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Jonathan Bernstein, MD, PhD

  • Jonathan A. Bernstein

Especialidades

Clinical Genetics

Trabajo y Educación

Formación Profesional

Stanford School of Medicine, Stanford, CA, 2003

Residencia

Lucile Packard Children's Hospital, Palo Alto, CA, 2006

Compañerismo

Lucile Packard Children's Hospital, Palo Alto, CA, 2008

Certificaciones Médicas

Clinical Genetics, American Board of Medical Genetics and Genomics

Pediatrics, American Board of Pediatrics

Condiciones Tratadas

Autism

Cardiovascular Genetic Issues

Cleft lip/cleft palate

Craniofacial disorders and craniosynostosis

Development delays and disorders

Todo Publicaciones

Teaching Biochemistry and Genetics to Students of Medicine, Pharmacy, and Dentistry 6th International Conference of the Association of Biochemistry Educators (ABE) Niederhoffer, E. C., Cline, S. D., Osheroff, N., Simmons, J. M., Diekman, A. B., Franklin, D. S., Abali, E. E., Bateman Jr., R. C., Fontes, J. D., Lindsley, J. E., Pearson, D., Rubenstein, P. A., Slaughter, C. A., Bernstein, J. A., Hyland, K. H., Park, V. M., Sobering, A. K., Weiler, T. A., Dasgupta, S.
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 (-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 Web of Science ID 000400480400029

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 Web of Science ID 000393352000001

View details for PubMedID 28157539

View details for PubMedCentralID PMC5294757

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 Web of Science ID 000394129900023

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 70kDa 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 Web of Science ID 000393834000001

View details for PubMedID 28126021

De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability. American journal of human genetics Kry, S., van Woerden, G. M., Besnard, T., Proietti Onori, M., Latypova, X., Towne, M. C., Cho, M. T., Prescott, T. E., Ploeg, M. A., Sanders, S., Stessman, H. A., Pujol, A., Distel, B., Robak, L. A., Bernstein, J. A., Denomm-Pichon, A. S., Lesca, G., Sellars, E. A., Berg, J., Carr, W., Busk, . L., van Bon, B. W., Waugh, J. L., Deardorff, M., Hoganson, G. E., Bosanko, K. B., Johnson, D. S., Dabir, T., Holla, . L., Sarkar, A., Tveten, K., de Bellescize, J., Braathen, G. J., Terhal, P. A., Grange, D. K., van Haeringen, A., Lam, C., Mirzaa, G., Burton, J., Bhoj, E. J., Douglas, J., Santani, A. B., Nesbitt, A. I., Helbig, K. L., Andrews, M. V., Begtrup, A., Tang, S., van Gassen, K. L., Juusola, J., Foss, K., Enns, G. M., Moog, U., Hinderhofer, K., Paramasivam, N., Lincoln, S., Kusako, B. H., Lindenbaum, P., Charpentier, E., Nowak, C. B., Cherot, E., Simonet, T., Ruivenkamp, C. A., Hahn, S., Brownstein, C. A., Xia, F., Schmitt, S., Deb, W., Bonneau, D., Nizon, M., Quinquis, D., Chelly, J., Rudolf, G., Sanlaville, D., Parent, P., Gilbert-Dussardier, B., Toutain, A., Sutton, V. R., Thies, J., Peart-Vissers, L. E., Boisseau, P., Vincent, M., Grabrucker, A. M., Dubourg, C., Tan, W. H., Verbeek, N. E., Granzow, M., Santen, G. W., Shendure, J., Isidor, B., Pasquier, L., Redon, R., Yang, Y., State, M. W., Kleefstra, T., Cogn, B., Petrovski, S., Retterer, K., Eichler, E. E., Rosenfeld, J. A., Agrawal, P. B., Bzieau, S., Odent, S., Elgersma, Y., Mercier, S. 2017; 101 (5): 76888

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 DOI 10.1016/j.ajhg.2017.10.003

View details for PubMedID 29100089

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., Walkiewicz, M., Xiao, R., Magoulas, P., Pan, S., Beuten, J., He, W., Bernstein, J. A., Schaaf, C. P., Scaglia, F., Eng, C. M., Yang, Y. 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 DOI 10.1002/ajmg.a.38388

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., Le Scouarnec, S., Cueff, C., Bernstein, D., Aalberts, J. J., Lecointe, S., Mrot, J., Bernstein, J. A., Oomen, T., Dina, C., Karakachoff, M., Desal, H., Al Habash, O., Delling, F. N., Capoulade, R., Suurmeijer, A. J., Milan, D., Norris, R. A., Markwald, R., Aikawa, E., Slaugenhaupt, S. A., Jeunemaitre, X., Hagge, A., Roussel, J. C., Trochu, J. N., Levine, R. A., Kyndt, F., Probst, V., Le Marec, H., 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 (33.39.8 vs. 5.04.9%, P<0.0001; hazard ratio 10.5 [95% confidence interval: 2.9-37.9]) owing mainly to a lifetime increased risk in men (76.814.1 vs. 9.18.7%, 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 DOI 10.1093/eurheartj/ehx505

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., Timms, A. E., Gripp, K., Baker, L., Park, K., Collins, S., Cheng, C., Stewart, F., Mehta, S. G., Saggar, A., Sztriha, L., Zombor, M., Caluseriu, O., Mesterman, R., Van Allen, M. I., Jacquinet, A., Ygberg, S., Bernstein, J. A., Wenger, A. M., Guturu, H., Bejerano, G., Gomez-Ospina, N., Lehman, A., Alfei, E., Pantaleoni, C., Conti, V., Guerrini, R., Moog, U., Graham, J. M., Hevner, R., Dobyns, W. B., O'Driscoll, M., Mirzaa, G. M. 2017; 140 (10): 261022

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 DOI 10.1093/brain/awx203

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., Jensik, P. J., Alaimo, J. T., Walkiewicz, M., Berger, S., Roeder, E., 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 DOI 10.1002/humu.23339

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., Khan, T. N., Szafranski, P., Slattery, L., Streff, H., Vetrini, F., Bernstein, J. A., Brown, C. W., Rosenfeld, J. A., Rednam, S., Scollon, S., Bergstrom, K. L., Parsons, D. W., Plon, S. E., Vieira, M. W., Quaio, C. R., Baratela, W. A., Acosta Guio, J. C., Armstrong, R., Mehta, S. G., Rump, P., Pfundt, R., Lewandowski, R., Fernandes, E. M., Shinde, D. N., Tang, S., Hoyer, J., Zweier, C., Reis, A., Bacino, C. A., Xiao, R., Breman, A. M., Smith, J. L., Katsanis, N., Bostwick, B., Popp, B., Davis, E. E., Yang, Y. 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 denovo 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 DOI 10.1016/j.ajhg.2017.08.014

View details for PubMedID 28942966

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

View details for PubMedCentralID PMC5171698

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., Brggenwirth, 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

Identification of a novel mutation in APTX gene associated with Ataxia-oculomotor apraxia. Cold Spring Harbor molecular case studies Inlora, J., Sailani, M. R., Khodadadi, H., Teymurinezhad, A., Takahashi, S., Bernstein, J. A., Garshasbi, M., 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 DOI 10.1101/mcs.a002014

View details for PubMedID 28652255

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 Mi2, 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 roleof 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 Web of Science ID 000385333700014

View details for PubMedID 27616479

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

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

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 Web of Science ID 000379948000019

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 Web of Science ID 000379420500016

View details for PubMedID 27159400

View details for PubMedCentralID PMC4979321

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 fouryears in all but one patient, who developed chorea at 14years. 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 Web of Science ID 000379452200016

View details for PubMedID 27068059

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

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 proteinsubunit beta-1, G. 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 G binding sites, which suggests that a likely disease mechanism is through the disruption of the protein interface required for G-G interaction (resulting in a constitutively active G) or through the disruption of residues relevant for interaction between G 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 Web of Science ID 000375869300017

View details for PubMedID 27108799

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, 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 18q22qter 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 18q22qter 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

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 Web of Science ID 000373098900018

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

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

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 g/mL) compared with those with PAPA syndrome (116 74 g/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 (EK) 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 Web of Science ID 000364787200024

View details for PubMedID 26025129

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 Web of Science ID 000362916200010

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
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., Altmller, J., Nrnberg, P., Weis, J., Hbner, 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

Clinical reappraisal of SHORT syndrome with PIK3R1 mutations: towards recommendation for molecular testing and management. Clinical genetics 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

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., Atti-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 , 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 , 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

View details for PubMedCentralID PMC4119063

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

-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 -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 -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 Web of Science ID 000311509200011

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

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

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

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 Web of Science ID 000300352600014

View details for PubMedID 21524234

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 Web of Science ID 000297978000039

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 Web of Science ID 000297199700009

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 Web of Science ID 000295326300032

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 Web of Science ID 000294182500031

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 Web of Science ID 000288170200040

View details for PubMedID 21307850

View details for PubMedCentralID PMC3077925

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 Web of Science ID 000284005700019

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 Web of Science ID 000220065300023

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 Web of Science ID 000177042400020

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 Web of Science ID 000174710000007

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