-recognized Mendelian disorder known to demonstrate both autosomal dominant and autosomal recessive inheritance. Typical manifestations include short stature, characteristic facies, and skeletal anomalies. Recessive inheritance has been associated with mutations in ROR2 while dominant inheritance has been observed for mutations in WNT5A, DVL1, and DVL3. Through trio whole genome sequencing, we identified a homozygous frameshifting single nucleotide deletion in WNT5A in a previously reported, deceased infant with a unique constellation of features comprising a 46,XY disorder of sex development with multiple congenital malformations including congenital diaphragmatic hernia, ambiguous genitalia, dysmorphic facies, shortened long bones, adactyly, and ventricular septal defect. The parents, who are both heterozygous for the deletion, appear clinically unaffected. In conjunction with published observations of Wnt5a double knockout mice, we provide evidence for the possibility of autosomal recessive inheritance in association with WNT5A loss-of-function mutations in RS.

  View details for PubMedID 29575631

• Genotype-phenotype correlations in individuals with pathogenic RERE variants. Human mutation Jordan, V. K., Fregeau, B. n., Ge, X. n., Giordano, J. n., Wapner, R. J., Balci, T. B., Carter, M. T., Bernat, J. A., Moccia, A. N., Srivastava, A. n., Martin, D. M., Bielas, S. L., Pappas, J. n., Svoboda, M. D., Rio, M. n., Boddaert, N. n., Cantagrel, V. n., Lewis, A. M., Scaglia, F. n., Kohler, J. N., Bernstein, J. A., Dries, A. M., Rosenfeld, J. A., DeFilippo, C. n., Thorson, W. n., Yang, Y. n., Sherr, E. H., Bi, W. n., Scott, D. A. 2018

  Abstract

  Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies and sensorineural hearing loss when compared to loss-of-function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine-rich region in the Atrophin-1 domain. We have also identified a recurrent two-amino-acid duplication in this region that is associated with the development of a CHARGE syndrome-like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype-phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7. This article is protected by copyright. All rights reserved.

  View details for PubMedID 29330883

• Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease. The New England journal of medicine Splinter, K. n., Adams, D. R., Bacino, C. A., Bellen, H. J., Bernstein, J. A., Cheatle-Jarvela, A. M., Eng, C. M., Esteves, C. n., Gahl, W. A., Hamid, R. n., Jacob, H. J., Kikani, B. n., Koeller, D. M., Kohane, I. S., Lee, B. H., Loscalzo, J. n., Luo, X. n., McCray, A. T., Metz, T. O., Mulvihill, J. J., Nelson, S. F., Palmer, C. G., Phillips, J. A., Pick, L. n., Postlethwait, J. H., Reuter, C. n., Shashi, V. n., Sweetser, D. A., Tifft, C. J., Walley, N. M., Wangler, M. F., Westerfield, M. n., Wheeler, M. T., Wise, A. L., Worthey, E. A., Yamamoto, S. n., Ashley, E. A. 2018

  Abstract

  Many patients remain without a diagnosis despite extensive medical evaluation. The Undiagnosed Diseases Network (UDN) was established to apply a multidisciplinary model in the evaluation of the most challenging cases and to identify the biologic characteristics of newly discovered diseases. The UDN, which is funded by the National Institutes of Health, was formed in 2014 as a network of seven clinical sites, two sequencing cores, and a coordinating center. Later, a central biorepository, a metabolomics core, and a model organisms screening center were added.We evaluated patients who were referred to the UDN over a period of 20 months. The patients were required to have an undiagnosed condition despite thorough evaluation by a health care provider. We determined the rate of diagnosis among patients who subsequently had a complete evaluation, and we observed the effect of diagnosis on medical care.A total of 1519 patients (53% female) were referred to the UDN, of whom 601 (40%) were accepted for evaluation. Of the accepted patients, 192 (32%) had previously undergone exome sequencing. Symptoms were neurologic in 40% of the applicants, musculoskeletal in 10%, immunologic in 7%, gastrointestinal in 7%, and rheumatologic in 6%. Of the 382 patients who had a complete evaluation, 132 received a diagnosis, yielding a rate of diagnosis of 35%. A total of 15 diagnoses (11%) were made by clinical review alone, and 98 (74%) were made by exome or genome sequencing. Of the diagnoses, 21% led to recommendations regarding changes in therapy, 37% led to changes in diagnostic testing, and 36% led to variant-specific genetic counseling. We defined 31 new syndromes.The UDN established a diagnosis in 132 of the 382 patients who had a complete evaluation, yielding a rate of diagnosis of 35%. (Funded by the National Institutes of Health Common Fund.).

  View details for PubMedID 30304647

• A New Approach to Rare Diseases of Children: The Undiagnosed Diseases Network. The Journal of pediatrics Reuter, C. M., Brimble, E. n., DeFilippo, C. n., Dries, A. M., Enns, G. M., Ashley, E. A., Bernstein, J. A., Fisher, P. G., Wheeler, M. T. 2018

  View details for PubMedID 29331327

• Isolated Congenital Anosmia and CNGA2 Mutation. Scientific reports Sailani, M. R., Jingga, I., MirMazlomi, S. H., Bitarafan, F., Bernstein, J. A., Snyder, M. P., Garshasbi, M. 2017; 7 (1): 2667-?

  Abstract

  Isolated congenital anosmia (ICA) is a rare condition that is associated with life-long inability to smell. Here we report a genetic characterization of a large Iranian family segregating ICA. Whole exome sequencing in five affected family members and five healthy members revealed a stop gain mutation in CNGA2 (OMIM 300338) (chrX:150,911,102; CNGA2. c.577C > T; p.Arg193*). The mutation segregates in an X-linked pattern, as all the affected family members are hemizygotes, whereas healthy family members are either heterozygote or homozygote for the reference allele. cnga2 knockout mice are congenitally anosmic and have abnormal olfactory system physiology, additionally Karstensen et al. recently reported two anosmic brothers sharing a CNGA2 truncating variant. Our study in concert with these findings provides strong support for role of CNGA2 gene with pathogenicity of ICA in humans. Together, these results indicate that mutations in key olfactory signaling pathway genes are responsible for human disease.

  View details for DOI 10.1038/s41598-017-02947-y

  View details for PubMedID 28572688

• Assembly of functionally integrated human forebrain spheroids NATURE Birey, F., Andersen, J., Makinson, C. D., Islam, S., Wei, W., Huber, N., Fan, H. C., Metzler, K. R., Panagiotakos, G., Thom, N., O'Rourke, N. A., Steinmetz, L. M., Bernstein, J. A., Hallmayer, J., Huguenard, J. R., Pasca, S. P. 2017; 545 (7652): 54-?

  Abstract

  The development of the nervous system involves a coordinated succession of events including the migration of GABAergic (γ-aminobutyric-acid-releasing) neurons from ventral to dorsal forebrain and their integration into cortical circuits. However, these interregional interactions have not yet been modelled with human cells. Here we generate three-dimensional spheroids from human pluripotent stem cells that resemble either the dorsal or ventral forebrain and contain cortical glutamatergic or GABAergic neurons. These subdomain-specific forebrain spheroids can be assembled in vitro to recapitulate the saltatory migration of interneurons observed in the fetal forebrain. Using this system, we find that in Timothy syndrome-a neurodevelopmental disorder that is caused by mutations in the CaV1.2 calcium channel-interneurons display abnormal migratory saltations. We also show that after migration, interneurons functionally integrate with glutamatergic neurons to form a microphysiological system. We anticipate that this approach will be useful for studying neural development and disease, and for deriving spheroids that resemble other brain regions to assemble circuits in vitro.

  View details for DOI 10.1038/nature22330

  View details for PubMedID 28445465

• Characterizing regression in Phelan McDermid Syndrome (22q13 deletion syndrome). Journal of psychiatric research Reierson, G., Bernstein, J., Froehlich-Santino, W., Urban, A., Purmann, C., Berquist, S., Jordan, J., O'Hara, R., Hallmayer, J. 2017; 91: 139-144

  Abstract

  To describe the frequency and characteristics of developmental regression in a sample of 50 patients with Phelan McDermid Syndrome (PMS) and investigate the possibility of association between regression, epilepsy, and electroencephalogram (EEG) abnormalities and deletion size.The Autism Diagnostic Interview-Revised (ADI-R) was used to evaluate regression in patients with a confirmed diagnosis of PMS. Information on seizure history and EEGs was obtained from medical record review. Deletion size was determined by DNA microarray.A history of regression at any age was present in 43% of all patients. Among those exhibiting regression, 67% had onset after the age of 30 months, affecting primarily motor and self-help skills. In 63% of all patients there was a history of seizures and a history of abnormal EEG was also present in 71%. No significant associations were found between regression and seizures or EEG abnormalities. Deletion size was significantly associated with EEG abnormalities, but not with regression or seizures.This study found a high rate of regression in PMS. In contrast to regression in autism, that often occurs earlier in development and affects language and social skills, we found regression in PMS most frequently has an onset in mid-childhood, affecting motor and self-help skills. We also found high rates of seizures and abnormal EEGs in patients with PMS. However, a history of abnormal EEG and seizures was not associated with an increased risk of regression. Larger deletion sizes were found to be significantly associated with a history of abnormal EEG.

  View details for DOI 10.1016/j.jpsychires.2017.03.010

  View details for PubMedID 28346892

• Association of AHSG with alopecia and mental retardation (APMR) syndrome. Human genetics Reza Sailani, M., Jahanbani, F., Nasiri, J., Behnam, M., Salehi, M., Sedghi, M., Hoseinzadeh, M., Takahashi, S., Zia, A., Gruber, J., Lynch, J. L., Lam, D., Winkelmann, J., Amirkiai, S., Pang, B., Rego, S., Mazroui, S., Bernstein, J. A., Snyder, M. P. 2017; 136 (3): 287-296

  Abstract

  Alopecia with mental retardation syndrome (APMR) is a very rare autosomal recessive condition that is associated with total or partial absence of hair from the scalp and other parts of the body as well as variable intellectual disability. Here we present whole-exome sequencing results of a large consanguineous family segregating APMR syndrome with seven affected family members. Our study revealed a novel predicted pathogenic, homozygous missense mutation in the AHSG (OMIM 138680) gene (AHSG: NM_001622:exon7:c.950G>A:p.Arg317His). The variant is predicted to affect a region of the protein required for protein processing and disrupts a phosphorylation motif. In addition, the altered protein migrates with an aberrant size relative to healthy individuals. Consistent with the phenotype, AHSG maps within APMR linkage region 1 (APMR 1) as reported before, and falls within runs of homozygosity (ROH). Previous families with APMR syndrome have been studied through linkage analyses and the linkage resolution did not allow pointing out to a single gene candidate. Our study is the first report to identify a homozygous missense mutation for APMR syndrome through whole-exome sequencing.

  View details for DOI 10.1007/s00439-016-1756-5

  View details for PubMedID 28054173

• The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease AMERICAN JOURNAL OF HUMAN GENETICS Ramoni, R. B., Mulvihill, J. J., Adams, D. R., Allard, P., Ashley, E. A., Bernstein, J. A., Gahl, W. A., Hamid, R., Loscalzo, J., McCray, A. T., Shashi, V., Tifft, C. J., Wise, A. L. 2017; 100 (2): 185-192

  Abstract

  Diagnosis at the edges of our knowledge calls upon clinicians to be data driven, cross-disciplinary, and collaborative in unprecedented ways. Exact disease recognition, an element of the concept of precision in medicine, requires new infrastructure that spans geography, institutional boundaries, and the divide between clinical care and research. The National Institutes of Health (NIH) Common Fund supports the Undiagnosed Diseases Network (UDN) as an exemplar of this model of precise diagnosis. Its goals are to forge a strategy to accelerate the diagnosis of rare or previously unrecognized diseases, to improve recommendations for clinical management, and to advance research, especially into disease mechanisms. The network will achieve these objectives by evaluating patients with undiagnosed diseases, fostering a breadth of expert collaborations, determining best practices for translating the strategy into medical centers nationwide, and sharing findings, data, specimens, and approaches with the scientific and medical communities. Building the UDN has already brought insights to human and medical geneticists. The initial focus has been on data sharing, establishing common protocols for institutional review boards and data sharing, creating protocols for referring and evaluating patients, and providing DNA sequencing, metabolomic analysis, and functional studies in model organisms. By extending this precision diagnostic model nationally, we strive to meld clinical and research objectives, improve patient outcomes, and contribute to medical science.

  View details for DOI 10.1016/j.athg.2017.01.006

  View details for PubMedID 28157539

• Sleep Disturbances in Individuals With Phelan-McDermid Syndrome: Correlation With Caregivers' Sleep Quality and Daytime Functioning SLEEP Bro, D., O'Hara, R., Primeau, M., Hanson-Kahn, A., Hallmayer, J., Bernstein, J. A. 2017; 40 (2)

  Abstract

  The aims of this study were to document sleep disturbances in individuals with Phelan-McDermid syndrome (PMS), to assess whether these individuals had been evaluated for sleep disorders, and to examine relationships between the sleep behavior of these individuals and the sleep behavior and daytime functioning of their caregivers.Participants were 193 caregivers of individuals with PMS recruited by the Phelan-McDermid Syndrome Foundation. Data were collected through a survey comprising 2 questionnaires: the Children's Sleep Habits Questionnaire (CSHQ) and the Parents' Sleep Habits Questionnaire. Data were analyzed using multiple linear regression analyses, Pearson correlation analyses, and independent-samples t-tests.Ninety percent of individuals with PMS showed evidence of marked sleep disturbance based on caregiver responses to the CSHQ. However, only 22% of individuals had undergone a formal sleep assessment. Reported increased sleep disturbance in individuals with PMS was a statistically significant predictor of reported increased sleep disturbance and daytime sleepiness in their caregivers.Sleep disturbance may be present in a substantial proportion of individuals with PMS and is negatively associated with caregivers' well-being. However, most individuals with PMS have not been evaluated for sleep disorders. When properly diagnosed, many sleep disorders can be alleviated with intervention. Thus, routine screening for and evaluation of sleep disturbances in individuals with PMS may have long-term positive impacts on the well-being of these individuals and their caregivers.

  View details for DOI 10.1093/sleep/zsw062

  View details for PubMedID 28364490

• De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease GENOME MEDICINE Takahashi, S., Andreoletti, G., Chen, R., Munehira, Y., Batra, A., Afzal, N. A., Beattie, R. M., Bernstein, J. A., Ennis, S., Snyder, M. 2017; 9

  Abstract

  Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disease of the gastrointestinal tract which includes ulcerative colitis and Crohn's disease. Genetic risk factors for IBD are not well understood.We performed a family-based whole exome sequencing (WES) analysis on a core family (Family A) to identify potential causal mutations and then analyzed exome data from a Caucasian pediatric cohort (136 patients and 106 controls) to validate the presence of mutations in the candidate gene, heat shock 70 kDa protein 1-like (HSPA1L). Biochemical assays of the de novo and rare (minor allele frequency, MAF < 0.01) mutation variant proteins further validated the predicted deleterious effects of the identified alleles.In the proband of Family A, we found a heterozygous de novo mutation (c.830C > T; p.Ser277Leu) in HSPA1L. Through analysis of WES data of 136 patients, we identified five additional rare HSPA1L mutations (p.Gly77Ser, p.Leu172del, p.Thr267Ile, p.Ala268Thr, p.Glu558Asp) in six patients. In contrast, rare HSPA1L mutations were not observed in controls, and were significantly enriched in patients (P = 0.02). Interestingly, we did not find non-synonymous rare mutations in the HSP70 isoforms HSPA1A and HSPA1B. Biochemical assays revealed that all six rare HSPA1L variant proteins showed decreased chaperone activity in vitro. Moreover, three variants demonstrated dominant negative effects on HSPA1L and HSPA1A protein activity.Our results indicate that de novo and rare mutations in HSPA1L are associated with IBD and provide insights into the pathogenesis of IBD, and also expand our understanding of the roles of HSP70s in human disease.

  View details for DOI 10.1186/s13073-016-0394-9

  View details for PubMedID 28126021

• The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nature genetics Redin, C., Brand, H., Collins, R. L., Kammin, T., Mitchell, E., Hodge, J. C., Hanscom, C., Pillalamarri, V., Seabra, C. M., Abbott, M., Abdul-Rahman, O. A., Aberg, E., Adley, R., Alcaraz-Estrada, S. L., Alkuraya, F. S., An, Y., Anderson, M., Antolik, C., Anyane-Yeboa, K., Atkin, J. F., Bartell, T., Bernstein, J. A., Beyer, E., Blumenthal, I., Bongers, E. M., Brilstra, E. H., Brown, C. W., Brüggenwirth, H. T., Callewaert, B., Chiang, C., Corning, K., Cox, H., Cuppen, E., Currall, B. B., Cushing, T., David, D., Deardorff, M. A., Dheedene, A., D'Hooghe, M., de Vries, B. B., Earl, D. L., Ferguson, H. L., Fisher, H., FitzPatrick, D. R., Gerrol, P., Giachino, D., Glessner, J. T., Gliem, T., Grady, M., Graham, B. H., Griffis, C., Gripp, K. W., Gropman, A. L., Hanson-Kahn, A., Harris, D. J., Hayden, M. A., Hill, R., Hochstenbach, R., Hoffman, J. D., Hopkin, R. J., Hubshman, M. W., Innes, A. M., Irons, M., Irving, M., Jacobsen, J. C., Janssens, S., Jewett, T., Johnson, J. P., Jongmans, M. C., Kahler, S. G., Koolen, D. A., Korzelius, J., Kroisel, P. M., Lacassie, Y., Lawless, W., Lemyre, E., Leppig, K., Levin, A. V., Li, H., Li, H., Liao, E. C., Lim, C., Lose, E. J., Lucente, D., Macera, M. J., Manavalan, P., Mandrile, G., Marcelis, C. L., Margolin, L., Mason, T., Masser-Frye, D., McClellan, M. W., Mendoza, C. J., Menten, B., Middelkamp, S., Mikami, L. R., Moe, E., Mohammed, S., Mononen, T., Mortenson, M. E., Moya, G., Nieuwint, A. W., Ordulu, Z., Parkash, S., Pauker, S. P., Pereira, S., Perrin, D., Phelan, K., Aguilar, R. E., Poddighe, P. J., Pregno, G., Raskin, S., Reis, L., Rhead, W., Rita, D., Renkens, I., Roelens, F., Ruliera, J., Rump, P., Schilit, S. L., Shaheen, R., Sparkes, R., Spiegel, E., Stevens, B., Stone, M. R., Tagoe, J., Thakuria, J. V., van Bon, B. W., van de Kamp, J., van der Burgt, I., van Essen, T., van Ravenswaaij-Arts, C. M., van Roosmalen, M. J., Vergult, S., Volker-Touw, C. M., Warburton, D. P., Waterman, M. J., Wiley, S., Wilson, A., Yerena-de Vega, M. d., Zori, R. T., Levy, B., Brunner, H. G., de Leeuw, N., Kloosterman, W. P., Thorland, E. C., Morton, C. C., Gusella, J. F., Talkowski, M. E. 2017; 49 (1): 36-45

  Abstract

  Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology.

  View details for DOI 10.1038/ng.3720

  View details for PubMedID 27841880

• Clinical and molecular characterization of de novo loss of function variants in HNRNPU. American journal of medical genetics. Part A Leduc, M. S., Chao, H. T., Qu, C. n., Walkiewicz, M. n., Xiao, R. n., Magoulas, P. n., Pan, S. n., Beuten, J. n., He, W. n., Bernstein, J. A., Schaaf, C. P., Scaglia, F. n., Eng, C. M., Yang, Y. n. 2017

  Abstract

  DNA alterations in the 1q43-q44 region are associated with syndromic neurodevelopmental disorders characterized by global developmental delay, intellectual disability, dysmorphic features, microcephaly, seizures, and agenesis of the corpus callosum. HNRNPU is located within the 1q43-q44 region and mutations in the gene have been reported in patients with early infantile epileptic encephalopathy. Here, we report on the clinical presentation of four patients with de novo heterozygous HNRNPU loss-of-function mutations detected by clinical whole exome sequencing: c.651_660del (p.Gly218Alafs*118), c.1089G>A (p.Trp363*), c.1714C>T (p.Arg572*), and c.2270_2271del (p.Pro757Argfs*7). All patients shared similar clinical features as previously reported including seizures, global developmental delay, intellectual disability, variable neurologic regression, behavior issues, and dysmorphic facial features. Features including heart defects and kidney abnormalities were not reported in our patients. These findings expands the clinical spectrum of HNRNPU-related disorder and shows that HNRNPU contributes to a subset of the clinical phenotypes associated with the contiguous 1q43-q44 deletion syndrome.

  View details for PubMedID 28815871

• New insights into mitral valve dystrophy: a Filamin-A genotype-phenotype and outcome study. European heart journal Le Tourneau, T. n., Le Scouarnec, S. n., Cueff, C. n., Bernstein, D. n., Aalberts, J. J., Lecointe, S. n., Mérot, J. n., Bernstein, J. A., Oomen, T. n., Dina, C. n., Karakachoff, M. n., Desal, H. n., Al Habash, O. n., Delling, F. N., Capoulade, R. n., Suurmeijer, A. J., Milan, D. n., Norris, R. A., Markwald, R. n., Aikawa, E. n., Slaugenhaupt, S. A., Jeunemaitre, X. n., Hagège, A. n., Roussel, J. C., Trochu, J. N., Levine, R. A., Kyndt, F. n., Probst, V. n., Le Marec, H. n., Schott, J. J. 2017

  Abstract

  Filamin-A (FLNA) was identified as the first gene of non-syndromic mitral valve dystrophy (FLNA-MVD). We aimed to assess the phenotype of FLNA-MVD and its impact on prognosis.We investigated the disease in 246 subjects (72 mutated) from four FLNA-MVD families harbouring three different FLNA mutations. Phenotype was characterized by a comprehensive echocardiography focusing on mitral valve apparatus in comparison with control relatives. In this X-linked disease valves lesions were severe in men and moderate in women. Most men had classical features of mitral valve prolapse (MVP), but without chordal rupture. By contrast to regular MVP, mitral leaflet motion was clearly restricted in diastole and papillary muscles position was closer to mitral annulus. Valvular abnormalities were similar in the four families, in adults and young patients from early childhood suggestive of a developmental disease. In addition, mitral valve lesions worsened over time as encountered in degenerative conditions. Polyvalvular involvement was frequent in males and non-diagnostic forms frequent in females. Overall survival was moderately impaired in men (P = 0.011). Cardiac surgery rate (mainly valvular) was increased (33.3 ± 9.8 vs. 5.0 ± 4.9%, P < 0.0001; hazard ratio 10.5 [95% confidence interval: 2.9-37.9]) owing mainly to a lifetime increased risk in men (76.8 ± 14.1 vs. 9.1 ± 8.7%, P < 0.0001).FLNA-MVD is a developmental and degenerative disease with complex phenotypic expression which can influence patient management. FLNA-MVD has unique features with both MVP and paradoxical restricted motion in diastole, sub-valvular mitral apparatus impairment and polyvalvular lesions in males. FLNA-MVD conveys a substantial lifetime risk of valve surgery in men.

  View details for PubMedID 29020406

• Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly. Brain : a journal of neurology Alcantara, D. n., Timms, A. E., Gripp, K. n., Baker, L. n., Park, K. n., Collins, S. n., Cheng, C. n., Stewart, F. n., Mehta, S. G., Saggar, A. n., Sztriha, L. n., Zombor, M. n., Caluseriu, O. n., Mesterman, R. n., Van Allen, M. I., Jacquinet, A. n., Ygberg, S. n., Bernstein, J. A., Wenger, A. M., Guturu, H. n., Bejerano, G. n., Gomez-Ospina, N. n., Lehman, A. n., Alfei, E. n., Pantaleoni, C. n., Conti, V. n., Guerrini, R. n., Moog, U. n., Graham, J. M., Hevner, R. n., Dobyns, W. B., O'Driscoll, M. n., Mirzaa, G. M. 2017; 140 (10): 2610–22

  Abstract

  Mutations of genes within the phosphatidylinositol-3-kinase (PI3K)-AKT-MTOR pathway are well known causes of brain overgrowth (megalencephaly) as well as segmental cortical dysplasia (such as hemimegalencephaly, focal cortical dysplasia and polymicrogyria). Mutations of the AKT3 gene have been reported in a few individuals with brain malformations, to date. Therefore, our understanding regarding the clinical and molecular spectrum associated with mutations of this critical gene is limited, with no clear genotype-phenotype correlations. We sought to further delineate this spectrum, study levels of mosaicism and identify genotype-phenotype correlations of AKT3-related disorders. We performed targeted sequencing of AKT3 on individuals with these phenotypes by molecular inversion probes and/or Sanger sequencing to determine the type and level of mosaicism of mutations. We analysed all clinical and brain imaging data of mutation-positive individuals including neuropathological analysis in one instance. We performed ex vivo kinase assays on AKT3 engineered with the patient mutations and examined the phospholipid binding profile of pleckstrin homology domain localizing mutations. We identified 14 new individuals with AKT3 mutations with several phenotypes dependent on the type of mutation and level of mosaicism. Our comprehensive clinical characterization, and review of all previously published patients, broadly segregates individuals with AKT3 mutations into two groups: patients with highly asymmetric cortical dysplasia caused by the common p.E17K mutation, and patients with constitutional AKT3 mutations exhibiting more variable phenotypes including bilateral cortical malformations, polymicrogyria, periventricular nodular heterotopia and diffuse megalencephaly without cortical dysplasia. All mutations increased kinase activity, and pleckstrin homology domain mutants exhibited enhanced phospholipid binding. Overall, our study shows that activating mutations of the critical AKT3 gene are associated with a wide spectrum of brain involvement ranging from focal or segmental brain malformations (such as hemimegalencephaly and polymicrogyria) predominantly due to mosaic AKT3 mutations, to diffuse bilateral cortical malformations, megalencephaly and heterotopia due to constitutional AKT3 mutations. We also provide the first detailed neuropathological examination of a child with extreme megalencephaly due to a constitutional AKT3 mutation. This child has one of the largest documented paediatric brain sizes, to our knowledge. Finally, our data show that constitutional AKT3 mutations are associated with megalencephaly, with or without autism, similar to PTEN-related disorders. Recognition of this broad clinical and molecular spectrum of AKT3 mutations is important for providing early diagnosis and appropriate management of affected individuals, and will facilitate targeted design of future human clinical trials using PI3K-AKT pathway inhibitors.

  View details for PubMedID 28969385

• Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype. Human mutation Chen, L. n., Jensik, P. J., Alaimo, J. T., Walkiewicz, M. n., Berger, S. n., Roeder, E. n., Faqeih, E. A., Bernstein, J. A., Smith, A. C., Mullegama, S. V., Saffen, D. W., Elsea, S. H. 2017

  Abstract

  Deformed epidermal autoregulatory factor-1 (DEAF1), a transcription factor essential for central nervous system and early embryonic development, has recently been implicated in a series of intellectual disability-related neurodevelopmental anomalies termed, in this study, as DEAF1-associated neurodevelopmental disorder (DAND). We identified six potentially deleterious DEAF1 variants in a cohort of individuals with DAND via clinical exome sequencing (CES) and in silico analysis, including two novel de novo variants: missense variant c.634G > A p.Gly212Ser in the SAND domain and deletion variant c.913_915del p.Lys305del in the NLS domain, as well as c.676C > T p.Arg226Trp, c.700T > A p.Trp234Arg, c.737G > C p.Arg246Thr, and c.791A > C p.Gln264Pro. Luciferase reporter, immunofluorescence staining, and electrophoretic mobility shift assays revealed that these variants had decreased transcriptional repression activity at the DEAF1 promoter and reduced affinity to consensus DEAF1 DNA binding sequences. In addition, c.913_915del p.K305del localized primarily to the cytoplasm and interacted with wild-type DEAF1. Our results demonstrate that variants located within the SAND or NLS domains significantly reduce DEAF1 transcriptional regulatory activities and are thus, likely to contribute to the underlying clinical concerns in DAND patients. These findings illustrate the importance of experimental characterization of variants with uncertain significance identified by CES to assess their potential clinical significance and possible use in diagnosis.

  View details for PubMedID 28940898

• Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features. American journal of human genetics Stankiewicz, P. n., Khan, T. N., Szafranski, P. n., Slattery, L. n., Streff, H. n., Vetrini, F. n., Bernstein, J. A., Brown, C. W., Rosenfeld, J. A., Rednam, S. n., Scollon, S. n., Bergstrom, K. L., Parsons, D. W., Plon, S. E., Vieira, M. W., Quaio, C. R., Baratela, W. A., Acosta Guio, J. C., Armstrong, R. n., Mehta, S. G., Rump, P. n., Pfundt, R. n., Lewandowski, R. n., Fernandes, E. M., Shinde, D. N., Tang, S. n., Hoyer, J. n., Zweier, C. n., Reis, A. n., Bacino, C. A., Xiao, R. n., Breman, A. M., Smith, J. L., Katsanis, N. n., Bostwick, B. n., Popp, B. n., Davis, E. E., Yang, Y. n. 2017

  Abstract

  Bromodomain PHD finger transcription factor (BPTF) is the largest subunit of nucleosome remodeling factor (NURF), a member of the ISWI chromatin-remodeling complex. However, the clinical consequences of disruption of this complex remain largely uncharacterized. BPTF is required for anterior-posterior axis formation of the mouse embryo and was shown to promote posterior neuroectodermal fate by enhancing Smad2-activated wnt8 expression in zebrafish. Here, we report eight loss-of-function and two missense variants (eight de novo and two of unknown origin) in BPTF on 17q24.2. The BPTF variants were found in unrelated individuals aged between 2.1 and 13 years, who manifest variable degrees of developmental delay/intellectual disability (10/10), speech delay (10/10), postnatal microcephaly (7/9), and dysmorphic features (9/10). Using CRISPR-Cas9 genome editing of bptf in zebrafish to induce a loss of gene function, we observed a significant reduction in head size of F0 mutants compared to control larvae. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and phospho-histone H3 (PH3) staining to assess apoptosis and cell proliferation, respectively, showed a significant increase in cell death in F0 mutants compared to controls. Additionally, we observed a substantial increase of the ceratohyal angle of the craniofacial skeleton in bptf F0 mutants, indicating abnormal craniofacial patterning. Taken together, our data demonstrate the pathogenic role of BPTF haploinsufficiency in syndromic neurodevelopmental anomalies and extend the clinical spectrum of human disorders caused by ablation of chromatin remodeling complexes.

  View details for PubMedID 28942966

• De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability. American journal of human genetics Küry, S. n., van Woerden, G. M., Besnard, T. n., Proietti Onori, M. n., Latypova, X. n., Towne, M. C., Cho, M. T., Prescott, T. E., Ploeg, M. A., Sanders, S. n., Stessman, H. A., Pujol, A. n., Distel, B. n., Robak, L. A., Bernstein, J. A., Denommé-Pichon, A. S., Lesca, G. n., Sellars, E. A., Berg, J. n., Carré, W. n., Busk, Ø. L., van Bon, B. W., Waugh, J. L., Deardorff, M. n., Hoganson, G. E., Bosanko, K. B., Johnson, D. S., Dabir, T. n., Holla, Ø. L., Sarkar, A. n., Tveten, K. n., de Bellescize, J. n., Braathen, G. J., Terhal, P. A., Grange, D. K., van Haeringen, A. n., Lam, C. n., Mirzaa, G. n., Burton, J. n., Bhoj, E. J., Douglas, J. n., Santani, A. B., Nesbitt, A. I., Helbig, K. L., Andrews, M. V., Begtrup, A. n., Tang, S. n., van Gassen, K. L., Juusola, J. n., Foss, K. n., Enns, G. M., Moog, U. n., Hinderhofer, K. n., Paramasivam, N. n., Lincoln, S. n., Kusako, B. H., Lindenbaum, P. n., Charpentier, E. n., Nowak, C. B., Cherot, E. n., Simonet, T. n., Ruivenkamp, C. A., Hahn, S. n., Brownstein, C. A., Xia, F. n., Schmitt, S. n., Deb, W. n., Bonneau, D. n., Nizon, M. n., Quinquis, D. n., Chelly, J. n., Rudolf, G. n., Sanlaville, D. n., Parent, P. n., Gilbert-Dussardier, B. n., Toutain, A. n., Sutton, V. R., Thies, J. n., Peart-Vissers, L. E., Boisseau, P. n., Vincent, M. n., Grabrucker, A. M., Dubourg, C. n., Tan, W. H., Verbeek, N. E., Granzow, M. n., Santen, G. W., Shendure, J. n., Isidor, B. n., Pasquier, L. n., Redon, R. n., Yang, Y. n., State, M. W., Kleefstra, T. n., Cogné, B. n., Petrovski, S. n., Retterer, K. n., Eichler, E. E., Rosenfeld, J. A., Agrawal, P. B., Bézieau, S. n., Odent, S. n., Elgersma, Y. n., Mercier, S. n. 2017; 101 (5): 768–88

  Abstract

  Calcium/calmodulin-dependent protein kinase II (CAMK2) is one of the first proteins shown to be essential for normal learning and synaptic plasticity in mice, but its requirement for human brain development has not yet been established. Through a multi-center collaborative study based on a whole-exome sequencing approach, we identified 19 exceedingly rare de novo CAMK2A or CAMK2B variants in 24 unrelated individuals with intellectual disability. Variants were assessed for their effect on CAMK2 function and on neuronal migration. For both CAMK2A and CAMK2B, we identified mutations that decreased or increased CAMK2 auto-phosphorylation at Thr286/Thr287. We further found that all mutations affecting auto-phosphorylation also affected neuronal migration, highlighting the importance of tightly regulated CAMK2 auto-phosphorylation in neuronal function and neurodevelopment. Our data establish the importance of CAMK2A and CAMK2B and their auto-phosphorylation in human brain function and expand the phenotypic spectrum of the disorders caused by variants in key players of the glutamatergic signaling pathway.

  View details for PubMedID 29100089

• Teaching Biochemistry and Genetics to Students of Dentistry, Medicine, and Pharmacy 6th International Conference of the Association of Biochemistry Educators (ABE) Clearwater Beach, FL, USA, May 7-11, 2017. Medical science educator Niederhoffer, E. C., Cline, S. D., Osheroff, N. n., Simmons, J. M., Diekman, A. B., Franklin, D. S., Abali, E. E., Bateman, R. C., Fontes, J. D., Lindsley, J. E., Pearson, D. n., Rubenstein, P. A., Slaughter, C. A., Bernstein, J. A., Hyland, K. M., Park, V. M., Sobering, A. K., Weiler, T. A., Dasgupta, S. n. 2017; 27 (4): 855–59

  View details for PubMedID 29291139

• WISP3 mutation associated with Pseudorheumatoid Dysplasia. Cold Spring Harbor molecular case studies Sailani, M. R., Chappell, J. n., Inlora, J. n., Lynch, L. n., Narasimha, A. n., Mazroui, S. n., Zia, A. n., Bernstein, J. n., Aryani, O. n., Snyder, M. P. 2017

  Abstract

  Progressive pseudorheumatoid dysplasia (PPD) is a skeletal dysplasia characterized by predominant involvement of articular cartilage with progressive joint stiffness. Here we report genetic characterization of a consanguineous family segregating an uncharacterized from of skeletal dysplasia. Whole exome sequencing of four affected siblings and their parents identified a loss of function homozygous mutation in the WISP3 gene, leading to diagnosis of PPD in the affected individuals. The identified variant (chr6: 112382301; WISP3:c.156C>A p.Cys52*) is rare and predicted to cause premature termination of the WISP3 protein.

  View details for PubMedID 29092958

• Identification of a novel mutation in APTX gene associated with Ataxia-oculomotor apraxia. Cold Spring Harbor molecular case studies Inlora, J. n., Sailani, M. R., Khodadadi, H. n., Teymurinezhad, A. n., Takahashi, S. n., Bernstein, J. A., Garshasbi, M. n., Snyder, M. P. 2017

  Abstract

  Hereditary ataxias are clinically and genetically heterogeneous family of disorders defined by the inability to control gait and muscle coordination. Given the non-specific symptoms of many hereditary ataxias, precise diagnosis relies on molecular genetic testing. To this end, we conducted whole exome sequencing (WES) on a large consanguineous Iranian family with hereditary ataxia and oculomotor apraxia. WES in five affected and six unaffected individuals resulted in the identification of a homozygous novel stop-gain mutation in APTX gene (c. 739T>A; p.Lys247Ter) that segregates with the phenotype. Mutations in APTX gene are associated with ataxia with oculomotor apraxia type 1 (AOA1).

  View details for PubMedID 28652255

• in a patient with a complex connective tissue phenotype. Cold Spring Harbor molecular case studies Zastrow, D. B., Zornio, P. A., Dries, A., Kohler, J., Fernandez, L., Waggott, D., Walkiewicz, M., Eng, C. M., Manning, M. A., Farrelly, E., Fisher, P. G., Ashley, E. A., Bernstein, J. A., Wheeler, M. T. 2017; 3 (1)

  Abstract

  Here we describe a patient who presented with a history of congenital diaphragmatic hernia, inguinal hernia, and recurrent umbilical hernia. She also has joint laxity, hypotonia, and dysmorphic features. A unifying diagnosis was not identified based on her clinical phenotype. As part of her evaluation through the Undiagnosed Diseases Network, trio whole-exome sequencing was performed. Pathogenic variants in FBN1 and TRPS1 were identified as causing two distinct autosomal dominant conditions, each with de novo inheritance. Fibrillin 1 (FBN1) mutations are associated with Marfan syndrome and a spectrum of similar phenotypes. TRPS1 mutations are associated with trichorhinophalangeal syndrome types I and III. Features of both conditions are evident in the patient reported here. Discrepant features of the conditions (e.g., stature) and the young age of the patient may have made a clinical diagnosis more difficult in the absence of exome-wide genetic testing.

  View details for DOI 10.1101/mcs.a001388

  View details for PubMedID 28050602

• Tumor-induced Osteomalacia in a 3-Year-Old With Unresectable Central Giant Cell Lesions. Journal of pediatric hematology/oncology Crossen, S. S., Zambrano, E., Newman, B., Bernstein, J. A., Messner, A. H., Bachrach, L. K., Twist, C. J. 2016: -?

  Abstract

  Tumor-induced osteomalacia (TIO) is a rare cause of hypophosphatemia involving overproduction of fibroblast growth factor 23. TIO has been described largely in adults with small mesenchymal tumors. We report a case of TIO in a child who presented with knee pain and radiographic findings concerning for rickets, and was found to have maxillomandibular giant cell lesions. The patient was treated with oral phosphorus and calcitriol, surgical debulking, and intralesional corticosteroids, which resulted in tumor regression and normalization of serum fibroblast growth factor 23and phosphorus. This case illustrates the occurrence of this rare paraneoplastic syndrome in children and adds to our knowledge about clinical manifestations and pathologic findings associated with pediatric TIO.

  View details for PubMedID 27820122

• M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nature genetics Jagadeesh, K. A., Wenger, A. M., Berger, M. J., Guturu, H., Stenson, P. D., Cooper, D. N., Bernstein, J. A., Bejerano, G. 2016

  Abstract

  Variant pathogenicity classifiers such as SIFT, PolyPhen-2, CADD, and MetaLR assist in interpretation of the hundreds of rare, missense variants in the typical patient genome by deprioritizing some variants as likely benign. These widely used methods misclassify 26 to 38% of known pathogenic mutations, which could lead to missed diagnoses if the classifiers are trusted as definitive in a clinical setting. We developed M-CAP, a clinical pathogenicity classifier that outperforms existing methods at all thresholds and correctly dismisses 60% of rare, missense variants of uncertain significance in a typical genome at 95% sensitivity.

  View details for DOI 10.1038/ng.3703

  View details for PubMedID 27776117

• Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene. Journal of medical genetics Balasubramanian, M., Lord, H., Levesque, S., Guturu, H., Thuriot, F., Sillon, G., Wenger, A. M., Sureka, D. L., Lester, T., Johnson, D. S., Bowen, J., Calhoun, A. R., Viskochil, D. H., Bejerano, G., Bernstein, J. A., Chitayat, D. 2016

  Abstract

  In 1993, Chitayat et al., reported a newborn with hyperphalangism, facial anomalies, and bronchomalacia. We identified three additional families with similar findings. Features include bilateral accessory phalanx resulting in shortened index fingers; hallux valgus; distinctive face; respiratory compromise.To identify the genetic aetiology of Chitayat syndrome and identify a unifying cause for this specific form of hyperphalangism.Through ongoing collaboration, we had collected patients with strikingly-similar phenotype. Trio-based exome sequencing was first performed in Patient 2 through Deciphering Developmental Disorders study. Proband-only exome sequencing had previously been independently performed in Patient 4. Following identification of a candidate gene variant in Patient 2, the same variant was subsequently confirmed from exome data in Patient 4. Sanger sequencing was used to validate this variant in Patients 1, 3; confirm paternal inheritance in Patient 5.A recurrent, novel variant NM_006494.2:c.266A>G p.(Tyr89Cys) in ERF was identified in five affected individuals: de novo (patient 1, 2 and 3) and inherited from an affected father (patient 4 and 5). p.Tyr89Cys is an aromatic polar neutral to polar neutral amino acid substitution, at a highly conserved position and lies within the functionally important ETS-domain of the protein. The recurrent ERF c.266A>C p.(Tyr89Cys) variant causes Chitayat syndrome.ERF variants have previously been associated with complex craniosynostosis. In contrast, none of the patients with the c.266A>G p.(Tyr89Cys) variant have craniosynostosis.We report the molecular aetiology of Chitayat syndrome and discuss potential mechanisms for this distinctive phenotype associated with the p.Tyr89Cys substitution in ERF.

  View details for DOI 10.1136/jmedgenet-2016-104143

  View details for PubMedID 27738187

• De Novo Mutations in CHD4, an ATP-Dependent Chromatin Remodeler Gene, Cause an Intellectual Disability Syndrome with Distinctive Dysmorphisms AMERICAN JOURNAL OF HUMAN GENETICS Weiss, K., Terhal, P. A., Cohen, L., Bruccoleri, M., Irving, M., Martinez, A. F., Rosenfeld, J. A., Machol, K., Yang, Y., Liu, P., Walkiewicz, M., Beuten, J., Gomez-Ospina, N., Haude, K., Fong, C., Enns, G. M., Bernstein, J. A., Fan, J., Gotway, G., Ghorbani, M., van Gassen, K., Monroe, G. R., van Haaften, G., Basel-Vanagaite, L., Yang, X., Campeau, P. M., Muenke, M. 2016; 99 (4): 934-941

  Abstract

  Chromodomain helicase DNA-binding protein 4 (CHD4) is an ATP-dependent chromatin remodeler involved in epigenetic regulation of gene transcription, DNA repair, and cell cycle progression. Also known as Mi2β, CHD4 is an integral subunit of a well-characterized histone deacetylase complex. Here we report five individuals with de novo missense substitutions in CHD4 identified through whole-exome sequencing and web-based gene matching. These individuals have overlapping phenotypes including developmental delay, intellectual disability, hearing loss, macrocephaly, distinct facial dysmorphisms, palatal abnormalities, ventriculomegaly, and hypogonadism as well as additional findings such as bone fusions. The variants, c.3380G>A (p.Arg1127Gln), c.3443G>T (p.Trp1148Leu), c.3518G>T (p.Arg1173Leu), and c.3008G>A, (p.Gly1003Asp) (GenBank: NM_001273.3), affect evolutionarily highly conserved residues and are predicted to be deleterious. Previous studies in yeast showed the equivalent Arg1127 and Trp1148 residues to be crucial for SNF2 function. Furthermore, mutations in the same positions were reported in malignant tumors, and a de novo missense substitution in an equivalent arginine residue in the C-terminal helicase domain of SMARCA4 is associated with Coffin Siris syndrome. Cell-based studies of the p.Arg1127Gln and p.Arg1173Leu mutants demonstrate normal localization to the nucleus and HDAC1 interaction. Based on these findings, the mutations potentially alter the complex activity but not its formation. This report provides evidence for the role of CHD4 in human development and expands an increasingly recognized group of Mendelian disorders involving chromatin remodeling and modification.

  View details for DOI 10.1016/j.ajhg.2016.08.001

  View details for PubMedID 27616479

• Impaired Health-Related Quality of Life in Children and Families Affected by Methylmalonic Acidemia. Journal of genetic counseling Splinter, K., Niemi, A., Cox, R., Platt, J., Shah, M., Enns, G. M., Kasahara, M., Bernstein, J. A. 2016; 25 (5): 936-944

  Abstract

  An understanding of health related quality of life (HRQoL) in children and families affected by methylmalonic acidemia (MMA) is important in planning counseling and therapeutic intervention. Liver transplantation (LT) is used as a treatment for MMA; however, its risks and benefits continue to be investigated. The purpose of this study was twofold: (1) to measure HRQoL in children and families affected by MMA using the Pediatric Quality of Life Inventory (PedsQL™) parent version, and (2) to assess the impact of LT on HRQoL by comparing LT and non-LT patient scores and free responses. Parents/caregivers reported lower scores on the majority of the PedsQL™ scales as compared to samples of healthy children, children with solid organ transplants for indications other than MMA, and families affected by chronic conditions. Scores for children with MMA were lowest in school and social functioning and scores for families were lowest in worry and activity impairment. There were no significant differences in LT and non-LT patient scores on the PedsQL™ scales. Our results document the negative impact of MMA on HRQoL.

  View details for DOI 10.1007/s10897-015-9921-x

  View details for PubMedID 26667650

• Clinical and radiographic delineation of Bent Bone Dysplasia-FGFR2 type or Bent Bone Dysplasia with Distinctive Clavicles and Angel-shaped Phalanges. American journal of medical genetics. Part A Krakow, D., Cohn, D. H., Wilcox, W. R., Noh, G. J., Raffel, L. J., Sarukhanov, A., Ivanova, M. H., Danielpour, M., Grange, D. K., Elliott, A. M., Bernstein, J. A., Rimoin, D. L., Merrill, A. E., Lachman, R. S. 2016; 170 (10): 2652-2661

  Abstract

  Bent Bone Dysplasia-FGFR2 type is a relatively recently described bent bone phenotype with diagnostic clinical, radiographic, and molecular characteristics. Here we report on 11 individuals, including the original four patients plus seven new individuals with three longer-term survivors. The prenatal phenotype included stillbirth, bending of the femora, and a high incidence of polyhydramnios, prematurity, and perinatal death in three of 11 patients in the series. The survivors presented with characteristic radiographic findings that were observed among those with lethality, including bent bones, distinctive (moustache-shaped) small clavicles, angel-shaped metacarpals and phalanges, poor mineralization of the calvarium, and craniosynostosis. Craniofacial abnormalities, hirsutism, hepatic abnormalities, and genitourinary abnormalities were noted as well. Longer-term survivors all needed ventilator support. Heterozygosity for mutations in the gene that encodes Fibroblast Growth Factor Receptor 2 (FGFR2) was identified in the nine individuals with available DNA. Description of these patients expands the prenatal and postnatal findings of Bent Bone Dysplasia-FGFR2 type and adds to the phenotypic spectrum among all FGFR2 disorders. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.37772

  View details for PubMedID 27240702

• Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. Genetics in medicine Wenger, A. M., Guturu, H., Bernstein, J. A., Bejerano, G. 2016

  Abstract

  Clinical exome sequencing is nondiagnostic for about 75% of patients evaluated for a possible Mendelian disorder. We examined the ability of systematic reevaluation of exome data to establish additional diagnoses.The exome and phenotypic data of 40 individuals with previously nondiagnostic clinical exomes were reanalyzed with current software and literature.A definitive diagnosis was identified for 4 of 40 participants (10%). In these cases the causative variant is de novo and in a relevant autosomal-dominant disease gene. The literature to tie the causative genes to the participants' phenotypes was weak, nonexistent, or not readily located at the time of the initial clinical exome reports. At the time of diagnosis by reanalysis, the supporting literature was 1 to 3 years old.Approximately 250 gene-disease and 9,200 variant-disease associations are reported annually. This increase in information necessitates regular reevaluation of nondiagnostic exomes. To be practical, systematic reanalysis requires further automation and more up-to-date variant databases. To maximize the diagnostic yield of exome sequencing, providers should periodically request reanalysis of nondiagnostic exomes. Accordingly, policies regarding reanalysis should be weighed in combination with factors such as cost and turnaround time when selecting a clinical exome laboratory.Genet Med advance online publication 21 July 2016Genetics in Medicine (2016); doi:10.1038/gim.2016.88.

  View details for DOI 10.1038/gim.2016.88

  View details for PubMedID 27441994

• Respiratory System Involvement in Costello Syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Gomez-Ospina, N., Kuo, C., Ananth, A. L., Myers, A., Brennan, M., Stevenson, D. A., Bernstein, J. A., Hudgins, L. 2016; 170 (7): 1849-1857

  Abstract

  Costello syndrome (CS) is a multisystem disorder caused by heterozygous germline mutations in the HRAS proto-oncogene. Respiratory system complications have been reported in individuals with CS, but a comprehensive description of the full spectrum and incidence of respiratory symptoms in these patients is not available. Here, we report the clinical course of four CS patients with respiratory complications as a major cause of morbidity. Review of the literature identified 56 CS patients with descriptions of their neonatal course and 17 patients in childhood/adulthood. We found that in the neonatal period, respiratory complications are seen in approximately 78% of patients with transient respiratory distress reported in 45% of neonates. Other more specific respiratory diagnoses were reported in 62% of patients, the majority of which comprised disorders of the upper and lower respiratory tract. Symptoms of upper airway obstruction were reported in CS neonates but were more commonly diagnosed in childhood/adulthood (71%). Analysis of HRAS mutations and their respiratory phenotype revealed that the common p.Gly12Ser mutation is more often associated with transient respiratory distress and other respiratory diagnoses. Respiratory failure and dependence on mechanical ventilation occurs almost exclusively with rare mutations. In cases of prenatally diagnosed CS, the high incidence of respiratory complications in the neonatal period should prompt anticipatory guidance and development of a postnatal management plan. This may be important in cases involving rarer mutations. Furthermore, the high frequency of airway obstruction in CS patients suggests that otorhinolaryngological evaluation and sleep studies should be considered. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.37655

  View details for PubMedID 27102959

• Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism JAMA NEUROLOGY Mirzaa, G. M., Campbell, C. D., Solovieff, N., Goold, C. P., Jansen, L. A., Menon, S., Timms, A. E., Conti, V., Biag, J. D., Olds, C., Boyle, E. A., Collins, S., Ishak, G., Poliachik, S. L., Girisha, K. M., Yeung, K., Chung, B. H., Rahikkala, E., Gunter, S. A., McDaniel, S. S., Macmurdo, C. F., Bernstein, J. A., Martin, B., Leary, R. J., Mahan, S., Liu, S., Weaver, M., Dorschner, M. O., Jhangiani, S., Muzny, D. M., Boerwinkle, E., Gibbs, R. A., Lupski, J. R., Shendure, J., Saneto, R. P., Novotny, E. J., Wilson, C. J., Sellers, W. R., Morrissey, M. P., Hevner, R. F., Ojemann, J. G., Guerrini, R., Murphy, L. O., Winckler, W., Dobyns, W. B. 2016; 73 (7): 836-845

  Abstract

  Focal cortical dysplasia (FCD), hemimegalencephaly, and megalencephaly constitute a spectrum of malformations of cortical development with shared neuropathologic features. These disorders are associated with significant childhood morbidity and mortality.To identify the underlying molecular cause of FCD, hemimegalencephaly, and diffuse megalencephaly.Patients with FCD, hemimegalencephaly, or megalencephaly (mean age, 11.7 years; range, 2-32 years) were recruited from Pediatric Hospital A. Meyer, the University of Hong Kong, and Seattle Children's Research Institute from June 2012 to June 2014. Whole-exome sequencing (WES) was performed on 8 children with FCD or hemimegalencephaly using standard-depth (50-60X) sequencing in peripheral samples (blood, saliva, or skin) from the affected child and their parents and deep (150-180X) sequencing in affected brain tissue. Targeted sequencing and WES were used to screen 93 children with molecularly unexplained diffuse or focal brain overgrowth. Histopathologic and functional assays of phosphatidylinositol 3-kinase-AKT (serine/threonine kinase)-mammalian target of rapamycin (mTOR) pathway activity in resected brain tissue and cultured neurons were performed to validate mutations.Whole-exome sequencing and targeted sequencing identified variants associated with this spectrum of developmental brain disorders.Low-level mosaic mutations of MTOR were identified in brain tissue in 4 children with FCD type 2a with alternative allele fractions ranging from 0.012 to 0.086. Intermediate-level mosaic mutation of MTOR (p.Thr1977Ile) was also identified in 3 unrelated children with diffuse megalencephaly and pigmentary mosaicism in skin. Finally, a constitutional de novo mutation of MTOR (p.Glu1799Lys) was identified in 3 unrelated children with diffuse megalencephaly and intellectual disability. Molecular and functional analysis in 2 children with FCD2a from whom multiple affected brain tissue samples were available revealed a mutation gradient with an epicenter in the most epileptogenic area. When expressed in cultured neurons, all MTOR mutations identified here drive constitutive activation of mTOR complex 1 and enlarged neuronal size.In this study, mutations of MTOR were associated with a spectrum of brain overgrowth phenotypes extending from FCD type 2a to diffuse megalencephaly, distinguished by different mutations and levels of mosaicism. These mutations may be sufficient to cause cellular hypertrophy in cultured neurons and may provide a demonstration of the pattern of mosaicism in brain and substantiate the link between mosaic mutations of MTOR and pigmentary mosaicism in skin.

  View details for DOI 10.1001/jamaneurol.2016.0363

  View details for PubMedID 27159400

• RASA1 somatic mutation and variable expressivity in capillary malformation/arteriovenous malformation (CM/AVM) syndrome. American journal of medical genetics. Part A Macmurdo, C. F., Wooderchak-Donahue, W., Bayrak-Toydemir, P., Le, J., Wallenstein, M. B., Milla, C., Teng, J. M., Bernstein, J. A., Stevenson, D. A. 2016; 170 (6): 1450-1454

  Abstract

  Germline mutations in RASA1 are associated with capillary malformation-arteriovenous malformation (CM-AVM) syndrome. CM-AVM syndrome is characterized by multi-focal capillary malformations and arteriovenous malformations. Lymphatic anomalies have been proposed as part of the phenotype. Intrafamilial variability has been reported, suggesting modifiers and somatic events. The objective of the study was to identify somatic RASA1 "second hits" from vascular malformations associated with CM-AVM syndrome, and describe phenotypic variability. Participants were examined and phenotyped. Genomic DNA was extracted from peripheral blood on all participants. Whole-exome sequencing was performed on the proband. Using Sanger sequencing, RASA1 exon 8 was PCR-amplified to track the c.1248T>G, p.Tyr416X germline variant through the family. A skin biopsy of a capillary malformation from the proband's mother was also obtained, and next-generation sequencing was performed on DNA from the affected tissue. A familial germline heterozygous novel pathogenic RASA1 variant, c.1248T>G (p.Tyr416X), was identified in the proband and her mother. The proband had capillary malformations, chylothorax, lymphedema, and overgrowth, while her affected mother had only isolated capillary malformations. Sequence analysis of DNA extracted from a skin biopsy of a capillary malformation of the affected mother showed a second RASA1 somatic mutation (c.2245C>T, p.Arg749X). These results and the extreme variable expressivity support the hypothesis that somatic "second hits" are required for the development of vascular anomalies associated with CM-AVM syndrome. In addition, the phenotypes of the affected individuals further clarify that lymphatic manifestations are also part of the phenotypic spectrum of RASA1-related disorders. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.37613

  View details for PubMedID 26969842

• Prenatally Diagnosed Cases of Binder Phenotype Complicated by Respiratory Distress in the Immediate Postnatal Period. Journal of ultrasound in medicine Blumenfeld, Y. J., Davis, A. S., Hintz, S. R., Milan, K., Messner, A. H., Barth, R. A., Hudgins, L., Chueh, J., Homeyer, M., Bernstein, J. A., Enns, G., Atwal, P., Manning, M. 2016; 35 (6): 1353-1358

  Abstract

  Binder phenotype, or maxillonasal dysostosis, is a distinctive pattern of facial development characterized by a short nose with a flat nasal bridge, an acute nasolabial angle, a short columella, a convex upper lip, and class III malocclusion. We report 3 cases of prenatally diagnosed Binder phenotype associated with perinatal respiratory impairment.

  View details for DOI 10.7863/ultra.15.02050

  View details for PubMedID 27162279

• Clinical Course of Six Children With GNAO1 Mutations Causing a Severe and Distinctive Movement Disorder PEDIATRIC NEUROLOGY Ananth, A. L., Robichaux-Viehoever, A., Kim, Y., Hanson-Kahn, A., Cox, R., Enns, G. M., Strober, J., Willing, M., Schlaggar, B. L., Wu, Y. W., Bernstein, J. A. 2016; 59: 81-84

  Abstract

  Mutations in GNAO1 have been described in 11 patients to date. Although most of these individuals had epileptic encephalopathy, four patients had a severe movement disorder as the prominent feature. We describe the largest series of patients with de novoGNAO1 mutations who have severe chorea, developmental delay, and hypotonia in the absence of epilepsy.Six patients with recurrent missense mutations in GNAO1 as detected by whole exome sequencing were identified at three institutions. We describe the presentation, clinical course, and response to treatment of these patients.All six patients exhibited global developmental delay and hypotonia from infancy. Chorea developed by age four years in all but one patient, who developed chorea at 14 years. Treatments with neuroleptics and tetrabenazine were most effective in the baseline management of chorea. The chorea became gradually progressive and marked by episodes of severe, refractory ballismus requiring intensive care unit admissions in four of six patients. Exacerbations indirectly led to the death of two patients.Patients with GNAO1 mutations can present with a severe, progressive movement disorder in the absence of epilepsy. Exacerbations may be refractory to treatment and can result in life-threatening secondary complications. Early and aggressive treatment of these exacerbations with direct admission to intensive care units for treatment with anesthetic drips may prevent some secondary complications. However the chorea and ballismus can be refractory to maximum medical therapy.

  View details for DOI 10.1016/j.pediatrneurol.2016.02.018

  View details for PubMedID 27068059

• Germline De Novo Mutations in GNB1 Cause Severe Neurodevelopmental Disability, Hypotonia, and Seizures AMERICAN JOURNAL OF HUMAN GENETICS Petrovski, S., Kury, S., Myers, C. T., Anyane-Yeboa, K., Cogne, B., Bialer, M., Xia, F., Hemati, P., Riviello, J., Mehaffey, M., Besnard, T., Becraft, E., Wadley, A., Politi, A. R., Colombo, S., Zhu, X., Ren, Z., Andrews, I., Dudding-Byth, T., Schneider, A. L., Wallace, G., Rosen, A. B., Schelley, S., Enns, G. M., Corre, P., Dalton, J., Mercier, S., Latypova, X., Schmitt, S., Guzman, E., Moore, C., Bier, L., Heinzen, E. L., Karachunski, P., Shur, N., Grebe, T., Basinger, A., Nguyen, J. M., Bezieau, S., Wierenga, K., Bernstein, J. A., Scheffer, I. E., Rosenfeld, J. A., Mefford, H. C., Isidor, B., Goldstein, D. B. 2016; 98 (5): 1001-1010

  Abstract

  Whole-exome sequencing of 13 individuals with developmental delay commonly accompanied by abnormal muscle tone and seizures identified de novo missense mutations enriched within a sub-region of GNB1, a gene encoding the guanine nucleotide-binding protein subunit beta-1, Gβ. These 13 individuals were identified among a base of 5,855 individuals recruited for various undiagnosed genetic disorders. The probability of observing 13 or more de novo mutations by chance among 5,855 individuals is very low (p = 7.1 × 10(-21)), implicating GNB1 as a genome-wide-significant disease-associated gene. The majority of these 13 mutations affect known Gβ binding sites, which suggests that a likely disease mechanism is through the disruption of the protein interface required for Gα-Gβγ interaction (resulting in a constitutively active Gβγ) or through the disruption of residues relevant for interaction between Gβγ and certain downstream effectors (resulting in reduced interaction with the effectors). Strikingly, 8 of the 13 individuals recruited here for a neurodevelopmental disorder have a germline de novo GNB1 mutation that overlaps a set of five recurrent somatic tumor mutations for which recent functional studies demonstrated a gain-of-function effect due to constitutive activation of G protein downstream signaling cascades for some of the affected residues.

  View details for DOI 10.1016/j.ajhg.2016.03.011

  View details for PubMedID 27108799

• Clinical, cytogenetic, and molecular outcomes in a series of 66 patients with Pierre Robin sequence and literature review: 22q11.2 deletion is less common than other chromosomal anomalies. American journal of medical genetics. Part A Gomez-Ospina, N., Bernstein, J. A. 2016; 170 (4): 870-880

  Abstract

  Pierre Robin sequence (PRS) is an important craniofacial anomaly that can be seen as an isolated finding or manifestation of multiple syndromes. 22q11.2 deletion and Stickler syndrome are cited as the two most common conditions associated with PRS, but their frequencies are debated. We performed a retrospective study of 66 patients with PRS and reviewed their genetic testing, diagnoses, and clinical findings. The case series is complemented by a comprehensive literature review of the nature and frequency of genetic diagnosis in PRS. In our cohort 65% of patients had associated anomalies; of these, a genetic diagnosis was established in 56%. Stickler syndrome was the most common diagnosis, comprising approximately 11% of all cases, followed by Treacher Collins syndrome (9%). The frequency of 22q11.2 deletion was 1.5%. Chromosome arrays, performed for 72% of idiopathic PRS with associated anomalies, revealed two cases of 18q22→qter deletion, a region not previously reported in association with PRS. A review of the cytogenetic anomalies identified in this population supports an association between the 4q33-qter, 17q24.3, 2q33.1, and 11q23 chromosomal loci and PRS. We found a low frequency of 22q11.2 deletion in PRS, suggesting it is less commonly implicated in this malformation. Our data also indicate a higher frequency of cytogenetic anomalies in PRS patients with associated anomalies, and a potential new link with the 18q22→qter locus. The present findings underscore the utility of chromosomal microarrays in cases of PRS with associated anomalies and suggest that delaying testing for apparently isolated cases should be considered. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.37538

  View details for PubMedID 26756138

• Novel X-linked syndrome of cardiac valvulopathy, keloid scarring, and reduced joint mobility due to filamin A substitution G1576R. American journal of medical genetics. Part A Atwal, P. S., Blease, S., Braxton, A., Graves, J., He, W., Person, R., Slattery, L., Bernstein, J. A., Hudgins, L. 2016; 170 (4): 891-895

  Abstract

  Filamin A (FLNA) is known to be involved in intracellular actin binding, cell migration, scaffolding, and signaling. We report a novel X-linked syndrome characterized by cardiac valvular disease, keloid scarring and reduced joint mobility in male second cousins due to a previously unreported mutation in FLNA. Whole exome sequencing was performed using standard methods and segregation analysis was performed in affected and non-affected family members. A novel hemizygous c.4726G>A (p.G1576R) mutation in FLNA was detected. Segregation analysis performed on multiple maternal family members showed c.4726G>A (p.G1576R) segregated with disease in an X-linked inheritance pattern. The findings in these cases are distinct from previously described FLNA related disorders by virtue of decreased joint mobility and spontaneous keloid scarring. They occur in association with a novel mutation and represent a novel genetic syndrome. © 2015 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.37491

  View details for PubMedID 26686323

• Clinical Delineation of the PACS1-Related Syndrome-Report on 19 Patients AMERICAN JOURNAL OF MEDICAL GENETICS PART A Schuurs-Hoeijmakers, J. H., Landsverk, M. L., Foulds, N., Kukolich, M. K., Gavrilova, R. H., Greville-Heygate, S., Hanson-Kahn, A., Bernstein, J. A., Glass, J., Chitayat, D., Burrow, T. A., Husami, A., Collins, K., Wusik, K., Van der Aa, N., Kooy, F., Brown, K. T., Gadzicki, D., Kini, U., Alvarez, S., Fernandez-Jaen, A., McGehee, F., Selby, K., Tarailo-Graovac, M., Van Allen, M., van Karnebeek, C. D., Stavropoulos, D. J., Marshall, C. R., Merico, D., Gregor, A., Zweier, C., Hopkin, R. J., Chu, Y. W., Chung, B. H., de Vries, B. B., Devriendt, K., Hurles, M. E., Brunner, H. G. 2016; 170 (3): 670-675

  Abstract

  We report on 19 individuals with a recurrent de novo c.607C>T mutation in PACS1. This specific mutation gives rise to a recognizable intellectual disability syndrome. There is a distinctive facial appearance (19/19), characterized by full and arched eyebrows, hypertelorism with downslanting palpebral fissures, long eye lashes, ptosis, low set and simple ears, bulbous nasal tip, wide mouth with downturned corners and a thin upper lip with an unusual "wavy" profile, flat philtrum, and diastema of the teeth. Intellectual disability, ranging from mild to moderate, was present in all. Hypotonia is common in infancy (8/19). Seizures are frequent (12/19) and respond well to anticonvulsive medication. Structural malformations are common, including heart (10/19), brain (12/16), eye (10/19), kidney (3/19), and cryptorchidism (6/12 males). Feeding dysfunction is presenting in infancy with failure to thrive (5/19), gastroesophageal reflux (6/19), and gastrostomy tube placement (4/19). There is persistence of oral motor dysfunction. We provide suggestions for clinical work-up and management and hope that the present study will facilitate clinical recognition of further cases. © 2016 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.37476

  View details for PubMedID 26842493

• A deleterious Nav1.1 mutation selectively impairs telencephalic inhibitory neurons derived from Dravet Syndrome patients. eLife Sun, Y., Pasca, S. P., Portmann, T., Goold, C., Worringer, K. A., Guan, W., Chan, K. C., Gai, H., Vogt, D., Chen, Y. J., Mao, R., Chan, K., Rubenstein, J. L., Madison, D. V., Hallmayer, J., Froehlich-Santino, W. M., Bernstein, J. A., Dolmetsch, R. E. 2016; 5

  Abstract

  Dravet Syndrome is an intractable form of childhood epilepsy associated with deleterious mutations in SCN1A, the gene encoding neuronal sodium channel Nav1.1. Earlier studies using human induced pluripotent stem cells (iPSCs) have produced mixed results regarding the importance of Nav1.1 in human inhibitory versus excitatory neurons. We studied a Nav1.1 mutation (p.S1328P) identified in a pair of twins with Dravet Syndrome and generated iPSC-derived neurons from these patients. Characterization of the mutant channel revealed a decrease in current amplitude and hypersensitivity to steady-state inactivation. We then differentiated Dravet-Syndrome and control iPSCs into telencephalic excitatory neurons or medial ganglionic eminence (MGE)-like inhibitory neurons. Dravet inhibitory neurons showed deficits in sodium currents and action potential firing, which were rescued by a Nav1.1 transgene, whereas Dravet excitatory neurons were normal. Our study identifies biophysical impairments underlying a deleterious Nav1.1 mutation and supports the hypothesis that Dravet Syndrome arises from defective inhibitory neurons.

  View details for DOI 10.7554/eLife.13073

  View details for PubMedID 27458797

• Single amino acid charge switch defines clinically distinct proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1)-associated inflammatory diseases JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Holzinger, D., Fassl, S. K., de Jager, W., Lohse, P., Roehrig, U. F., Gattorno, M., Omenetti, A., Chiesa, S., Schena, F., Austermann, J., Vogl, T., Kuhns, D. B., Holland, S. M., Rodriguez-Gallego, C., Lopez-Almaraz, R., Arostegui, J. I., Colino, E., Roldan, R., Fessatou, S., Isidor, B., Poignant, S., Ito, K., Epple, H., Bernstein, J. A., Jeng, M., Frankovich, J., Lionetti, G., Church, J. A., Ong, P. Y., LaPlant, M., Abinun, M., Skinner, R., Bigley, V., Sachs, U. J., Hinze, C., Hoppenreijs, E., Ehrchen, J., Foell, D., Chae, J. J., Ombrello, A., Aksentijevich, I., Sunderkoetter, C., Roth, J. 2015; 136 (5): 1337-1345

  Abstract

  Hyperzincemia and hypercalprotectinemia (Hz/Hc) is a distinct autoinflammatory entity involving extremely high serum concentrations of the proinflammatory alarmin myeloid-related protein (MRP) 8/14 (S100A8/S100A9 and calprotectin).We sought to characterize the genetic cause and clinical spectrum of Hz/Hc.Proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1) gene sequencing was performed in 14 patients with Hz/Hc, and their clinical phenotype was compared with that of 11 patients with pyogenic arthritis, pyoderma gangrenosum, and acne (PAPA) syndrome. PSTPIP1-pyrin interactions were analyzed by means of immunoprecipitation and Western blotting. A structural model of the PSTPIP1 dimer was generated. Cytokine profiles were analyzed by using the multiplex immunoassay, and MRP8/14 serum concentrations were analyzed by using an ELISA.Thirteen patients were heterozygous for a missense mutation in the PSTPIP1 gene, resulting in a p.E250K mutation, and 1 carried a mutation resulting in p.E257K. Both mutations substantially alter the electrostatic potential of the PSTPIP1 dimer model in a region critical for protein-protein interaction. Patients with Hz/Hc have extremely high MRP8/14 concentrations (2045 ± 1300 μg/mL) compared with those with PAPA syndrome (116 ± 74 μg/mL) and have a distinct clinical phenotype. A specific cytokine profile is associated with Hz/Hc. Hz/Hc mutations altered protein binding of PSTPIP1, increasing interaction with pyrin through phosphorylation of PSTPIP1.Mutations resulting in charge reversal in the y-domain of PSTPIP1 (E→K) and increased interaction with pyrin cause a distinct autoinflammatory disorder defined by clinical and biochemical features not found in patients with PAPA syndrome, indicating a unique genotype-phenotype correlation for mutations in the PSTPIP1 gene. This is the first inborn autoinflammatory syndrome in which inflammation is driven by uncontrolled release of members of the alarmin family.

  View details for DOI 10.1016/j.jaci.2015.04.016

  View details for PubMedID 26025129

• Prenatal hydrops foetalis associated with infantile free sialic acid storage disease. Journal of obstetrics and gynaecology Chock, V. Y., MILAN, K. E., Folkins, A. K., Hazard, F. K., Bernstein, J. A., Hintz, S. R. 2015; 35 (8): 850-852

  View details for DOI 10.3109/01443615.2015.1017558

  View details for PubMedID 26076308

• Clinical reappraisal of SHORT syndrome with PIK3R1 mutations: towards recommendation for molecular testing and management. Clinical genetics Avila, M., Dyment, D. A., Sagen, J. V., St-Onge, J., Moog, U., Chung, B. H., Mansour, S., Albanese, A., Garcia, S., Ortiz Martin, D., Lopez, A. A., Claudi, T., König, R., White, S. M., Sawyer, S. L., Bernstein, J. A., Slattery, L., Jobling, R. K., Yoon, G., Curry, C. J., Le Merrer, M., Le Luyer, B., Héron, D., Mathieu-Dramard, M., Bitoun, P., Odent, S., Amiel, J., Kuentz, P., Thevenon, J., Laville, M., Reznik, Y., Fagour, C., Nunes, M. L., Delesalle, D., Manouvrier, S., Lascols, O., Huet, F., Binquet, C., Faivre, L., Rivière, J. B., Vigouroux, C., Njølstad, P. R., Innes, A. M., Thauvin-Robinet, C. 2015

  Abstract

  SHORT syndrome has historically been defined by its acronym: short stature (S), hyperextensibility of joints and/or inguinal hernia (H), ocular depression (O), Rieger abnormality (R) and teething delay (T). More recently several research groups have identified PIK3R1 mutations as responsible for SHORT syndrome. Knowledge of the molecular etiology of SHORT syndrome has permitted a reassessment of the clinical phenotype. The detailed phenotypes of 32 individuals with SHORT syndrome and PIK3R1 mutation, including eight newly ascertained individuals, were studied to fully define the syndrome and the indications for PIK3R1 testing. The major features described in the SHORT acronym were not universally seen and only half (52%) had 4 or more of the classic features. The commonly observed clinical features of SHORT syndrome seen in the cohort included IUGR < 10(th) percentile, postnatal growth restriction, lipoatrophy and the characteristic facial gestalt. Anterior chamber defects and insulin resistance or diabetes were also observed but were not as prevalent. The less specific, or minor features of SHORT syndrome include teething delay, thin wrinkled skin, speech delay, sensorineural deafness, hyperextensibility of joints and inguinal hernia. Given the high risk of diabetes mellitus, regular monitoring of glucose metabolism is warranted. An echocardiogram, ophthalmological and hearing assessments are also recommended.

  View details for DOI 10.1111/cge.12688

  View details for PubMedID 26497935

• DYRK1A haploinsufficiency causes a new recognizable syndrome with microcephaly, intellectual disability, speech impairment, and distinct facies EUROPEAN JOURNAL OF HUMAN GENETICS Ji, J., Lee, H., Argiropoulos, B., Dorrani, N., Mann, J., Martinez-Agosto, J. A., Gomez-Ospina, N., Gallant, N., Bernstein, J. A., Hudgins, L., Slattery, L., Isidor, B., Le Caignec, C., David, A., Obersztyn, E., Wisniowiecka-Kowalnik, B., Fox, M., Deignan, J. L., Vilain, E., Hendricks, E., Harr, M. H., Noon, S. E., Jackson, J. R., Wilkens, A., Mirzaa, G., Salamon, N., Abramson, J., Zackai, E. H., Krantz, I., Innes, A. M., Nelson, S. F., Grody, W. W., Quintero-Rivera, F. 2015; 23 (11): 1473-1481

  Abstract

  Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A (DYRK1A ) is a highly conserved gene located in the Down syndrome critical region. It has an important role in early development and regulation of neuronal proliferation. Microdeletions of chromosome 21q22.12q22.3 that include DYRK1A (21q22.13) are rare and only a few pathogenic single-nucleotide variants (SNVs) in the DYRK1A gene have been described, so as of yet, the landscape of DYRK1A disruptions and their associated phenotype has not been fully explored. We have identified 14 individuals with de novo heterozygous variants of DYRK1A; five with microdeletions, three with small insertions or deletions (INDELs) and six with deleterious SNVs. The analysis of our cohort and comparison with published cases reveals that phenotypes are consistent among individuals with the 21q22.12q22.3 microdeletion and those with translocation, SNVs, or INDELs within DYRK1A. All individuals shared congenital microcephaly at birth, intellectual disability, developmental delay, severe speech impairment, short stature, and distinct facial features. The severity of the microcephaly varied from -2 SD to -5 SD. Seizures, structural brain abnormalities, eye defects, ataxia/broad-based gait, intrauterine growth restriction, minor skeletal abnormalities, and feeding difficulties were present in two-thirds of all affected individuals. Our study demonstrates that haploinsufficiency of DYRK1A results in a new recognizable syndrome, which should be considered in individuals with Angelman syndrome-like features and distinct facial features. Our report represents the largest cohort of individuals with DYRK1A disruptions to date, and is the first attempt to define consistent genotype-phenotype correlations among subjects with 21q22.13 microdeletions and DYRK1A SNVs or small INDELs.European Journal of Human Genetics advance online publication, 6 May 2015; doi:10.1038/ejhg.2015.71.

  View details for DOI 10.1038/ejhg.2015.71

  View details for PubMedID 25944381

• Factors Associated with Uptake of Genetics Services for Hypertrophic Cardiomyopathy. Journal of genetic counseling Khouzam, A., Kwan, A., Baxter, S., Bernstein, J. A. 2015; 24 (5): 797-809

  Abstract

  Hypertrophic cardiomyopathy (HCM) is a common cardiovascular disorder with variable expressivity and incomplete penetrance. Clinical guidelines recommend consultation with a genetics professional as part of an initial assessment for HCM, yet there remains an underutilization of genetics services. We conducted a study to assess factors associated with this underutilization within the framework of the Health Belief Model (HBM). An online survey was completed by 306 affected individuals and at risk family members. Thirty-seven percent of individuals (113/306) had visited a genetics professional for reasons related to HCM. Genetic testing was performed on 53 % (162/306). Individuals who had undergone testing were more likely to have seen a genetics professional (p < 0.001), had relatives with an HCM diagnosis (p = 0.002), and have a known familial mutation (p < 0.001). They were also more likely to agree that genetic testing would satisfy their curiosity (p < 0.001), provide reassurance (p < 0.001), aid family members in making healthcare decisions (p < 0.001), and encourage them to engage in a healthier lifestyle (p = 0.002). The HBM components of cues to action and perceived benefits and barriers had the greatest impact on uptake of genetic testing. In order to ensure optimal counseling and care for individuals and families with HCM, awareness and education around HCM and genetic services should be promoted in both physicians and patients alike.

  View details for DOI 10.1007/s10897-014-9810-8

  View details for PubMedID 25566741

• 46,XY disorders of sex development and congenital diaphragmatic hernia: A case with dysmorphic facies, truncus arteriosus, bifid thymus, gut malrotation, rhizomelia, and adactyly AMERICAN JOURNAL OF MEDICAL GENETICS PART A Esplin, E. D., Chaib, H., Haney, M., Martin, B., Homeyer, M., Urban, A. E., Bernstein, J. A. 2015; 167A (6): 1360-1364

  Abstract

  The association of 46,XY disorder of sex development (DSD) with congenital diaphragmatic hernia (CDH) is rare, but has been previously described with and without other congenital anomalies. Literature review identified five cases of 46,XY DSD associated with CDH and other congenital anomalies. These five cases share characteristics including CDH, 46,XY karyotype with external female appearing or ambiguous genitalia, cardiac anomalies, and decreased life span. The present case had novel features including truncus arteriosus, bifid thymus, gut malrotation, and limb anomalies consisting of rhizomelia and adactyly. With this case report, we present a review of the literature of cases of 46,XY DSD and CDH in association with multiple congenital abnormalities. This case may represent a unique syndrome of 46,XY DSD and diaphragmatic hernia or a more severe presentation of a syndrome represented in the previously reported cases. © 2015 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.37037

  View details for Web of Science ID 000355276700028

• Increased body mass in infancy and early toddlerhood in Angelman syndrome patients with uniparental disomy and imprinting center defects. American journal of medical genetics. Part A Brennan, M., Adam, M. P., Seaver, L. H., Myers, A., Schelley, S., Zadeh, N., Hudgins, L., Bernstein, J. A. 2015; 167A (1): 142-146

  Abstract

  The diagnosis of Angelman syndrome (AS) is based on clinical features and genetic testing. Developmental delay, severe speech impairment, ataxia, atypical behavior and microcephaly by two years of age are typical. Feeding difficulties in young infants and obesity in late childhood can also be seen. The NIH Angelman-Rett-Prader-Willi Consortium and others have documented genotype-phenotype associations including an increased body mass index in children with uniparental disomy (UPD) or imprinting center (IC) defects. We recently encountered four cases of infantile obesity in non-deletion AS cases, and therefore examined body mass measures in a cohort of non-deletion AS cases. We report on 16 infants and toddlers (ages 6 to 44 months; 6 female, and 10 male) with severe developmental delay. Birth weights were appropriate for gestational age in most cases, >97th% in one case and not available in four cases. The molecular subclass case distribution consisted of: UPD (n = 2), IC defect (n = 3), UPD or IC defect (n = 3), and UBE3A mutation (n = 8). Almost all (7 out of 8) UPD, IC and UPD/IC cases went on to exhibit >90th% age- and gender-appropriate weight for height or BMI within the first 44 months. In contrast, no UBE3A mutation cases exhibited obesity or pre-obesity measures (percentiles ranged from <3% to 55%). These findings demonstrate that increased body mass may be evident as early as the first year of life and highlight the utility of considering the diagnosis of AS in the obese infant or toddler with developmental delay, especially when severe. Although a mechanism explaining the association of UPD, and IC defects with obesity has not been identified, recognition of this correlation may inform investigation of imprinting at the PWS/AS locus and obesity. © 2014 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.36831

  View details for PubMedID 25402239

• Cold-aggravated pain in humans caused by a hyperactive NaV1.9 channel mutant. Nature communications Leipold, E., Hanson-Kahn, A., Frick, M., Gong, P., Bernstein, J. A., Voigt, M., Katona, I., Oliver Goral, R., Altmüller, J., Nürnberg, P., Weis, J., Hübner, C. A., Heinemann, S. H., Kurth, I. 2015; 6: 10049-?

  Abstract

  Gain-of-function mutations in the human SCN11A-encoded voltage-gated Na(+) channel NaV1.9 cause severe pain disorders ranging from neuropathic pain to congenital pain insensitivity. However, the entire spectrum of the NaV1.9 diseases has yet to be defined. Applying whole-exome sequencing we here identify a missense change (p.V1184A) in NaV1.9, which leads to cold-aggravated peripheral pain in humans. Electrophysiological analysis reveals that p.V1184A shifts the voltage dependence of channel opening to hyperpolarized potentials thereby conferring gain-of-function characteristics to NaV1.9. Mutated channels diminish the resting membrane potential of mouse primary sensory neurons and cause cold-resistant hyperexcitability of nociceptors, suggesting a mechanistic basis for the temperature dependence of the pain phenotype. On the basis of direct comparison of the mutations linked to either cold-aggravated pain or pain insensitivity, we propose a model in which the physiological consequence of a mutation, that is, augmented versus absent pain, is critically dependent on the type of NaV1.9 hyperactivity.

  View details for DOI 10.1038/ncomms10049

  View details for PubMedID 26645915

• Perinatal features of the RASopathies: Noonan syndrome, cardiofaciocutaneous syndrome and Costello syndrome. American journal of medical genetics. Part A Myers, A., Bernstein, J. A., Brennan, M., Curry, C., Esplin, E. D., Fisher, J., Homeyer, M., Manning, M. A., Muller, E. A., Niemi, A., Seaver, L. H., Hintz, S. R., Hudgins, L. 2014; 164A (11): 2814-2821

  Abstract

  The RASopathies are a family of developmental disorders caused by heritable defects of the RAS/MAPK signaling pathway. While the postnatal presentation of this group of disorders is well known, the prenatal and neonatal findings are less widely recognized. We report on the perinatal presentation of 10 patients with Noonan syndrome (NS), nine with Cardiofaciocutaneous syndrome (CFCS) and three with Costello syndrome (CS), in conjunction with the results of a comprehensive literature review. The majority of perinatal findings in NS, CS, and CFCS are shared: polyhydramnios; prematurity; lymphatic dysplasia; macrosomia; relative macrocephaly; respiratory distress; hypotonia, as well as cardiac and renal anomalies. In contrast, fetal arrhythmia and neonatal hypoglycemia are relatively specific to CS. NS, CS, and CFCS should all be considered as a possible diagnosis in pregnancies with a normal karyotype and ultrasound findings of a RASopathy. Recognition of the common perinatal findings of these disorders should facilitate both their prenatal and neonatal diagnosis. © 2014 Wiley Periodicals, Inc.

  View details for DOI 10.1002/ajmg.a.36737

  View details for PubMedID 25250515

• Inappropriate p53 activation during development induces features of CHARGE syndrome. Nature Van Nostrand, J. L., Brady, C. A., Jung, H., Fuentes, D. R., Kozak, M. M., Johnson, T. M., Lin, C., Lin, C., Swiderski, D. L., Vogel, H., Bernstein, J. A., Attié-Bitach, T., Chang, C., Wysocka, J., Martin, D. M., Attardi, L. D. 2014; 514 (7521): 228-232

  Abstract

  CHARGE syndrome is a multiple anomaly disorder in which patients present with a variety of phenotypes, including ocular coloboma, heart defects, choanal atresia, retarded growth and development, genitourinary hypoplasia and ear abnormalities. Despite 70-90% of CHARGE syndrome cases resulting from mutations in the gene CHD7, which encodes an ATP-dependent chromatin remodeller, the pathways underlying the diverse phenotypes remain poorly understood. Surprisingly, our studies of a knock-in mutant mouse strain that expresses a stabilized and transcriptionally dead variant of the tumour-suppressor protein p53 (p53(25,26,53,54)), along with a wild-type allele of p53 (also known as Trp53), revealed late-gestational embryonic lethality associated with a host of phenotypes that are characteristic of CHARGE syndrome, including coloboma, inner and outer ear malformations, heart outflow tract defects and craniofacial defects. We found that the p53(25,26,53,54) mutant protein stabilized and hyperactivated wild-type p53, which then inappropriately induced its target genes and triggered cell-cycle arrest or apoptosis during development. Importantly, these phenotypes were only observed with a wild-type p53 allele, as p53(25,26,53,54)(/-) embryos were fully viable. Furthermore, we found that CHD7 can bind to the p53 promoter, thereby negatively regulating p53 expression, and that CHD7 loss in mouse neural crest cells or samples from patients with CHARGE syndrome results in p53 activation. Strikingly, we found that p53 heterozygosity partially rescued the phenotypes in Chd7-null mouse embryos, demonstrating that p53 contributes to the phenotypes that result from CHD7 loss. Thus, inappropriate p53 activation during development can promote CHARGE phenotypes, supporting the idea that p53 has a critical role in developmental syndromes and providing important insight into the mechanisms underlying CHARGE syndrome.

  View details for DOI 10.1038/nature13585

  View details for PubMedID 25119037

• Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genetics in medicine Enns, G. M., Shashi, V., Bainbridge, M., Gambello, M. J., Zahir, F. R., Bast, T., Crimian, R., Schoch, K., Platt, J., Cox, R., Bernstein, J. A., Scavina, M., Walter, R. S., Bibb, A., Jones, M., Hegde, M., Graham, B. H., Need, A. C., Oviedo, A., Schaaf, C. P., Boyle, S., Butte, A. J., Chen, R., Clark, M. J., Haraksingh, R., Cowan, T. M., He, P., Langlois, S., Zoghbi, H. Y., Snyder, M., Gibbs, R. A., Freeze, H. H., Goldstein, D. B. 2014; 16 (10): 751-758

  Abstract

  Purpose:The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1.Methods:Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data.Results:All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele.Conclusion:NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.Genet Med advance online publication 20 March 2014Genetics in Medicine (2014); doi:10.1038/gim.2014.22.

  View details for DOI 10.1038/gim.2014.22

  View details for PubMedID 24651605

• Clinical whole-exome sequencing: are we there yet? Genetics in medicine Atwal, P. S., Brennan, M., Cox, R., Niaki, M., Platt, J., Homeyer, M., Kwan, A., Parkin, S., Schelley, S., Slattery, L., Wilnai, Y., Bernstein, J. A., Enns, G. M., Hudgins, L. 2014; 16 (9): 717-719

  Abstract

  Background:Clinical laboratories began offering whole-exome sequencing in 2011 at a cost between $4,500 and $9,000. Reported detection rates for deleterious mutations range from 25 to 50%. Based on the experience of our clinical genetics service, actual success rates may be lower than estimated rates. We report results from our own experience along with a survey of clinical geneticists to ascertain (i) current success rates for causal gene detection in a clinical setting; (ii) if there are insurance authorization issues; and (iii) if turnaround times quoted by the clinical laboratories are accurate; we also gauge provider opinions toward clinical whole-exome sequencing.Methods:We reviewed our results and the results of a survey that was electronically distributed to 47 clinical genetics centers.Results:A total of 35 exome reports were available. If all positive results are collated, we observe a success rate of 22.8%. One result incorrectly identified a known benign variant as pathogenic. Some insurers covered all testing, whereas others denied any insurance coverage. Only three (23.1%) of our reports were available within the laboratory's quoted turnaround times. More than 50% of clinicians queried in our survey had not ordered whole-exome sequencing at the current time, many stating concerns regarding interpretation, insurance coverage, and cost.Conclusion:Clinical whole-exome sequencing has proven diagnostic utility; however, currently many clinicians have concerns regarding interpretation of results, insurance coverage, and cost.Genet Med advance online publication 13 February 2014Genetics in Medicine (2014); doi:10.1038/gim.2014.10.

  View details for DOI 10.1038/gim.2014.10

  View details for PubMedID 24525916

• A recurrent fibrillin-1 mutation in severe early onset Marfan syndrome. Journal of pediatric genetics Sureka, D., Stheneur, C., Odent, S., Arno, G., Murphy, D., Bernstein, J. A. 2014; 3 (3): 157-162

  Abstract

  The recurrent substitution of isoleucine for threonine at codon 1048 (I1048T) substitution has been linked to severe, early onset Marfan syndrome, however, the existence of strong genotype-phenotype associations in Marfan syndrome (MFS) is not widely agreed upon. Our aim is to substantiate the association between the I1048T substitution and a severe clinical presentation to facilitate care planning and genetic counseling. We review the clinical findings from seven cases of early-onset MFS with a recurrent I1048T substitution. The presented findings include those from one newly diagnosed case, significant new detail from three additional cases, and a review of published findings in three cases. All seven individuals with the I1048T substitution had mitral insufficiency, arachnodactyly and characteristic facies consistent with early-onset MFS. Our findings support the existence of a genotype-phenotype correlation between the I1048T substitution and early-onset MFS. Recognition of this relationship has implications for genetic counseling and clinical care. Additionally, exploration of how the I1048T substitution results in a severe phenotype may lead to further insight into the pathophysiology of MFS.

  View details for DOI 10.3233/PGE-14095

  View details for PubMedID 27625872

• Clinical interpretation and implications of whole-genome sequencing. JAMA Dewey, F. E., Grove, M. E., Pan, C., Goldstein, B. A., Bernstein, J. A., Chaib, H., Merker, J. D., Goldfeder, R. L., Enns, G. M., David, S. P., Pakdaman, N., Ormond, K. E., Caleshu, C., Kingham, K., Klein, T. E., Whirl-Carrillo, M., Sakamoto, K., Wheeler, M. T., Butte, A. J., Ford, J. M., Boxer, L., Ioannidis, J. P., Yeung, A. C., Altman, R. B., Assimes, T. L., Snyder, M., Ashley, E. A., Quertermous, T. 2014; 311 (10): 1035-1045

  Abstract

  Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication.To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings.An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings.Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up.Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95% CI, 0.40-0.64), and reclassified 69% of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001).In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine.

  View details for DOI 10.1001/jama.2014.1717

  View details for PubMedID 24618965

• SHANK3 and IGF1 restore synaptic deficits in neurons from 22q13 deletion syndrome patients. Nature Shcheglovitov, A., Shcheglovitova, O., Yazawa, M., Portmann, T., Shu, R., Sebastiano, V., Krawisz, A., Froehlich, W., Bernstein, J. A., Hallmayer, J. F., Dolmetsch, R. E. 2013; 503 (7475): 267-271

  Abstract

  Phelan-McDermid syndrome (PMDS) is a complex neurodevelopmental disorder characterized by global developmental delay, severely impaired speech, intellectual disability, and an increased risk of autism spectrum disorders (ASDs). PMDS is caused by heterozygous deletions of chromosome 22q13.3. Among the genes in the deleted region is SHANK3, which encodes a protein in the postsynaptic density (PSD). Rare mutations in SHANK3 have been associated with idiopathic ASDs, non-syndromic intellectual disability, and schizophrenia. Although SHANK3 is considered to be the most likely candidate gene for the neurological abnormalities in PMDS patients, the cellular and molecular phenotypes associated with this syndrome in human neurons are unknown. We generated induced pluripotent stem (iPS) cells from individuals with PMDS and autism and used them to produce functional neurons. We show that PMDS neurons have reduced SHANK3 expression and major defects in excitatory, but not inhibitory, synaptic transmission. Excitatory synaptic transmission in PMDS neurons can be corrected by restoring SHANK3 expression or by treating neurons with insulin-like growth factor 1 (IGF1). IGF1 treatment promotes formation of mature excitatory synapses that lack SHANK3 but contain PSD95 and N-methyl-D-aspartate (NMDA) receptors with fast deactivation kinetics. Our findings provide direct evidence for a disruption in the ratio of cellular excitation and inhibition in PMDS neurons, and point to a molecular pathway that can be recruited to restore it.

  View details for DOI 10.1038/nature12618

  View details for PubMedID 24132240

• ß-Galactosidosis in Patient with Intermediate GM1 and MBD Phenotype. JIMD reports Moore, T., Bernstein, J. A., Casson-Parkin, S., Cowan, T. M. 2013; 7: 77-79

  Abstract

  A 5-year-old girl with clinical and biochemical phenotypes encompassing both GM1-gangliosidosis (GM1) and Morquio B disease (MBD) is described. Mild generalized skeletal dysplasia and keratan sulfaturia were consistent with a diagnosis of MBD, while developmental delay and GM1-specific oligosacchariduria were consistent with GM1 gangliosidosis. No observable β-galactosidase activity was detected in leukocytes, and two mutations, p.R201H (c.602G>A) and p.G311R (c.931G>A), were identified by gene sequencing. The R201H substitution has been previously reported in patients with both GM1 and MBD, and G311R is a novel mutation. Our patient represents a further example of the clinical heterogeneity that can result from mutations at the β-galactosidase locus.

  View details for DOI 10.1007/8904_2012_145

  View details for PubMedID 23430499

• Underutilization of Genetics Services for Autism: The Importance of Parental Awareness and Provider Recommendation JOURNAL OF GENETIC COUNSELING Vande Wydeven, K., Kwan, A., Hardan, A. Y., Bernstein, J. A. 2012; 21 (6): 803-813

  Abstract

  Reasons for the underutilization of genetics services by families of children with autism spectrum disorders (ASD) are not well understood. We report the identification of factors associated with this underuse. Survey-based study of parents and/or guardians of children with ASD. One hundred fifty-five families completed the questionnaire. Thirty-one of 155 (20%) children had seen a genetics professional. Forty-nine of 154 (32%) children had undergone genetic testing. Parents whose child saw a genetics professional were more likely to 1) Have a primary provider refer for or suggest a genetics evaluation 2) Have asked for a referral, and/or 3) Know another person with a genetic cause of ASD. amilies of children with ASD who have not received genetics services are less aware of their availability and utility. They are also less likely to have their provider recommend a clinical genetics evaluation. Efforts should be taken to increase awareness of both health providers and parents regarding the usefulness of genetics services for ASD.

  View details for DOI 10.1007/s10897-012-9494-x

  View details for PubMedID 22415587

• ALX4 gain-of-function mutations in nonsyndromic craniosynostosis HUMAN MUTATION Yagnik, G., Ghuman, A., Kim, S., Stevens, C. G., Kimonis, V., Stoler, J., Sanchez-Lara, P. A., Bernstein, J. A., Naydenov, C., Drissi, H., Cunningham, M. L., Kim, J., Boyadjiev, S. A. 2012; 33 (12): 1626-1629

  Abstract

  Craniosynostosis is the early fusion of one or more sutures of the infant skull and is a common defect occurring in approximately 1 of every 2,500 live births. Nonsyndromic craniosynostosis (NSC) accounts for approximately 80% of all cases and is thought to have strong genetic determinants that are yet to be identified. ALX4 is a homeodomain transcription factor with known involvement in osteoblast regulation. By direct sequencing of the ALX4 coding region in sagittal or sagittal-suture-involved nonsyndromic craniosynostosis probands, we identified novel, nonsynonymous, familial variants in three of 203 individuals with NSC. Using dual-luciferase assay we show that two of these variants (V7F and K211E) confer a significant gain-of-function effect on ALX4. Our results suggest that ALX4 variants may have an impact on the genetic etiology of NSC.

  View details for DOI 10.1002/humu.22166

  View details for Web of Science ID 000310975900002

  View details for PubMedID 22829454

  View details for PubMedCentralID PMC3495992

• Spectrum of Mutations in the Renin-Angiotensin System Genes in Autosomal Recessive Renal Tubular Dysgenesis HUMAN MUTATION Gribouval, O., Moriniere, V., Pawtowski, A., Arrondel, C., Sallinen, S., Saloranta, C., Clericuzio, C., Viot, G., Tantau, J., Blesson, S., Cloarec, S., Machet, M. C., Chitayat, D., Thauvin, C., Laurent, N., Sampson, J. R., Bernstein, J. A., Clemenson, A., Prieur, F., Daniel, L., Levy-Mozziconacci, A., Lachlan, K., Alessandri, J. L., Cartault, F., Riviere, J. P., Picard, N., Baumann, C., Delezoide, A. L., Belar Ortega, M., Chassaing, N., Labrune, P., Yu, S., Firth, H., Wellesley, D., Bitzan, M., Alfares, A., Braverman, N., Krogh, L., Tolmie, J., Gaspar, H., Doray, B., Majore, S., Bonneau, D., Triau, S., Loirat, C., David, A., Bartholdi, D., Peleg, A., Brackman, D., Stone, R., DeBerardinis, R., Corvol, P., Michaud, A., Antignac, C., Gubler, M. C. 2012; 33 (2): 316-326

  Abstract

  Autosomal recessive renal tubular dysgenesis (RTD) is a severe disorder of renal tubular development characterized by early onset and persistent fetal anuria leading to oligohydramnios and the Potter sequence, associated with skull ossification defects. Early death occurs in most cases from anuria, pulmonary hypoplasia, and refractory arterial hypotension. The disease is linked to mutations in the genes encoding several components of the renin-angiotensin system (RAS): AGT (angiotensinogen), REN (renin), ACE (angiotensin-converting enzyme), and AGTR1 (angiotensin II receptor type 1). Here, we review the series of 54 distinct mutations identified in 48 unrelated families. Most of them are novel and ACE mutations are the most frequent, observed in two-thirds of families (64.6%). The severity of the clinical course was similar whatever the mutated gene, which underlines the importance of a functional RAS in the maintenance of blood pressure and renal blood flow during the life of a human fetus. Renal hypoperfusion, whether genetic or secondary to a variety of diseases, precludes the normal development/ differentiation of proximal tubules. The identification of the disease on the basis of precise clinical and histological analyses and the characterization of the genetic defects allow genetic counseling and early prenatal diagnosis.

  View details for DOI 10.1002/humu.21661

  View details for Web of Science ID 000300705600004

  View details for PubMedID 22095942

• Analysis of the Alternative Splicing of an FGFR2 Transcript Due to a Novel 5 ' Splice Site Mutation (1084+1G > A): Case Report CLEFT PALATE-CRANIOFACIAL JOURNAL Traynis, I., Bernstein, J. A., Gardner, P., Schrijver, I. 2012; 49 (1): 104-108

  Abstract

  Craniosynostosis is characterized by premature fusion of one or more cranial sutures and is associated with mutations in fibroblast growth factor receptor (FGFR) genes. Here we describe a novel mutation (1084+1G>A) in the FGFR2 gene of a patient with isolated bicoronal synostosis. We detected two isoforms that result from the mutation and are characterized, respectively, by exon skipping and the use of a cryptic splice site. Interestingly, the alternatively spliced forms of FGFR2 appear to induce fusion of the cranial sutures suggesting that the mutation acts via a gain-of-function mechanism rather than a loss of protein functionality.

  View details for DOI 10.1597/10-217

  View details for PubMedID 21524234

• Rapid Implementation of Inpatient Electronic Physician Documentation at an Academic Hospital APPLIED CLINICAL INFORMATICS Hahn, J. S., Bernstein, J. A., MCKENZIE, R. B., King, B. J., Longhurst, C. A. 2012; 3 (2): 175-185

  Abstract

  Electronic physician documentation is an essential element of a complete electronic medical record (EMR). At Lucile Packard Children's Hospital, a teaching hospital affiliated with Stanford University, we implemented an inpatient electronic documentation system for physicians over a 12-month period. Using an EMR-based free-text editor coupled with automated import of system data elements, we were able to achieve voluntary, widespread adoption of the electronic documentation process. When given the choice between electronic versus dictated report creation, the vast majority of users preferred the electronic method. In addition to increasing the legibility and accessibility of clinical notes, we also decreased the volume of dictated notes and scanning of handwritten notes, which provides the opportunity for cost savings to the institution.

  View details for DOI 10.4338/ACI-2012-02-CR-0003

  View details for Web of Science ID 000317183500003

  View details for PubMedID 23620718

• Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome NATURE MEDICINE Pasca, S. P., Portmann, T., Voineagu, I., Yazawa, M., Shcheglovitov, A., Pasca, A. M., Cord, B., Palmer, T. D., Chikahisa, S., Nishino, S., Bernstein, J. A., Hallmayer, J., Geschwind, D. H., Dolmetsch, R. E. 2011; 17 (12): 1657-U176

  Abstract

  Monogenic neurodevelopmental disorders provide key insights into the pathogenesis of disease and help us understand how specific genes control the development of the human brain. Timothy syndrome is caused by a missense mutation in the L-type calcium channel Ca(v)1.2 that is associated with developmental delay and autism. We generated cortical neuronal precursor cells and neurons from induced pluripotent stem cells derived from individuals with Timothy syndrome. Cells from these individuals have defects in calcium (Ca(2+)) signaling and activity-dependent gene expression. They also show abnormalities in differentiation, including decreased expression of genes that are expressed in lower cortical layers and in callosal projection neurons. In addition, neurons derived from individuals with Timothy syndrome show abnormal expression of tyrosine hydroxylase and increased production of norepinephrine and dopamine. This phenotype can be reversed by treatment with roscovitine, a cyclin-dependent kinase inhibitor and atypical L-type-channel blocker. These findings provide strong evidence that Ca(v)1.2 regulates the differentiation of cortical neurons in humans and offer new insights into the causes of autism in individuals with Timothy syndrome.

  View details for DOI 10.1038/nm.2576

  View details for PubMedID 22120178

• Newborn with prenatally diagnosed choroidal fissure cyst and panhypopituitarism and review of the literature. AJP reports Chitkara, R., Rajani, A., Bernstein, J., Shah, S., Hahn, J. S., Barnes, P., Hintz, S. R. 2011; 1 (2): 111-114

  Abstract

  Little has been reported on fetal diagnosis of choroidal fissure cysts and prediction of the clinical complications that can result. We describe the case of a near-term male infant with prenatally diagnosed choroidal fissure cyst and bilateral clubfeet. His prolonged course in the neonatal intensive care nursery was marked by severe panhypopituitarism, late-onset diabetes insipidus, placement of a cystoperitoneal shunt, and episodes of sepsis. Postnatal genetic evaluation also revealed an interstitial deletion involving most of band 10q26.12 and the proximal half of band 10q26.13. The patient had multiple readmissions for medical and surgical indications and died at 6 months of age. This case represents the severe end of the spectrum of medical complications for children with choroidal fissure cysts. It highlights not only the importance of comprehensive evaluation and multidisciplinary management and counseling in such cases, but also the need for heightened vigilance in these patients.

  View details for DOI 10.1055/s-0031-1293512

  View details for PubMedID 23705098

• Ectopia Lentis as the Presenting and Primary Feature in Marfan Syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Zadeh, N., Bernstein, J. A., Niemi, A. K., Dugan, S., Kwan, A., Liang, D., Hyland, J. C., Hoyme, H. E., Hudgins, L., Manning, M. A. 2011; 155A (11): 2661-2668

  Abstract

  Marfan syndrome (MFS) is a multisystem connective tissue disorder with primary involvement of the ocular, cardiovascular, and skeletal systems. We report on eight patients, all presenting initially with bilateral ectopia lentis (EL) during early childhood. These individuals did not have systemic manifestations of MFS, and did not fulfill the revised Ghent diagnostic criteria. However, all patients had demonstratable, disease-causing missense mutations in the FBN1 gene. Based on molecular results, cardiovascular imaging was recommended and led to the identification of mild aortic root changes in seven of the eight patients. The remaining patient had mitral valve prolapse with a normal appearing thoracic aorta. The findings presented in this paper validate the necessity of FBN1 gene testing in all individuals presenting with isolated EL. As we observed, these individuals are at increased risk of cardiovascular complications. Furthermore, we also noted that the majority of our patient cohort's mutations occurred in the 5' portion of the FBN1 gene, and were found to affect highly conserved cysteine residues, which may indicate a possible genotype-phenotype correlation. We conclude that in patients with isolated features of EL, FBN1 mutation analysis is necessary to aid in providing prompt diagnosis, and to identify patients at risk for potentially life-threatening complications. Additionally, knowledge of the type and location of an FBN1 mutation may be useful in providing further clinical correlation regarding phenotypic progression and appropriate medical management.

  View details for DOI 10.1002/ajmg.a.34245

  View details for PubMedID 21932315

• Horseshoe Kidney and a Rare TSC2 Variant in Two Unrelated Individuals With Tuberous Sclerosis Complex AMERICAN JOURNAL OF MEDICAL GENETICS PART A Niemi, A., Northrup, H., Hudgins, L., Bernstein, J. A. 2011; 155A (10): 2534-2537

  Abstract

  Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem disorder characterized by abnormalities involving the skin, brain, kidney (angiomyolipomas, cysts), and heart. Horseshoe kidney has not been considered to be a common renal manifestation of TSC but it has been previously reported in two patients with TSC. We report on two unrelated females with typical manifestations of TSC, horseshoe kidney, and an identical variant c.5138G>A in exon 39 (p.Arg1713His) of TSC2 gene. These cases provide evidence that horseshoe kidney is associated with TSC and add to the evidence for the pathogenicity of this variant. Furthermore, one of the patients also had a diaphragmatic hernia which has been reported twice in the medical literature in individuals with TSC. It is possible that a diaphragmatic hernia is another rare manifestation of TSC and that TSC should be included in the differential diagnosis of infants with a diaphragmatic hernia. Given that both a horseshoe kidney and a diaphragmatic hernia are findings that can be detected prenatally on an ultrasound examination, our findings may have implications for prenatal genetic counseling.

  View details for DOI 10.1002/ajmg.a.34197

  View details for PubMedID 21910228

• Familial Cardiac Valvulopathy Due to Filamin A Mutation AMERICAN JOURNAL OF MEDICAL GENETICS PART A Bernstein, J. A., Bernstein, D., Hehr, U., Hudgins, L. 2011; 155A (9): 2236-2241

  Abstract

  We report on the clinical findings in siblings affected by the recently characterized X-linked form of hereditary cardiac valvular dystrophy or cardiac valve disease (OMIM 314400) due to mutations in the FLNA gene and review the literature on this condition. Although FLNA related cardiac valve disease is presumed to be a rare disorder, it is likely underdiagnosed. Several features of this condition may aid in its identification. FLNA related valvular disease can be recognized on the basis of its distinctive inheritance, early age of onset, and frequent multi-valve involvement.

  View details for DOI 10.1002/ajmg.a.34132

  View details for PubMedID 21815255

• Using induced pluripotent stem cells to investigate cardiac phenotypes in Timothy syndrome NATURE Yazawa, M., Hsueh, B., Jia, X., Pasca, A. M., Bernstein, J. A., Hallmayer, J., Dolmetsch, R. E. 2011; 471 (7337): 230-U120

  Abstract

  Individuals with congenital or acquired prolongation of the QT interval, or long QT syndrome (LQTS), are at risk of life-threatening ventricular arrhythmia. LQTS is commonly genetic in origin but can also be caused or exacerbated by environmental factors. A missense mutation in the L-type calcium channel Ca(V)1.2 leads to LQTS in patients with Timothy syndrome. To explore the effect of the Timothy syndrome mutation on the electrical activity and contraction of human cardiomyocytes, we reprogrammed human skin cells from Timothy syndrome patients to generate induced pluripotent stem cells, and differentiated these cells into cardiomyocytes. Electrophysiological recording and calcium (Ca(2+)) imaging studies of these cells revealed irregular contraction, excess Ca(2+) influx, prolonged action potentials, irregular electrical activity and abnormal calcium transients in ventricular-like cells. We found that roscovitine, a compound that increases the voltage-dependent inactivation of Ca(V)1.2 (refs 6-8), restored the electrical and Ca(2+) signalling properties of cardiomyocytes from Timothy syndrome patients. This study provides new opportunities for studying the molecular and cellular mechanisms of cardiac arrhythmias in humans, and provides a robust assay for developing new drugs to treat these diseases.

  View details for DOI 10.1038/nature09855

  View details for PubMedID 21307850

• Clues to an Early Diagnosis of Kallmann Syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Kaplan, J. D., Bernstein, J. A., Kwan, A., Hudgins, L. 2010; 152A (11): 2796-2801

  Abstract

  Kallmann syndrome (KS) is defined by the association of idiopathic hypogonadotropic hypogonadism and anosmia/hyposmia. Diagnosis is frequently delayed, however, because hypogonadotropic hypogonadism is usually not apparent until puberty and individuals with anosmia/hyposmia are often unaware of this sensory deficit. Mutations in at least six genes have been associated with KS; however, the sensitivity of molecular testing is only about 30% and, therefore, the diagnosis is largely based on clinical findings. We describe the findings in six individuals with KS, which demonstrate the utility of associated anomalies in making this diagnosis. Analysis of our case series and literature review suggests the consideration of KS for males with microphallus and/or cryptorchidism and for any patient with hearing loss, renal agenesis, and/or synkinesis. Conversely, patients with features of KS should have an audiology evaluation and a renal ultrasound.

  View details for DOI 10.1002/ajmg.a.33442

  View details for PubMedID 20949504

• Two-Tier Approach to the Newborn Screening of Methylenetetrahydrofolate Reductase Deficiency and Other Remethylation Disorders with Tandem Mass Spectrometry JOURNAL OF PEDIATRICS Tortorelli, S., Turgeon, C. T., Lim, J. S., Baumgart, S., Day-Salvatore, D., Abdenur, J., Bernstein, J. A., Lorey, F., Lichter-Konecki, U., Oglesbee, D., Raymond, K., Matem, D., Schimmenti, L., Rinaldo, P., Gavrilov, D. K. 2010; 157 (2): 271-275

  Abstract

  To validate a 2-tier approach for newborn screening (NBS) of remethylation defects.The original NBS dried blood spots of 5 patients with a proven diagnosis of a remethylation disorder and 1 patient with biochemical evidence of such disorder were analyzed retrospectively to determine disease ranges for methionine (Met; 4.7-8.1 micromol/L; 1 percentile of healthy population, 11.1 micromol/L), the methionine/phenylalanine ratio (Met/Phe; 0.09-0.16; 1 percentile of healthy population, 0.22), and total homocysteine (tHcy; 42-157 micromol/L; 99 percentile of normal population, 14.7 micromol/L). These preliminary disease ranges showed a sufficient degree of segregation from healthy population data, allowing the selection of cutoff values. A simple algorithm was then developed to reflex cases to a second-tier testing for tHcy, which has been applied prospectively for 14 months.A total of 86 333 NBS samples were tested between January 2007 and March 2008, and 233 of them (0.27%) met the criteria for second-tier testing of tHcy. All cases revealed concentrations of tHcy <15 micromol/L and were considered unaffected. No false-negative results have been reported with a state-wide system based on 2 combined metabolic clinics and laboratories that cover the entire Minnesota population and border areas of neighboring states.Pending more conclusive evidence from the prospective identification of additional true-positive cases, NBS for remethylation disorders appears to be feasible with existing methodologies, with only a marginal increase of the laboratory workload.

  View details for DOI 10.1016/j.jpeds.2010.02.027

  View details for Web of Science ID 000279871700023

  View details for PubMedID 20394947

• Index of suspicion. Pediatrics in review Zadeh, N., Bernstein, J. A., Stiasny, D., Callaghan, M. U., Flores, C. E., Tytko, J. M., Mannarino, F. P., Moore, J. 2010; 31 (4): 167-172

  View details for DOI 10.1542/pir.31-4-167

  View details for PubMedID 20360413

• Improved physician work flow after integrating sign-out notes into the electronic medical record. Joint Commission journal on quality and patient safety / Joint Commission Resources Bernstein, J. A., Imler, D. L., Sharek, P., Longhurst, C. A. 2010; 36 (2): 72-78

  Abstract

  In recent years, electronic sign-out notes have been identified as a means of enhancing the effective transfer of patient care between providers. Such a tool was developed and implemented within the electronic medical record (EMR) system, and its impact on physician work flow was assessed.A printable sign-out report was implemented within the EMR system at a tertiary academic children's hospital. Month 1 post go-live survey data were collected in June and July 2006, and 6-month post go-live survey data were collected in November and December 2006. Use of the sign-out form to document handoff data between go-live and Month 16 (September 2007) was measured using log data from the EMR. Housestaff physicians were asked to report the impact of the tool on their work flow and satisfaction with the sign-out process through a Web-based survey.The sign-out report was steadily adopted following its introduction. Between the first and second surveys, use of EMR-integrated sign-out increased from 37% to 81% of respondents for day-to-night sign-out (chi2 = 12.79, p < .001) and from 14% to 39% for night-to-day sign-out (chi 2 = 5.08, p < .05). With increased use of the report, housestaff reported less time devoted to redundant data entry and increased satisfaction with the sign-out process.EMR-integrated sign-out documents offer the advantages of other electronic network-accessible systems and can also incorporate information already in the medical record in an automated manner. Although the primary motivation for introducing standardized, EMR-integrated sign-out documents is to enhance the safety of patient handoffs, the perception of improved physician work flow is also a benefit of such an intervention.

  View details for PubMedID 20180439

• Clinical and Molecular Heterogeneity in Patients with the CblD Inborn Error of Cobalamin Metabolism JOURNAL OF PEDIATRICS Miousse, I. R., Watkins, D., Coelho, D., Rupar, T., Crombez, E. A., Vilain, E., Bernstein, J. A., Cowan, T., Lee-Messer, C., Enns, G. M., Fowler, B., Rosenblatt, D. S. 2009; 154 (4): 551-556

  Abstract

  To describe 3 patients with the cblD disorder, a rare inborn error of cobalamin metabolism caused by mutations in the MMADHC gene that can result in isolated homocystinuria, isolated methylmalonic aciduria, or combined homocystinuria and methylmalonic aciduria.Patient clinical records were reviewed. Biochemical and somatic cell genetic studies were performed on cultured fibroblasts. Sequence analysis of the MMADHC gene was performed on patient DNA.Patient 1 presented with isolated methylmalonic aciduria, patient 3 with isolated homocystinuria, and patient 2 with combined methylmalonic aciduria and homocystinuria. Studies of cultured fibroblasts confirmed decreased synthesis of adenosylcobalamin in patient 1, decreased synthesis of methylcobalamin in patient 3, and decreased synthesis of both cobalamin derivatives in patient 2. The diagnosis of cblD was established in each patient by complementation analysis. Mutations in the MMADHC gene were identified in all patients.The results emphasize the heterogeneous clinical, cellular and molecular phenotype of the cblD disorder. The results of molecular analysis of the MMADHC gene are consistent with the hypothesis that mutations affecting the N terminus of the MMADHC protein are associated with methylmalonic aciduria, and mutations affecting the C terminus are associated with homocystinuria.

  View details for DOI 10.1016/j.jpeds.2008.10.043

  View details for Web of Science ID 000264808000020

  View details for PubMedID 19058814

• GENOMIC ANALYSIS OF MRNA DECAY IN E. COLI WITH DNA MICROARRAYS RNA TURNOVER IN BACTERIA, ARCHAEA AND ORGANELLES Lin, P., Singh, D., Bernstein, J. A., Lin-Chao, S. 2008; 447: 47-?

  Abstract

  The decay of mRNA plays an important role in the regulation of gene expression. Although relatively ignored for many years and regarded as a simple ribonucleotide salvage pathway, mRNA decay has been established in recent years as a well-defined cellular process that plays an integral role in determining gene expression. The recent application of microarray methods to the study of diverse organisms will help us to better understand these gene regulatory circuits and the influence of transcript stability on gene expression. DNA microarray technology is the method of choice to study individual mRNA half-lives on a global scale. It is important to standardize these methods to generate reproducible and reliable results. In this chapter, we describe experimental designs for the analysis of mRNA decay on a genome-wide scale and provide detailed protocols for each experimental step. We also present an analysis of the decay of chromosomally encoded mRNAs in E. coli.

  View details for DOI 10.1016/S0076-6879(08)02203-9

  View details for Web of Science ID 000262438300003

  View details for PubMedID 19161837

• Global analysis of Escherichia coli RNA degradosome function using DNA microarrays PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bernstein, J. A., Lin, P. H., Cohen, S. N., Lin-Chao, S. 2004; 101 (9): 2758-2763

  Abstract

  RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes.

  View details for DOI 10.1073/pnas.0308747101

  View details for PubMedID 14981237

• Life after transcription - revisiting the fate of messenger RNA TRENDS IN GENETICS Khodursky, A. B., Bernstein, J. A. 2003; 19 (3): 113-115

  Abstract

  Recently, several groups have used high-density DNA microarrays to study mRNA turnover. These new data suggest that decay contributes significantly to determining mRNA levels, and they should prompt us to refocus our attention on the regulatory potential of mRNA decay.

  View details for Web of Science ID 000181584500001

  View details for PubMedID 12615000

• Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management. Methods in molecular biology (Clifton, N.J.) Khodursky, A. B., Bernstein, J. A., Peter, B. J., Rhodius, V., Wendisch, V. F., Zimmer, D. P. 2003; 224: 61-78

  View details for PubMedID 12710666

• Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S., Cohen, S. N. 2002; 99 (15): 9697-9702

  Abstract

  Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the approximately 4,300 predicted E. coli messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of E. coli, although approximately 80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in E. coli, nor the free energy of folding of 5' or 3' untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability.

  View details for DOI 10.1073/pnas.112318199

  View details for PubMedID 12119387

• RNase G complementation of me null mutation identifies functional interrelationships with RNase E in Escherichia coli MOLECULAR MICROBIOLOGY Lee, K., Bernstein, J. A., Cohen, S. N. 2002; 43 (6): 1445-1456

  Abstract

  The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-complemented cells accumulated precursors of 5S ribosomal RNA (rRNA) and the RNA component of RNase P (i.e. M1 RNA), indicating that normal processing of these Rne-cleaved RNAs was not restored by RNase G; additionally, neither 5S rRNA nor M1 RNA was generated from precursors by RNase G cleavage in vitro. Using DNA microarrays containing 4405 Escherichia coli open reading frames (ORFs), we identified mRNAs whose steady-state level was affected by Rne, Rng or the N-terminal catalytic domain of RNase E. Most transcript species affected by RNase E deficiency were also elevated in an rne deletion mutant complemented by Rng. However, approximately 100 mRNAs that accumulated in Rne-deficient cells were decreased by rng-complemention, thus identifying targets whose processing or degradation may be the basis for RNase E essentiality. Remarkably prominent in this group were mRNAs implicated in energy-generating pathways or in the synthesis or degradation of macromolecules.

  View details for PubMedID 11952897

• Use of traditional medicine in Mongolia: a survey COMPLEMENTARY THERAPIES IN MEDICINE Bernstein, J. A., Stibich, M. A., LeBaron, S. 2002; 10 (1): 42-45

  Abstract

  To conduct a pilot investigation of the frequency with which individuals visit practitioners of Western and traditional Mongolian medicine and their motivations for making these visits.Survey based interviews were conducted in a sample of 90 adults.Darkhan, Mongolia.Measures included the annual frequency of visits to practitioners of traditional and Western medicine as well as ratings of the importance of seven factors in choosing what type of practitioner to use.During the past year, 51% of subjects interviewed had used Western services exclusively, 8% had used traditional services exclusively, and 38% had used both types of services. Users and non-users of traditional medicine did not vary in terms of age, gender, occupation or rural vs urban residence. Traditional medicine users rated the knowledge base of traditional practitioners higher than did nonusers (5.3/7 vs 4.5/7, P < 0.01). A patient's specific illness appears to be important in deciding what type of treatment he will seek.Traditional medicine appears to be a more significant component of Mongolian health care than is reported in the international literature and consequently may deserve additional attention in future studies of the country's medical system.

  View details for DOI 10.1054/ctim.2002.0508

  View details for Web of Science ID 000177550400008

  View details for PubMedID 12442822