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1. Mammalian target of rapamycin pathway mutations cause hemimegalencephaly and focal cortical dysplasia

Author

D'Gama, AM, Geng, Y, Couto, JA, Martin, B, Boyle, EA, Lacoursiere, CM, Hossain, A, Hatem, NE, Barry, BJ, Kwiatkowski, DJ, Vinters, HV, Barkovich, AJ, Shendure, J, Mathern, GW, Walsh, CA, and Poduri, A

Subjects
Clinical Sciences, Neurosciences, Neurology & Neurosurgery
Abstract

Focal malformations of cortical development, including focal cortical dysplasia (FCD) and hemimegalencephaly (HME), are important causes of intractable childhood epilepsy. Using targeted and exome sequencing on DNA from resected brain samples and nonbrain samples from 53 patients with FCD or HME, we identified pathogenic germline and mosaic mutations in multiple PI3K/AKT pathway genes in 9 patients, and a likely pathogenic variant in 1 additional patient. Our data confirm the association of DEPDC5 with sporadic FCD but also implicate this gene for the first time in HME. Our findings suggest that modulation of the mammalian target of rapamycin pathway may hold promise for malformation-associated epilepsy. Ann Neurol 2015;77:720-725

Published
2015

2. Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional Regulation

Author

Ahituv, Nadav, Birnbaum, RY, Patwardhan, RP, Kim, MJ, Findlay, GM, Martin, B, Zhao, J, Bell, RJA, Smith, RP, Ku, AA, and Shendure, J

Abstract

© 2014 Birnbaum et al.In addition to their protein coding function, exons can also serve as transcriptional enhancers. Mutations in these exonic-enhancers (eExons) could alter both protein function and transcription. However, the functional consequence of

Published
2014

3. Human iPSC Derived Enamel Organoid Guided by Single-Cell Atlas of Human Tooth Development

Author

Alghadeer, A, primary, Hanson-Drury, S, additional, Ehnes, D, additional, Zhao, YT, additional, Patni, AP, additional, O’Day, D, additional, Spurrell, CH, additional, Gogate, AA, additional, Phal, A, additional, Zhang, H, additional, Devi, A, additional, Wang, Y, additional, Starita, L, additional, Doherty, D, additional, Glass, I, additional, Shendure, J, additional, Baker, D, additional, Regier, MC, additional, Mathieu, J, additional, and Ruohola-Baker, H, additional

Published
2022
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6. Guidelines for investigating causality of sequence variants in human disease

Author

MacArthur, D.G., Manolio, T.A., Dimmock, D.P., Rehm, H.L., Shendure, J., Abecasis, G.R., Adams, D.R., Altman, R.B., Antonarakis, S.E., Ashley, E.A., Barrett, J.C., Biesecker, L.G., Conrad, D.F., Cooper, G.M., Cox, N.J., Daly, M.J., Gerstein, M.B., Goldstein, D.B., Hirschhorn, J.N., Leal, S.M., Pennacchio, L.A., Stamatoyannopoulos, J.A., Sunyaev, S.R., Valle, D., Voight, B.F., Winckler, W., and Gunter, C.

Subjects
Genomics -- Investigations -- Research, Genetic translation -- Research, Disease transmission -- Research -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variantlevel support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development., High-throughput sequencing approaches can generate detailed catalogues of genetic variation in both disease patients and the general population. However, for these technologies to have the greatest medical impact we must [...]

Published
2014
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8. Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity

Author

Bachmann-Gagescu, R, Dempsey, J C, Phelps, I G, OʼRoak, B J, Knutzen, D M, Rue, T C, Ishak, G E, Isabella, C R, Gorden, N, Adkins, J, Boyle, E A, de Lacy, N, OʼDay, D, Alswaid, A, Ramadevi A, Radha, Lingappa, L, Lourenço, C, Martorell, L, Garcia-Cazorla, À, Ozyürek, H, Haliloğlu, G, Tuysuz, B, Topçu, M, Chance, P, Parisi, M A, Glass, I A, Shendure, J, and Doherty, D

Published
2015
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11. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

Author

Esposito, D, Weile, J, Shendure, J, Starita, LM, Papenfuss, AT, Roth, FP, Fowler, DM, Rubin, AF, Esposito, D, Weile, J, Shendure, J, Starita, LM, Papenfuss, AT, Roth, FP, Fowler, DM, and Rubin, AF

Abstract

Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB ( https://www.mavedb.org ), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.

Published
2019

12. Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation

Author

Gelman, H, Dines, JN, Berg, J, Berger, AH, Brnich, S, Hisama, FM, James, RG, Rubin, AF, Shendure, J, Shirts, B, Fowler, DM, Starita, LM, Gelman, H, Dines, JN, Berg, J, Berger, AH, Brnich, S, Hisama, FM, James, RG, Rubin, AF, Shendure, J, Shirts, B, Fowler, DM, and Starita, LM

Abstract

Variants of uncertain significance represent a massive challenge to medical genetics. Multiplexed functional assays, in which the functional effects of thousands of genomic variants are assessed simultaneously, are increasingly generating data that can be used as additional evidence for or against variant pathogenicity. Such assays have the potential to resolve variants of uncertain significance, thereby increasing the clinical utility of genomic testing. Existing standards from the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) and new guidelines from the Clinical Genome Resource (ClinGen) establish the role of functional data in variant interpretation, but do not address the specific challenges or advantages of using functional data derived from multiplexed assays. Here, we build on these existing guidelines to provide recommendations to experimentalists for the production and reporting of multiplexed functional data and to clinicians for the evaluation and use of such data. By following these recommendations, experimentalists can produce transparent, complete, and well-validated datasets that are primed for clinical uptake. Our recommendations to clinicians and diagnostic labs on how to evaluate the quality of multiplexed functional datasets, and how different datasets could be incorporated into the ACMG/AMP variant-interpretation framework, will hopefully clarify whether and how such data should be used. The recommendations that we provide are designed to enhance the quality and utility of multiplexed functional data, and to promote their judicious use.

Published
2019

14. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

Author

CRyPTIC Consortium, 100000 Genomes Project, Allix-Beguec, C, Arandjelovic, I, Bi, L, Beckert, P, Bonnet, M, Bradley, P, Cabibbe, AM, Cancino-Munoz, I, Caulfield, MJ, Chaiprasert, A, Cirillo, DM, Clifton, D, Comas, I, Crook, DW, De Filippo, MR, de Neeling, H, Diel, R, Drobniewski, FA, Faksri, K, Farhat, MR, Fleming, J, Fowler, P, Fowler, TA, Gao, Q, Gardy, J, Gascoyne-Binzi, D, Gibertoni-Cruz, A-L, Gil-Brusola, A, Golubchik, T, Gonzalo, X, Grandjean, L, He, G, Guthrie, JL, Hoosdally, S, Hunt, M, Iqbal, Z, Ismail, N, Johnston, J, Khanzada, FM, Khor, CC, Kohl, TA, Kong, C, Lipworth, S, Liu, Q, Maphalala, G, Martinez, E, Mathys, V, Merker, M, Miotto, P, Mistry, N, Moore, DAJ, Murray, M, Niemann, S, Ong, RT-H, Peto, TEA, Posey, JE, Prammananan, T, Pym, A, Rodrigues, C, Rodrigues, M, Rodwell, T, Rossolini, GM, Padilla, ES, Schito, M, Shen, X, Shendure, J, Sintchenko, V, Sloutsky, A, Smith, EG, Snyder, M, Soetaert, K, Starks, AM, Supply, P, Suriyapol, P, Tahseen, S, Tang, P, Teo, Y-Y, Thuong, TNT, Thwaites, G, Tortoli, E, Omar, SV, van Soolingen, D, Walker, AS, Walker, TM, Wilcox, M, Wilson, DJ, Wyllie, D, Yang, Y, Zhang, H, Zhao, Y, and Zhu, B

Abstract

Background: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.\ud \ud \ud \ud Methods: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.\ud \ud \ud \ud Results: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted.\ud \ud \ud \ud Conclusions: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.)

Published
2018

15. De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability

Author

Kury, S., Woerden, G.M. van, Besnard, T., Onori, M.P., Latypova, X., Towne, M.C., Cho, M.T., Prescott, T.E., Ploeg, M.A., Sanders, S., Stessman, H.A.F., Pujol, A., Distel, ben, Robak, L.A., Bernstein, J.A., Denomme-Pichon, A.S., Lesca, G., Sellars, E.A., Berg, J., Carre, W., Busk, O.L., Bon, B.W.M. van, Waugh, J.L., Deardorff, M., Hoganson, G.E., Bosanko, K.B., Johnson, D.S., Dabir, T., Holla, O.L., Sarkar, A., Tveten, K., Bellescize, J. de, Braathen, G.J., Terhal, P.A., Grange, D.K., Haeringen, A. van, 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., Gassen, K.L.I. van, 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.L., 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.L.M., Boisseau, P., Vincent, M., Grabrucker, A.M., Dubourg, C., Tan, W.H., Verbeek, N.E., Granzow, M., Santen, G.W.E., Shendure, J., Isidor, B., Pasquier, L., Redon, R., Yang, Y.P., State, M.W., Kleefstra, T., Cogne, B., Petrovski, S., Retterer, K., Eichler, E.E., Rosenfeld, J.A., Agrawal, P.B., Bezieau, S., Odent, S., Elgersma, Y., Mercier, S., Undiagnosed Dis Network, GEM HUGO, Deciphering Dev Dis Study, Service de génétique médicale [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), Department of Neuroscience [Rotterdam, the Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Expertise Center for Neurodevelopmental Disorders [Rotterdam, the Netherlands] (ENCORE), Genomics Program and Division of Genetics [Boston, USA], Harvard Medical School [Boston] (HMS)-Boston Children's Hospital-The Manton Center for Orphan Disease Research, Gene Discovery Core [Boston, MA, USA] ( The Manton Center for Orphan Disease Research), Harvard Medical School [Boston] (HMS)-Boston Children's Hospital, GeneDx [Gaithersburg, MD, USA], Department of Medical Genetics [Skien, Norway], Telemark Hospital Trust [Skien, Norway], Department of Psychiatry [San Francisco, CA, USA], University of California [San Francisco] (UCSF), University of California-University of California, Department of Genome Sciences [Seattle] (GS), University of Washington [Seattle], Department of Pharmacology [Omaha, NE, USA], Creighton University Medical School [Omaha, NE, USA], Neurometabolic Diseases Laboratory [Barcelona, Spain], Institut d'Investigació Biomèdica de Bellvitge [Barcelone] (IDIBELL), Centre for Biomedical Research on Rare Diseases [Barcelona, Spain] (CIBERER), Hospital Sant Joan de Déu [Barcelona], Institució Catalana de Recerca i Estudis Avançats (ICREA), Department of Medical Biochemistry [Amsterdam, the Netherlands] (Academic Medical Center), University of Amsterdam [Amsterdam] (UvA), Department of Molecular and Human Genetics [Houston, USA], Baylor College of Medecine, Department of Pediatrics [Stanford], Stanford Medicine, Stanford University-Stanford University, Département de Biochimie et Génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Angers (UA), Service de Génétique [HCL, Lyon] (Centre de Référence des Anomalies du Développement), Hospices civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Section of Genetics and Metabolism [Little Rock, AR, USA], University of Arkansas for Medical Sciences (UAMS), Molecular and Clinical Medicine [Dundee, UK] (School of Medicine), University of Dundee [UK]-Ninewells Hospital & Medical School [Dundee, UK], Laboratoire de Génétique Moléculaire & Génomique [CHU Rennes], CHU Pontchaillou [Rennes], Department of Human Genetics [Nijmegen], Radboud University Medical Center [Nijmegen], Department of Neurology [Boston], Harvard Medical School [Boston] (HMS)-Massachusetts General Hospital [Boston], Department of Pediatrics [Philadelphia, PA, USA] (Division of Genetics), Children’s Hospital of Philadelphia (CHOP ), Department of Pediatrics [Chicago, IL, USA] (College of Medicine), University of Illinois [Chicago] (UIC), University of Illinois System-University of Illinois System, Sheffield Children's NHS Foundation Trust, Northern Ireland Regional Genetics Centre [Belfast, UK], Belfast City Hospital-Belfast Health and Social Care Trust, Nottingham Regional Genetics Service [Nottingham, UK], City Hospital Campus [Nottingham, UK]-Nottingham University Hospitals NHS Trust [UK], Département d'Epilepsie, Sommeil et Neurophysiologie Pédiatrique [HCL, Lyon], Hospices Civils de Lyon (HCL), Department of Genetics [Utrecht, the Netherlands], University Medical Center [Utrecht], Department of Pediatrics [Saint Louis, MO, USA] (Division of Genetics and Genomic Medicine), Washington University in Saint Louis (WUSTL), Department of Clinical Genetics [Leiden, the Netherlands], Leiden University Medical Center (LUMC), Department of Pediatrics [Seattle, WA, USA] (Division of Genetic Medicine), University of Washington [Seattle]-Seattle Children’s Hospital, Center for Integrative Brain Research [Seattle, WA, USA], University of Washington [Seattle]-Seattle Children's Research Institute, The Center for Applied Genomics [Philadelphia, PA, USA], Division of Human Genetics [Philadelphia, PA, USA], Department of Pathology and Laboratory Medicine [Philadelphia, PA, USA], University of Pennsylvania [Philadelphia]-Perelman School of Medicine, University of Pennsylvania [Philadelphia], Department of Pathology and Laboratory Medicine [Philadelphia, PA, USA] (Perelman School of Medicine), Division of Clinical Genomics [Aliso Viejo, CA, USA], Ambry Genetics [Aliso Viejo, CA, USA], Division of Neurology [Philadelphia, PA, USA], Institute of Human Genetics [Heidelberg, Germany], Universität Heidelberg [Heidelberg], University of Heidelberg, Medical Faculty, unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Diagnostic Génétique [CHU Strasbourg], Université de Strasbourg (UNISTRA)-CHU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Service de Neurologie [CHU Strasbourg], Hôpital de Hautepierre [Strasbourg]-Centre Hospitalier Universitaire de Strasbourg (CHU de Strasbourg ), Département de génétique médicale en pédiatrie [CHRU Brest], Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Service de Génétique [CHU Poitiers], Centre hospitalier universitaire de Poitiers (CHU Poitiers), Service de Génétique [CHRU Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Department of Biological Sciences [Limerick, Ireland], University of Limerick (UL), Bernal Institute [Limerick, Ireland], Howard Hughes Medical Institute [Seattle], Howard Hughes Medical Institute (HHMI), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Service de Génétique Clinique [CHU Rennes] (Réseau de Génétique et Génomique Médicale), Hôpitaux Universitaires du Grand Ouest, The Wellcome Trust Sanger Institute [Cambridge], Department of Medicine [Melbourne, Australia], University of Melbourne-Austin Health, Division of Newborn Medicine [Boston, MA, USA], Immunobiology of Human αβ and γδ T Cells and Immunotherapeutic Applications (CRCINA-ÉQUIPE 1), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Neurosciences, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Univ Angers, Okina, University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de génétique moléculaire et génomique médicale [CHU Rennes], Nottingham University Hospitals NHS Trust (NUH)-City Hospital Campus [Nottingham, UK], Universiteit Leiden-Universiteit Leiden, Department of Pediatrics [Seattle, WA, USA], University of Pennsylvania-Perelman School of Medicine, University of Pennsylvania, Universität Heidelberg [Heidelberg] = Heidelberg University, Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Service de génétique clinique [Rennes], Université de Rennes (UR)-CHU Pontchaillou [Rennes]-hôpital Sud, Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), Amsterdam Gastroenterology Endocrinology Metabolism, Medical Biochemistry, and Bernardo, Elizabeth

Subjects
0301 basic medicine, Male, de novo mutations, AMPAR, medicine.disease_cause, Inbred C57BL, Mice, 0302 clinical medicine, Intellectual disability, CAMK2A, Exome, Phosphorylation, Genetics (clinical), Genetics, Neurons, Mutation, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Brain, Phenotype, NMDAR, intellectual disability, Female, Signal transduction, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Signal Transduction, Glutamic Acid, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Article, Cell Line, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, medicine, Journal Article, Animals, Humans, Protein kinase A, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], synaptic plasticity, medicine.disease, Mice, Inbred C57BL, CAMK2, CAMK2B, 030104 developmental biology, HEK293 Cells, Synaptic plasticity, Calcium-Calmodulin-Dependent Protein Kinase Type 2, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Contains fulltext : 182539.pdf (Publisher’s version ) (Closed access) 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.

Published
2017
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19. BRCA Testing by Single-Molecule Molecular Inversion Probes

Author

Neveling, K., Mensenkamp, A.R., Derks, R, Kwint, M.P., Ouchene, H., Steehouwer, M., Lier, L.A. van, Bosgoed, E.A.J., Rikken, A., Tychon, M.W.J., Zafeiropoulou, D., Castelein, S., Hehir-Kwa, J.Y., Thung, G.W., Hofste, T., Lelieveld, S.H., Bertens, S.M., Adan, I.B., Eijkelenboom, A., Tops, B.B.J., Yntema, H.G., Stokowy, T., Knappskog, P.M., Hoberg-Vetti, H., Steen, V.M., Boyle, E., Martin, B., Ligtenberg, M.J.L., Shendure, J., Nelen, M.R., Hoischen, A., Neveling, K., Mensenkamp, A.R., Derks, R, Kwint, M.P., Ouchene, H., Steehouwer, M., Lier, L.A. van, Bosgoed, E.A.J., Rikken, A., Tychon, M.W.J., Zafeiropoulou, D., Castelein, S., Hehir-Kwa, J.Y., Thung, G.W., Hofste, T., Lelieveld, S.H., Bertens, S.M., Adan, I.B., Eijkelenboom, A., Tops, B.B.J., Yntema, H.G., Stokowy, T., Knappskog, P.M., Hoberg-Vetti, H., Steen, V.M., Boyle, E., Martin, B., Ligtenberg, M.J.L., Shendure, J., Nelen, M.R., and Hoischen, A.

Abstract

Contains fulltext : 169902.pdf (publisher's version ) (Closed access), BACKGROUND: Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS: The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS: Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS: smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.

Published
2017

20. De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability

Author

Küry, S. (Sébastien), Woerden, G.M. (Geeske) van, Besnard, T. (Thomas), Proietti-Onori, M. (Martina), Latypova, X. (Xénia), Towne, M.C. (Meghan C.), Cho, M.T. (Megan T.), Prescott, T. (Trine), Ploeg, M.A. (Melissa), Sanders, S. (Stephan), Stessman, H.A.F. (Holly A F), Pujol, A. (Aurora), Distel, B. (Ben), Robak, L.A. (Laurie A.), Bernstein, J.A. (Jonathan A.), Denommé-Pichon, A.-S. (Anne-Sophie), Lesca, G. (Gaëtan), Sellars, E.A. (Elizabeth A.), Berg, J. (Jonathan), Carré, W. (Wilfrid), Busk, ØL. (Øyvind Løvold), Bon, B. (Bregje) van, Waugh, J.L. (Jeff L.), Deardorff, M.A. (Matthew), Hoganson, G.E. (George E.), Bosanko, K.B. (Katherine B.), Johnson, D.S. (Diana S.), Dabir, T. (Tabib), Holla, ØL. (Øystein Lunde), Sarkar, A. (Ajoy), Tveten, K. (Kristian), de Bellescize, J. (Julitta), Braathen, G.J. (Geir J.), Terhal, P. (Paulien), Grange, D.K. (Dorothy K.), Haeringen, A. (Arie) van, Lam, C. (Christina), Mirzaa, G.M. (Ghayda), Burton, J. (Jennifer), Bhoj, E.J. (Elizabeth J.), Douglas, J. (Jessica), Santani, A.B. (Avni B.), Nesbitt, A.I. (Addie I.), Helbig, K.L. (Katherine L.), Andrews, M.V. (Marisa V.), Begtrup, A. (Amber), Tang, S. (Sha), van Gassen, K.L.I. (Koen L.I.), Juusola, J. (Jane), Foss, K. (Kimberly), Enns, G. (Gregory), Moog, U. (Ute), Hinderhofer, K. (Katrin), Paramasivam, N. (Nagarajan), Lincoln, S. (Sharyn), Kusako, B.H. (Brandon H.), Lindenbaum, P. (Pierre), Charpentier, E. (Eric), Nowak, C.B. (Catherine B.), Cherot, E. (Elouan), Simonet, T. (Thomas), Ruivenkamp, C.A. (Claudia), Hahn, S. (Sihoun), Brownstein, C.A. (Catherine A.), Xia, F. (Fan), Schmitt, S. (Sébastien), Deb, W. (Wallid), Bonneau, D. (Dominique), Nizon, M. (Mathilde), Quinquis, D. (Delphine), Chelly, J. (Jamel), Rudolf, G. (Gabrielle), Sanlaville, D. (Damien), Parent, P. (Philippe), Gilbert-Dussardier, B. (Brigitte), Toutain, A. (Annick), Sutton, V.R. (V. Reid), Thies, J. (Jenny), Peart-Vissers, L.E.L.M. (Lisenka E L M), Boisseau, P. (Pierre), Vincent, M. (Marie), Grabrucker, A.M. (Andreas M.), Dubourg, C. (Christèle), Tan, W.-H. (Wen-Hann), Verbeek, N.E. (Nienke), Granzow, M. (Martin), Santen, G.W.E. (Gijs), Shendure, J. (Jay), Isidor, B. (Bertrand), Pasquier, L. (Laurent), Redon, R. (Richard), Yang, Y. (Yaping), State, M.W. (Matthew), Kleefstra, T. (Tjitske), Cogné, B. (Benjamin), Petrovski, S. (Slavé), Retterer, K. (Kyle), Eichler, E.E. (Evan), Rosenfeld, J.A. (Jill), Agrawal, P.B. (Pankaj B.), Bézieau, S. (Stéphane), Odent, S. (Sylvie), Elgersma, Y. (Ype), Mercier, S. (Sandra), Küry, S. (Sébastien), Woerden, G.M. (Geeske) van, Besnard, T. (Thomas), Proietti-Onori, M. (Martina), Latypova, X. (Xénia), Towne, M.C. (Meghan C.), Cho, M.T. (Megan T.), Prescott, T. (Trine), Ploeg, M.A. (Melissa), Sanders, S. (Stephan), Stessman, H.A.F. (Holly A F), Pujol, A. (Aurora), Distel, B. (Ben), Robak, L.A. (Laurie A.), Bernstein, J.A. (Jonathan A.), Denommé-Pichon, A.-S. (Anne-Sophie), Lesca, G. (Gaëtan), Sellars, E.A. (Elizabeth A.), Berg, J. (Jonathan), Carré, W. (Wilfrid), Busk, ØL. (Øyvind Løvold), Bon, B. (Bregje) van, Waugh, J.L. (Jeff L.), Deardorff, M.A. (Matthew), Hoganson, G.E. (George E.), Bosanko, K.B. (Katherine B.), Johnson, D.S. (Diana S.), Dabir, T. (Tabib), Holla, ØL. (Øystein Lunde), Sarkar, A. (Ajoy), Tveten, K. (Kristian), de Bellescize, J. (Julitta), Braathen, G.J. (Geir J.), Terhal, P. (Paulien), Grange, D.K. (Dorothy K.), Haeringen, A. (Arie) van, Lam, C. (Christina), Mirzaa, G.M. (Ghayda), Burton, J. (Jennifer), Bhoj, E.J. (Elizabeth J.), Douglas, J. (Jessica), Santani, A.B. (Avni B.), Nesbitt, A.I. (Addie I.), Helbig, K.L. (Katherine L.), Andrews, M.V. (Marisa V.), Begtrup, A. (Amber), Tang, S. (Sha), van Gassen, K.L.I. (Koen L.I.), Juusola, J. (Jane), Foss, K. (Kimberly), Enns, G. (Gregory), Moog, U. (Ute), Hinderhofer, K. (Katrin), Paramasivam, N. (Nagarajan), Lincoln, S. (Sharyn), Kusako, B.H. (Brandon H.), Lindenbaum, P. (Pierre), Charpentier, E. (Eric), Nowak, C.B. (Catherine B.), Cherot, E. (Elouan), Simonet, T. (Thomas), Ruivenkamp, C.A. (Claudia), Hahn, S. (Sihoun), Brownstein, C.A. (Catherine A.), Xia, F. (Fan), Schmitt, S. (Sébastien), Deb, W. (Wallid), Bonneau, D. (Dominique), Nizon, M. (Mathilde), Quinquis, D. (Delphine), Chelly, J. (Jamel), Rudolf, G. (Gabrielle), Sanlaville, D. (Damien), Parent, P. (Philippe), Gilbert-Dussardier, B. (Brigitte), Toutain, A. (Annick), Sutton, V.R. (V. Reid), Thies, J. (Jenny), Peart-Vissers, L.E.L.M. (Lisenka E L M), Boisseau, P. (Pierre), Vincent, M. (Marie), Grabrucker, A.M. (Andreas M.), Dubourg, C. (Christèle), Tan, W.-H. (Wen-Hann), Verbeek, N.E. (Nienke), Granzow, M. (Martin), Santen, G.W.E. (Gijs), Shendure, J. (Jay), Isidor, B. (Bertrand), Pasquier, L. (Laurent), Redon, R. (Richard), Yang, Y. (Yaping), State, M.W. (Matthew), Kleefstra, T. (Tjitske), Cogné, B. (Benjamin), Petrovski, S. (Slavé), Retterer, K. (Kyle), Eichler, E.E. (Evan), Rosenfeld, J.A. (Jill), Agrawal, P.B. (Pankaj B.), Bézieau, S. (Stéphane), Odent, S. (Sylvie), Elgersma, Y. (Ype), and Mercier, S. (Sandra)

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.

Published
2017
Full Text
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21. Quantification of differential gene expression by multiplexed targeted resequencing of cDNA

Author

Arts, P., Raadt, J. van der, Gestel, S.H.C. van, Steehouwer, M., Shendure, J., Hoischen, A., Albers, C.A., Arts, P., Raadt, J. van der, Gestel, S.H.C. van, Steehouwer, M., Shendure, J., Hoischen, A., and Albers, C.A.

Abstract

Contains fulltext : 174649.pdf (publisher's version ) (Open Access), Whole-transcriptome or RNA sequencing (RNA-Seq) is a powerful and versatile tool for functional analysis of different types of RNA molecules, but sample reagent and sequencing cost can be prohibitive for hypothesis-driven studies where the aim is to quantify differential expression of a limited number of genes. Here we present an approach for quantification of differential mRNA expression by targeted resequencing of complementary DNA using single-molecule molecular inversion probes (cDNA-smMIPs) that enable highly multiplexed resequencing of cDNA target regions of approximately 100 nucleotides and counting of individual molecules. We show that accurate estimates of differential expression can be obtained from molecule counts for hundreds of smMIPs per reaction and that smMIPs are also suitable for quantification of relative gene expression and allele-specific expression. Compared with low-coverage RNA-Seq and a hybridization-based targeted RNA-Seq method, cDNA-smMIPs are a cost-effective high-throughput tool for hypothesis-driven expression analysis in large numbers of genes (10 to 500) and samples (hundreds to thousands).

Published
2017

22. An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes

Author

Wheway, G, Schmidts, M, Mans, DA, Szymanska, K, Nguyen, TT, Racher, H, Phelps, IG, Toedt, G, Kennedy, J, Wunderlich, KA, Sorusch, N, Abdelhamed, ZA, Natarajan, S, Herridge, W, van Reeuwijk, J, Horn, N, Boldt, K, Parry, DA, Letteboer, SJ, Roosing, S, Adams, M, Bell, SM, Bond, J, Higgins, J, Morrison, EE, Tomlinson, DC, Slaats, GG, van Dam, TJ, Huang, L, Kessler, K, Giessl, A, Logan, CV, Boyle, EA, Shendure, J, Anazi, S, Aldahmesh, M, Al Hazzaa, S, Hegele, RA, Ober, C, Frosk, P, Mhanni, AA, Chodirker, BN, Chudley, AE, Lamont, R, Bernier, FP, Beaulieu, CL, Gordon, P, Pon, RT, Donahue, C, Barkovich, AJ, Wolf, L, Toomes, C, Thiel, CT, Boycott, KM, McKibbin, M, Inglehearn, CF, UK10K Consortium, University ofWashington Center forMendelian Genomics, Stewart, F, Omran, H, Huynen, MA, Sergouniotis, PI, Alkuraya, FS, Parboosingh, JS, Innes, AM, Willoughby, CE, Giles, RH, Webster, AR, Ueffing, M, Blacque, O, Gleeson, JG, Wolfrum, U, Beales, PL, Gibson, T, Doherty, D, Mitchison, HM, Roepman, R, and Johnson, CA

Abstract

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.

Published
2015

23. Long-read sequence assembly of the gorilla genome

Author

Gordon, D., primary, Huddleston, J., additional, Chaisson, M. J. P., additional, Hill, C. M., additional, Kronenberg, Z. N., additional, Munson, K. M., additional, Malig, M., additional, Raja, A., additional, Fiddes, I., additional, Hillier, L. W., additional, Dunn, C., additional, Baker, C., additional, Armstrong, J., additional, Diekhans, M., additional, Paten, B., additional, Shendure, J., additional, Wilson, R. K., additional, Haussler, D., additional, Chin, C.-S., additional, and Eichler, E. E., additional

Published
2016
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24. A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer

Author

Weren, R.D.A., Ligtenberg, M.J., Kets, C.M., Voer, R.M. de, Verwiel, E.T.P., Spruijt, L., Zelst-Stams, W.A.G. van, Jongmans, M.C.J., Gilissen, C., Hehir, J.Y., Hoischen, A., Shendure, J., Boyle, E.A., Kamping, E.J., Nagtegaal, I.D., Tops, B.B.J., Nagengast, F.M., Geurts van Kessel, A.H.M., Krieken, J.H.J.M. van, Kuiper, R.P., Hoogerbrugge, N., Weren, R.D.A., Ligtenberg, M.J., Kets, C.M., Voer, R.M. de, Verwiel, E.T.P., Spruijt, L., Zelst-Stams, W.A.G. van, Jongmans, M.C.J., Gilissen, C., Hehir, J.Y., Hoischen, A., Shendure, J., Boyle, E.A., Kamping, E.J., Nagtegaal, I.D., Tops, B.B.J., Nagengast, F.M., Geurts van Kessel, A.H.M., Krieken, J.H.J.M. van, Kuiper, R.P., and Hoogerbrugge, N.

Abstract

Contains fulltext : 155056.pdf (publisher's version ) (Closed access), The genetic cause underlying the development of multiple colonic adenomas, the premalignant precursors of colorectal cancer (CRC), frequently remains unresolved in patients with adenomatous polyposis. Here we applied whole-exome sequencing to 51 individuals with multiple colonic adenomas from 48 families. In seven affected individuals from three unrelated families, we identified a homozygous germline nonsense mutation in the base-excision repair (BER) gene NTHL1. This mutation was exclusively found in a heterozygous state in controls (minor allele frequency of 0.0036; n = 2,329). All three families showed recessive inheritance of the adenomatous polyposis phenotype and progression to CRC in at least one member. All three affected women developed an endometrial malignancy or premalignancy. Genetic analysis of three carcinomas and five adenomas from different affected individuals showed a non-hypermutated profile enriched for cytosine-to-thymine transitions. We conclude that a homozygous loss-of-function germline mutation in the NTHL1 gene predisposes to a new subtype of BER-associated adenomatous polyposis and CRC.

Published
2015

25. An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes

Author

Wheway, G., Schmidts, M., Mans, D.A., Szymanska, K., Nguyen, T.M., Racher, H., Phelps, I.G., Toedt, G., Kennedy, J., Wunderlich, K.A., Sorusch, N., Abdelhamed, Z.A., Natarajan, S., Herridge, W., Reeuwijk, J. van, Horn, N., Boldt, K., Parry, D.A., Letteboer, S.J.F., Roosing, S., Adams, M., Bell, S.M., Bond, J., Higgins, J., Morrison, E.E., Tomlinson, D.C., Slaats, G.G., Dam, T.J.P. van, Huang, L., Kessler, K., Giessl, A., Logan, C.V., Boyle, E.A., Shendure, J., Anazi, S., Aldahmesh, M., Hazzaa, S. Al, Hegele, R.A., Ober, C., Frosk, P., Mhanni, A.A., Chodirker, B.N., Chudley, A.E., Lamont, R., Bernier, F.P., Beaulieu, C.L., Gordon, P., Pon, R.T., Donahue, C., Barkovich, A.J., Wolf, L., Toomes, C., Thiel, C.T., Boycott, K.M., McKibbin, M., Inglehearn, C.F., Stewart, F., Omran, H., Huynen, M.A., Sergouniotis, P.I., Alkuraya, F.S., Parboosingh, J.S., Innes, A.M., Willoughby, C.E., Giles, R.H., Webster, A.R., Ueffing, M., Blacque, O., Gleeson, J.G., Wolfrum, U., Beales, P.L., Gibson, T., Doherty, D., Mitchison, H.M., Roepman, R., Johnson, C.A., Wheway, G., Schmidts, M., Mans, D.A., Szymanska, K., Nguyen, T.M., Racher, H., Phelps, I.G., Toedt, G., Kennedy, J., Wunderlich, K.A., Sorusch, N., Abdelhamed, Z.A., Natarajan, S., Herridge, W., Reeuwijk, J. van, Horn, N., Boldt, K., Parry, D.A., Letteboer, S.J.F., Roosing, S., Adams, M., Bell, S.M., Bond, J., Higgins, J., Morrison, E.E., Tomlinson, D.C., Slaats, G.G., Dam, T.J.P. van, Huang, L., Kessler, K., Giessl, A., Logan, C.V., Boyle, E.A., Shendure, J., Anazi, S., Aldahmesh, M., Hazzaa, S. Al, Hegele, R.A., Ober, C., Frosk, P., Mhanni, A.A., Chodirker, B.N., Chudley, A.E., Lamont, R., Bernier, F.P., Beaulieu, C.L., Gordon, P., Pon, R.T., Donahue, C., Barkovich, A.J., Wolf, L., Toomes, C., Thiel, C.T., Boycott, K.M., McKibbin, M., Inglehearn, C.F., Stewart, F., Omran, H., Huynen, M.A., Sergouniotis, P.I., Alkuraya, F.S., Parboosingh, J.S., Innes, A.M., Willoughby, C.E., Giles, R.H., Webster, A.R., Ueffing, M., Blacque, O., Gleeson, J.G., Wolfrum, U., Beales, P.L., Gibson, T., Doherty, D., Mitchison, H.M., Roepman, R., and Johnson, C.A.

Abstract

Item does not contain fulltext, Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.

Published
2015

28. De novo tbr1 mutations in sporadic autism disrupt protein functions

Author

Deriziotis, P., O'Roak, B.J., Graham, S.A., Estruch, S.B., Dimitropoulou, D., Bernier, R.A., Gerdts, J., Shendure, J., Eichler, E.E., Fisher, S.E., Deriziotis, P., O'Roak, B.J., Graham, S.A., Estruch, S.B., Dimitropoulou, D., Bernier, R.A., Gerdts, J., Shendure, J., Eichler, E.E., and Fisher, S.E.

Abstract

Contains fulltext : 133084.pdf (publisher's version ) (Open Access)

Published
2014

29. Refining analyses of copy number variation identifies specific genes associated with developmental delay.

Author

Coe, B.P., Witherspoon, K., Rosenfeld, J.A., Bon, B.W.M. van, Silfhout, A.T. van, Bosco, P., Friend, K.L., Baker, C., Buono, S., Vissers, L.E.L.M., Schuurs-Hoeijmakers, J.H.M., Hoischen, A., Pfundt, R., Krumm, N., Carvill, G.L., Li, D., Amaral, D., Brown, N., Lockhart, P.J., Scheffer, I.E., Alberti, A., Shaw, M., Pettinato, R., Tervo, R., Leeuw, N. de, Reijnders, M.R., Torchia, B.S., Peeters, H., Thompson, E., O'Roak, B.J., Fichera, M., Hehir-Kwa, J.Y., Shendure, J., Mefford, H.C., Haan, E., Gécz, J., Vries, L.B.A. de, Romano, C, Eichler, E.E., Coe, B.P., Witherspoon, K., Rosenfeld, J.A., Bon, B.W.M. van, Silfhout, A.T. van, Bosco, P., Friend, K.L., Baker, C., Buono, S., Vissers, L.E.L.M., Schuurs-Hoeijmakers, J.H.M., Hoischen, A., Pfundt, R., Krumm, N., Carvill, G.L., Li, D., Amaral, D., Brown, N., Lockhart, P.J., Scheffer, I.E., Alberti, A., Shaw, M., Pettinato, R., Tervo, R., Leeuw, N. de, Reijnders, M.R., Torchia, B.S., Peeters, H., Thompson, E., O'Roak, B.J., Fichera, M., Hehir-Kwa, J.Y., Shendure, J., Mefford, H.C., Haan, E., Gécz, J., Vries, L.B.A. de, Romano, C, and Eichler, E.E.

Abstract

Contains fulltext : 136682.pdf (publisher's version ) (Closed access)

Published
2014

30. Disruptive CHD8 mutations define a subtype of autism early in development.

Author

Bernier, R., Golzio, C., Xiong, B., Stessman, H.A., Coe, B.P., Penn, O., Witherspoon, K., Gerdts, J., Baker, C., Silfhout, A.T. van, Schuurs-Hoeijmakers, J.H.M., Fichera, M., Bosco, P., Buono, S., Alberti, A., Failla, P., Peeters, H., Steyaert, J., Vissers, L.E.L.M., Francescatto, L., Mefford, H.C., Rosenfeld, J.A., Bakken, T., O'Roak, B.J., Pawlus, M., Moon, R., Shendure, J., Amaral, D.G., Lein, E., Rankin, J., Romano, C, Vries, L.B.A. de, Katsanis, N., Eichler, E.E., Bernier, R., Golzio, C., Xiong, B., Stessman, H.A., Coe, B.P., Penn, O., Witherspoon, K., Gerdts, J., Baker, C., Silfhout, A.T. van, Schuurs-Hoeijmakers, J.H.M., Fichera, M., Bosco, P., Buono, S., Alberti, A., Failla, P., Peeters, H., Steyaert, J., Vissers, L.E.L.M., Francescatto, L., Mefford, H.C., Rosenfeld, J.A., Bakken, T., O'Roak, B.J., Pawlus, M., Moon, R., Shendure, J., Amaral, D.G., Lein, E., Rankin, J., Romano, C, Vries, L.B.A. de, Katsanis, N., and Eichler, E.E.

Abstract

Item does not contain fulltext

Published
2014

31. Systematic deep sequence analysis of the role of somatic mutation in cerebral cortical malformations

Author

Jamuar, S.S., Lam, A.N.T., Kircher, M., D'Gama, A.M., Wang, J, Barry, J., Zhang, X., Hill, R.S., Partlow, J.N., Rozzo, A., Servattalab, S, Mehta, B, Topcu, M, Amrom, Dina, Andermann, Eva, Dan, Bernard, Guerrini, R, Scheffer, Ingrid E, Berkovic, S F, Leventer, Richard Jacob R., Shen, Y.-T., Lin Wu, B, Brain Malformation Study Group, B, Barkovich, A James, Sahin, Mustafa, Chang, B.S., Bamshad, M., Nickerson, D.A., Shendure, J., Poduri, A., Yu, T.W., Walsh, C A, Jamuar, S.S., Lam, A.N.T., Kircher, M., D'Gama, A.M., Wang, J, Barry, J., Zhang, X., Hill, R.S., Partlow, J.N., Rozzo, A., Servattalab, S, Mehta, B, Topcu, M, Amrom, Dina, Andermann, Eva, Dan, Bernard, Guerrini, R, Scheffer, Ingrid E, Berkovic, S F, Leventer, Richard Jacob R., Shen, Y.-T., Lin Wu, B, Brain Malformation Study Group, B, Barkovich, A James, Sahin, Mustafa, Chang, B.S., Bamshad, M., Nickerson, D.A., Shendure, J., Poduri, A., Yu, T.W., and Walsh, C A

Abstract

BACKGROUND: Although there is increasing recognition of the role of somatic mutations in genetic disorders, the prevalence of somatic mutations in neurodevelopmental disease and the optimal techniques to detect somatic mosaicism have not been systematically evaluated. METHODS: Using a customized panel of known and candidate genes associated with brain malformations, we applied targeted high-coverage sequencing (depth, ≥200x) to leukocytederived DNA samples from 158 persons with brain malformations, including the double-cortex syndrome (subcortical band heterotopia, 30 persons), polymicrogyria with megalencephaly (20), periventricular nodular heterotopia (61), and pachygyria (47). We validated candidate mutations with the use of Sanger sequencing and, for variants present at unequal read depths, subcloning followed by colony sequencing. RESULTS: Validated, causal mutations were found in 27 persons (17%; range, 10 to 30% for each phenotype). Mutations were somatic in 8 of the 27 (30%), predominantly in persons with the double-cortex syndrome (in whom we found mutations in DCX and LIS1), persons with periventricular nodular heterotopia (FLNA), and persons with pachygyria (TUBB2B). Of the somatic mutations we detected, 5 (63%) were undetectable with the use of traditional Sanger sequencing but were validated through subcloning and subsequent sequencing of the subcloned DNA. We found potentially causal mutations in the candidate genes DYNC1H1, KIF5C, and other kinesin genes in persons with pachygyria. CONCLUSIONS: Targeted sequencing was found to be useful for detecting somatic mutations in patients with brain malformations. High-coverage sequencing panels provide an important complement to whole-exome and whole-genome sequencing in the evaluation of somatic mutations in neuropsychiatric disease. Copyright © 2014 Massachusetts Medical Society., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2014

32. Refining analyses of copy number variation identifies specific genes associated with developmental delay

Author

Coe, BP, Witherspoon, K, Rosenfeld, JA, van Bon, BWM, Vulto-van Silfhout, AT, Bosco, P, Friend, KL, Baker, C, Buono, S, Vissers, LELM, Schuurs-Hoeijmakers, JH, Hoischen, A, Pfundt, R, Krumm, N, Carvill, GL, Li, D, Amaral, D, Brown, N, Lockhart, PJ, Scheffer, IE, Alberti, A, Shaw, M, Pettinato, R, Tervo, R, de Leeuw, N, Reijnders, MRF, Torchia, BS, Peeters, H, O'Roak, BJ, Fichera, M, Hehir-Kwa, JY, Shendure, J, Mefford, HC, Haan, E, Gecz, J, de Vries, BBA, Romano, C, Eichler, EE, Coe, BP, Witherspoon, K, Rosenfeld, JA, van Bon, BWM, Vulto-van Silfhout, AT, Bosco, P, Friend, KL, Baker, C, Buono, S, Vissers, LELM, Schuurs-Hoeijmakers, JH, Hoischen, A, Pfundt, R, Krumm, N, Carvill, GL, Li, D, Amaral, D, Brown, N, Lockhart, PJ, Scheffer, IE, Alberti, A, Shaw, M, Pettinato, R, Tervo, R, de Leeuw, N, Reijnders, MRF, Torchia, BS, Peeters, H, O'Roak, BJ, Fichera, M, Hehir-Kwa, JY, Shendure, J, Mefford, HC, Haan, E, Gecz, J, de Vries, BBA, Romano, C, and Eichler, EE

Abstract

Copy number variants (CNVs) are associated with many neurocognitive disorders; however, these events are typically large, and the underlying causative genes are unclear. We created an expanded CNV morbidity map from 29,085 children with developmental delay in comparison to 19,584 healthy controls, identifying 70 significant CNVs. We resequenced 26 candidate genes in 4,716 additional cases with developmental delay or autism and 2,193 controls. An integrated analysis of CNV and single-nucleotide variant (SNV) data pinpointed 10 genes enriched for putative loss of function. Follow-up of a subset of affected individuals identified new clinical subtypes of pediatric disease and the genes responsible for disease-associated CNVs. These genetic changes include haploinsufficiency of SETBP1 associated with intellectual disability and loss of expressive language and truncations of ZMYND11 in individuals with autism, aggression and complex neuropsychiatric features. This combined CNV and SNV approach facilitates the rapid discovery of new syndromes and genes involved in neuropsychiatric disease despite extensive genetic heterogeneity.

Published
2014

35. GABRA1 and STXBP1: Novel genetic causes of Dravet syndrome

Author

Carvill, G. L., primary, Weckhuysen, S., additional, McMahon, J. M., additional, Hartmann, C., additional, Moller, R. S., additional, Hjalgrim, H., additional, Cook, J., additional, Geraghty, E., additional, O'Roak, B. J., additional, Petrou, S., additional, Clarke, A., additional, Gill, D., additional, Sadleir, L. G., additional, Muhle, H., additional, von Spiczak, S., additional, Nikanorova, M., additional, Hodgson, B. L., additional, Gazina, E. V., additional, Suls, A., additional, Shendure, J., additional, Dibbens, L. M., additional, De Jonghe, P., additional, Helbig, I., additional, Berkovic, S. F., additional, Scheffer, I. E., additional, and Mefford, H. C., additional

Published
2014
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36. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1.

Author

Mefford H.C., Andrade D.M., Freeman J.L., Sadleir L.G., Shendure J., Berkovic S.F., Scheffer I.E., Carvill G.L., Heavin S.B., Yendle S.C., McMahon J.M., O'Roak B.J., Cook J., Khan A., Dorschner M.O., Weaver M., Calvert S., Malone S., Wallace G., Stanley T., Bye A.M.E., Bleasel A., Howell K.B., Kivity S., Mackay M.T., Rodriguez-Casero V., Webster R., Korczyn A., Afawi Z., Zelnick N., Lerman-Sagie T., Lev D., Moller R.S., Gill D., Mefford H.C., Andrade D.M., Freeman J.L., Sadleir L.G., Shendure J., Berkovic S.F., Scheffer I.E., Carvill G.L., Heavin S.B., Yendle S.C., McMahon J.M., O'Roak B.J., Cook J., Khan A., Dorschner M.O., Weaver M., Calvert S., Malone S., Wallace G., Stanley T., Bye A.M.E., Bleasel A., Howell K.B., Kivity S., Mackay M.T., Rodriguez-Casero V., Webster R., Korczyn A., Afawi Z., Zelnick N., Lerman-Sagie T., Lev D., Moller R.S., and Gill D.

Abstract

Epileptic encephalopathies are a devastating group of epilepsies with poor prognosis, of which the majority are of unknown etiology. We perform targeted massively parallel resequencing of 19 known and 46 candidate genes for epileptic encephalopathy in 500 affected individuals (cases) to identify new genes involved and to investigate the phenotypic spectrum associated with mutations in known genes. Overall, we identified pathogenic mutations in 10% of our cohort. Six of the 46 candidate genes had 1 or more pathogenic variants, collectively accounting for 3% of our cohort. We show that de novo CHD2 and SYNGAP1 mutations are new causes of epileptic encephalopathies, accounting for 1.2% and 1% of cases, respectively. We also expand the phenotypic spectra explained by SCN1A, SCN2A and SCN8A mutations. To our knowledge, this is the largest cohort of cases with epileptic encephalopathies to undergo targeted resequencing. Implementation of this rapid and efficient method will change diagnosis and understanding of the molecular etiologies of these disorders. © 2013 Nature America, Inc. All rights reserved.

Published
2013

37. Targeted resequencing in epileptic encephalopathies reveals marked genetic heterogeneity and novel genes.

Author

Scheffer I.E., Shendure J., Berkovic S.F., Mefford H.C., Carvill G.L., Heavin S.B., Yendle S.C., O'Roak B.J., Cook J., Khan A., Dorschner M.O., Weaver M.A., Calvert S., Malone S., Wallace G., Stanley T., Bye A.M., Bleasel A., Howell K.B., Kivity S., Mackay M.T., Rodriguez-Casero V., Webster R., Korczyn A., Zelnick N., Lerman-Sagie T., Lev D., SteensbjerreMoller R., Andrade D.M., Freeman J.L., Sadleir L.G., Scheffer I.E., Shendure J., Berkovic S.F., Mefford H.C., Carvill G.L., Heavin S.B., Yendle S.C., O'Roak B.J., Cook J., Khan A., Dorschner M.O., Weaver M.A., Calvert S., Malone S., Wallace G., Stanley T., Bye A.M., Bleasel A., Howell K.B., Kivity S., Mackay M.T., Rodriguez-Casero V., Webster R., Korczyn A., Zelnick N., Lerman-Sagie T., Lev D., SteensbjerreMoller R., Andrade D.M., Freeman J.L., and Sadleir L.G.

Abstract

Purpose: Epileptic encephalopathies (EEs) are a devastating group of epilepsies characterized by refractory seizures, cognitive arrest or regression, associated with ongoing epileptic activity, and a poor prognosis. De novo mutations in a number of genes, as well as rare, de novo copy number changes, are known to cause EE. However, the vast majority of cases have an unknown etiology. Method(s): We performed targeted massively parallel resequencing of 18 known and 47 candidate EE genes in 500 patients to identify novel genes, and investigate the phenotypic spectrum of known genes. Result(s): Overall, we identify pathogenic mutations in 10% of our cohort. Pathogenic variants were found in seven of our 47 candidate genes, collectively accounting for 3% of EE in our cohort. Most notably, we identify mutations in 1.2% of our cohort in a novel gene that acts in the chromatin remodeling pathway. Also, de novo mutations were detected in 1% of the cohort in SYNGAP1, a gene identified in individuals with intellectual disability. The remaining pathogenic variants were detected in known EE genes. For some, including SCN1A, SCN2A, and SCN8A, we expand the phenotypic spectrum, presenting novel clinical features associated with these genes. Conclusion(s): We have developed a rapid, cost-effective ($1/gene/proband) and efficient targeted resequencing approach to define the molecular etiology of EE. These results will transform molecular diagnostic approaches and facilitate the management of families affected by this devastating disorder. Furthermore, we have identified the chromatin remodeling pathway as a novel biological process involved in epileptogenesis. Future studies of this pathway will provide new avenues for development of therapeutic interventions.

Published
2013

38. GRIN2A mutations cause epilepsy-aphasia spectrum disorders

Author

Carvill, GL, Regan, BM, Yendle, SC, O'Roak, BJ, Lozovaya, N, Bruneau, N, Burnashev, N, Khan, A, Cook, J, Geraghty, E, Sadleir, LG, Turner, SJ, Tsai, M-H, Webster, R, Ouvrier, R, Damiano, JA, Berkovic, SF, Shendure, J, Hildebrand, MS, Szepetowski, P, Scheffer, IE, Mefford, HC, Carvill, GL, Regan, BM, Yendle, SC, O'Roak, BJ, Lozovaya, N, Bruneau, N, Burnashev, N, Khan, A, Cook, J, Geraghty, E, Sadleir, LG, Turner, SJ, Tsai, M-H, Webster, R, Ouvrier, R, Damiano, JA, Berkovic, SF, Shendure, J, Hildebrand, MS, Szepetowski, P, Scheffer, IE, and Mefford, HC

Abstract

Epilepsy-aphasia syndromes (EAS) are a group of rare, severe epileptic encephalopathies of unknown etiology with a characteristic electroencephalogram (EEG) pattern and developmental regression particularly affecting language. Rare pathogenic deletions that include GRIN2A have been implicated in neurodevelopmental disorders. We sought to delineate the pathogenic role of GRIN2A in 519 probands with epileptic encephalopathies with diverse epilepsy syndromes. We identified four probands with GRIN2A variants that segregated with the disorder in their families. Notably, all four families presented with EAS, accounting for 9% of epilepsy-aphasia cases. We did not detect pathogenic variants in GRIN2A in other epileptic encephalopathies (n = 475) nor in probands with benign childhood epilepsy with centrotemporal spikes (n = 81). We report the first monogenic cause, to our knowledge, for EAS. GRIN2A mutations are restricted to this group of cases, which has important ramifications for diagnostic testing and treatment and provides new insights into the pathogenesis of this debilitating group of conditions.

Published
2013

39. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1

Author

Carvill, GL, Heavin, SB, Yendle, SC, McMahon, JM, O'Roak, BJ, Cook, J, Khan, A, Dorschner, MO, Weaver, M, Calvert, S, Malone, S, Wallace, G, Stanley, T, Bye, AME, Bleasel, A, Howell, KB, Kivity, S, Mackay, MT, Rodriguez-Casero, V, Webster, R, Korczyn, A, Afawi, Z, Zelnick, N, Lerman-Sagie, T, Lev, D, Moller, RS, Gill, D, Andrade, DM, Freeman, JL, Sadleir, LG, Shendure, J, Berkovic, SF, Scheffer, IE, Mefford, HC, Carvill, GL, Heavin, SB, Yendle, SC, McMahon, JM, O'Roak, BJ, Cook, J, Khan, A, Dorschner, MO, Weaver, M, Calvert, S, Malone, S, Wallace, G, Stanley, T, Bye, AME, Bleasel, A, Howell, KB, Kivity, S, Mackay, MT, Rodriguez-Casero, V, Webster, R, Korczyn, A, Afawi, Z, Zelnick, N, Lerman-Sagie, T, Lev, D, Moller, RS, Gill, D, Andrade, DM, Freeman, JL, Sadleir, LG, Shendure, J, Berkovic, SF, Scheffer, IE, and Mefford, HC

Abstract

Epileptic encephalopathies are a devastating group of epilepsies with poor prognosis, of which the majority are of unknown etiology. We perform targeted massively parallel resequencing of 19 known and 46 candidate genes for epileptic encephalopathy in 500 affected individuals (cases) to identify new genes involved and to investigate the phenotypic spectrum associated with mutations in known genes. Overall, we identified pathogenic mutations in 10% of our cohort. Six of the 46 candidate genes had 1 or more pathogenic variants, collectively accounting for 3% of our cohort. We show that de novo CHD2 and SYNGAP1 mutations are new causes of epileptic encephalopathies, accounting for 1.2% and 1% of cases, respectively. We also expand the phenotypic spectra explained by SCN1A, SCN2A and SCN8A mutations. To our knowledge, this is the largest cohort of cases with epileptic encephalopathies to undergo targeted resequencing. Implementation of this rapid and efficient method will change diagnosis and understanding of the molecular etiologies of these disorders.

Published
2013

40. Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species

Author

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. -C, Corbeil, J., Fabbro, C. D., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. -W, Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., MacCallum, I., MacManes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. -M, Yuan, J., Zhang, G., Zhang, H., Zhou, S., Korf, I. F., Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. -C, Corbeil, J., Fabbro, C. D., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. -W, Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., MacCallum, I., MacManes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. -M, Yuan, J., Zhang, G., Zhang, H., Zhou, S., and Korf, I. F.

Abstract

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., QC 20170307

Published
2013
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41. De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

Author

Riviere, J.B., van Bon, B.W., Hoischen, A., Kholmanskikh, S.S., O'Roak, B.J., Gilissen, C.F.H.A., Gijsen, S., Sullivan, C.T., Christian, S.L., Abdul-Rahman, O.A., Atkin, J.F., Chassaing, N., Drouin-Garraud, V., Fry, A.E., Fryns, J.P., Gripp, K.W., Kempers, M., Kleefstra, T., Mancini, G.M.S., Nowaczyk, M.J., van Ravenswaaij-Arts, C.M., Roscioli, T., Marble, M., Rosenfeld, J.A., Siu, V.M., Vries, L.B.A. de, Shendure, J., Verloes, A., Veltman, J.A., Brunner, H.G., Ross, M.E., Pilz, D.T., Dobyns, W.B., Riviere, J.B., van Bon, B.W., Hoischen, A., Kholmanskikh, S.S., O'Roak, B.J., Gilissen, C.F.H.A., Gijsen, S., Sullivan, C.T., Christian, S.L., Abdul-Rahman, O.A., Atkin, J.F., Chassaing, N., Drouin-Garraud, V., Fry, A.E., Fryns, J.P., Gripp, K.W., Kempers, M., Kleefstra, T., Mancini, G.M.S., Nowaczyk, M.J., van Ravenswaaij-Arts, C.M., Roscioli, T., Marble, M., Rosenfeld, J.A., Siu, V.M., Vries, L.B.A. de, Shendure, J., Verloes, A., Veltman, J.A., Brunner, H.G., Ross, M.E., Pilz, D.T., and Dobyns, W.B.

Abstract

Item does not contain fulltext, Brain malformations are individually rare but collectively common causes of developmental disabilities. Many forms of malformation occur sporadically and are associated with reduced reproductive fitness, pointing to a causative role for de novo mutations. Here, we report a study of Baraitser-Winter syndrome, a well-defined disorder characterized by distinct craniofacial features, ocular colobomata and neuronal migration defect. Using whole-exome sequencing of three proband-parent trios, we identified de novo missense changes in the cytoplasmic actin-encoding genes ACTB and ACTG1 in one and two probands, respectively. Sequencing of both genes in 15 additional affected individuals identified disease-causing mutations in all probands, including two recurrent de novo alterations (ACTB, encoding p.Arg196His, and ACTG1, encoding p.Ser155Phe). Our results confirm that trio-based exome sequencing is a powerful approach to discover genes causing sporadic developmental disorders, emphasize the overlapping roles of cytoplasmic actin proteins in development and suggest that Baraitser-Winter syndrome is the predominant phenotype associated with mutation of these two genes.

Published
2012

42. Mutation discovery in mice by whole exome sequencing

Author

Fairfield, H, Gilbert, GJ, Barter, M, Corrigan, RR, Curtain, M, Ding, Y, D'Ascenzo, M, Gerhardt, DJ, He, C, Huang, W, Richmond, T, Rowe, L, Probst, FJ, Bergstrom, DE, Murray, SA, Bult, C, Richardson, J, Kile, BT, Gut, I, Hager, J, Sigurdsson, S, Mauceli, E, Di Palma, F, Lindblad-Toh, K, Cunningham, ML, Cox, TC, Justice, MJ, Spector, MS, Lowe, SW, Albert, T, Donahue, LR, Jeddeloh, J, Shendure, J, Reinholdt, LG, Fairfield, H, Gilbert, GJ, Barter, M, Corrigan, RR, Curtain, M, Ding, Y, D'Ascenzo, M, Gerhardt, DJ, He, C, Huang, W, Richmond, T, Rowe, L, Probst, FJ, Bergstrom, DE, Murray, SA, Bult, C, Richardson, J, Kile, BT, Gut, I, Hager, J, Sigurdsson, S, Mauceli, E, Di Palma, F, Lindblad-Toh, K, Cunningham, ML, Cox, TC, Justice, MJ, Spector, MS, Lowe, SW, Albert, T, Donahue, LR, Jeddeloh, J, Shendure, J, and Reinholdt, LG

Abstract

We report the development and optimization of reagents for in-solution, hybridization-based capture of the mouse exome. By validating this approach in a multiple inbred strains and in novel mutant strains, we show that whole exome sequencing is a robust approach for discovery of putative mutations, irrespective of strain background. We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis.

Published
2011

43. A novel missense variant in the PNPLA1 gene underlies congenital ichthyosis in three consanguineous families.

Author

Ahmad, F., Ansar, M., Mehmood, S., Izoduwa, A., Lee, K., Nasir, A., Abrar, M., Ullah, A., Aziz, A., Smith, J.D., Shendure, J., Bamshad, M.J., Nicekrson, D.A., Santos ‐ Cortez, R.L.P., Leal, S.M., and Ahmad, W.

Subjects
AUTOSOMAL recessive polycystic kidney, ICHTHYOSIS, MISSENSE mutation, GENETICS
Abstract

A letter to the editor is presented which discusses a study regarding the missense variant of PNPLA1 gene that can cause autosomal recessive congenital ichthyosis (ARCI).

Published
2016
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48. Proffered papers and posters presented at the Sixth International Symposium on Hereditary Breast and Ovarian Cancer—BRCA: Challenges and Opportunities : Presented by the Hereditary Breast and Ovarian Cancer Foundation in collaboration with the Program in Cancer Genetics, McGill University; Centre Mont-Royal, Montreal, QC; 10–13 May 2016

Author

Starita L, Islam M, Fields S, Parvin J, Shendure J, Vierstraete J, Willaert A, Vleminckx K, Vermassen P, Pieters L, Coucke P, Vral A, Claes K, and Chalas E

49. Exome-wide DNA capture and next generation sequencing in domestic and wild species

Author

Ng Sarah B, Chen Shanyuan, Beja-Pereira Albano, Cosart Ted, Shendure Jay, and Luikart Gordon

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses. We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (Bos taurus) to capture (enrich for), and subsequently sequence, thousands of exons of B. taurus, B. indicus, and Bison bison (wild bison). Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits. Results We successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the B. taurus genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes. Conclusions This study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.

Published
2011
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50. Genomic regions associated with microdeletion/microduplication syndromes exhibit extreme diversity of structural variation

Author

Catherine J. Chu, Naomi Meeks, Feyza Yilmaz, Yulia Mostovoy, Chin Lin, Pui-Yan Kwok, Curtis R. Coughlin, Elizabeth A. Geiger, Tamim H. Shaikh, Stephen K. Chow, Urvashi Surti, Kathryn C. Chatfield, and Shendure, J

Subjects
Heart Defects, Congenital, Williams Syndrome, Developmental Disabilities, Population, Locus (genetics), Chromosome Disorders, Biology, Chromosomes, Structural variation, Craniofacial Abnormalities, 03 medical and health sciences, Congenital, Chromosome Breakpoints, Segmental Duplications, Genomic, 0302 clinical medicine, Gene mapping, Seizures, Intellectual Disability, Genotype, Genetics, Humans, 2.1 Biological and endogenous factors, Aetiology, Repeated sequence, education, genomic disorders, segmental duplications, 030304 developmental biology, Segmental duplication, Heart Defects, Investigation, Chromosomes, Human, Pair 15, 0303 health sciences, education.field_of_study, Pair 16, Mental Disorders, Breakpoint, Human Genome, Pair 15, structural variation, 030220 oncology & carcinogenesis, Genomic Structural Variation, Genomic, genome mapping, Chromosome Deletion, Chromosomes, Human, Pair 16, Human, Developmental Biology
Abstract

Segmental duplications (SDs) are a class of long, repetitive DNA elements whose paralogs share a high level of sequence similarity with each other. SDs mediate chromosomal rearrangements that lead to structural variation in the general population as well as genomic disorders associated with multiple congenital anomalies, including the 7q11.23 (Williams–Beuren Syndrome, WBS), 15q13.3, and 16p12.2 microdeletion syndromes. Population-level characterization of SDs has generally been lacking because most techniques used for analyzing these complex regions are both labor and cost intensive. In this study, we have used a high-throughput technique to genotype complex structural variation with a single molecule, long-range optical mapping approach. We characterized SDs and identified novel structural variants (SVs) at 7q11.23, 15q13.3, and 16p12.2 using optical mapping data from 154 phenotypically normal individuals from 26 populations comprising five super-populations. We detected several novel SVs for each locus, some of which had significantly different prevalence between populations. Additionally, we localized the microdeletion breakpoints to specific paralogous duplicons located within complex SDs in two patients with WBS, one patient with 15q13.3, and one patient with 16p12.2 microdeletion syndromes. The population-level data presented here highlights the extreme diversity of large and complex SVs within SD-containing regions. The approach we outline will greatly facilitate the investigation of the role of inter-SD structural variation as a driver of chromosomal rearrangements and genomic disorders.

Published
2021

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