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Manoli I, Sysol JR, Head PE, Epping MW, Gavrilova O, Crocker MK, Sloan JL, Koutsoukos SA, Wang C, Ktena YP, Mendelson S, Pass AR, Zerfas PM, Hoffmann V, Vernon HJ, Fletcher LA, Reynolds JC, Tsokos MG, Stratakis CA, Voss SD, Chen KY, Brown RJ, Hamosh A, Berry GT, Chen XS, Yanovski JA, Venditti CP. Lipodystrophy in methylmalonic acidemia associated with elevated FGF21 and abnormal methylmalonylation. JCI Insight 2024; 9:e174097. [PMID: 38271099 DOI: 10.1172/jci.insight.174097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
A distinct adipose tissue distribution pattern was observed in patients with methylmalonyl-CoA mutase deficiency, an inborn error of branched-chain amino acid (BCAA) metabolism, characterized by centripetal obesity with proximal upper and lower extremity fat deposition and paucity of visceral fat, that resembles familial multiple lipomatosis syndrome. To explore brown and white fat physiology in methylmalonic acidemia (MMA), body composition, adipokines, and inflammatory markers were assessed in 46 patients with MMA and 99 matched controls. Fibroblast growth factor 21 levels were associated with acyl-CoA accretion, aberrant methylmalonylation in adipose tissue, and an attenuated inflammatory cytokine profile. In parallel, brown and white fat were examined in a liver-specific transgenic MMA mouse model (Mmut-/- TgINS-Alb-Mmut). The MMA mice exhibited abnormal nonshivering thermogenesis with whitened brown fat and had an ineffective transcriptional response to cold stress. Treatment of the MMA mice with bezafibrates led to clinical improvement with beiging of subcutaneous fat depots, which resembled the distribution seen in the patients. These studies defined what we believe to be a novel lipodystrophy phenotype in patients with defects in the terminal steps of BCAA oxidation and demonstrated that beiging of subcutaneous adipose tissue in MMA could readily be induced with small molecules.
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Affiliation(s)
- Irini Manoli
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Justin R Sysol
- Metabolic Medicine Branch, National Human Genome Research Institute
| | | | | | - Oksana Gavrilova
- Mouse Metabolism Core, National Institute of Diabetes and Digestive and Kidney Diseases
| | - Melissa K Crocker
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development; and
| | - Jennifer L Sloan
- Metabolic Medicine Branch, National Human Genome Research Institute
| | | | - Cindy Wang
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Yiouli P Ktena
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Sophia Mendelson
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development; and
| | - Alexandra R Pass
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Patricia M Zerfas
- Office of Research Services, Division of Veterinary Resources, NIH, Bethesda, Maryland, USA
| | - Victoria Hoffmann
- Office of Research Services, Division of Veterinary Resources, NIH, Bethesda, Maryland, USA
| | - Hilary J Vernon
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Laura A Fletcher
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases
| | | | - Maria G Tsokos
- Ultrastructural Pathology Section, Center for Cancer Research; and
| | - Constantine A Stratakis
- Section on Endocrinology & Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Stephan D Voss
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kong Y Chen
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases
| | - Rebecca J Brown
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaoyuan Shawn Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, Maryland, USA
| | - Jack A Yanovski
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development; and
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware JS. Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genet Med 2024; 26:101029. [PMID: 37982373 PMCID: PMC11039201 DOI: 10.1016/j.gim.2023.101029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023] Open
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom.
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Katherine S Josephs
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, United Kingdom
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; Open Targets, Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David W Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia; University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, United Kingdom
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
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3
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Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos A, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon S, Castellanos F, Caufield JH, Chan LE, Chute C, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He Y(O, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus M, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts A, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res 2024; 52:D1333-D1346. [PMID: 37953324 PMCID: PMC10767975 DOI: 10.1093/nar/gkad1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.
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Affiliation(s)
| | | | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Joel Anderton
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Anita M Bagley
- Shriners Children's Northern California, Sacramento, CA, USA
| | - Eduard Bakštein
- National Institute of Mental Health, Klecany, Czech Republic
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC 27517, USA
| | - Gareth Baynam
- Rare Care Centre, Perth Children's Hospital, Perth, Australia
| | | | - Michael Berk
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Holli Bertram
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Somer Bishop
- Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience, San Francisco, CA, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - David F Bodenstein
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | | | - Kaan Boztug
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Jolana Čady
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Tiffany J Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, NY, NY, USA
| | | | - Seth J Carbon
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - J Harry Caufield
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Jaime Cruz-Rojo
- UDISGEN (Dysmorphology and Genetics Unit), 12 de Octubre Hospital, Madrid, Spain
| | - Noémi Dahan-Oliel
- Department of Clinical Research, Shriners Hospitals for Children, Montreal, Quebec, Canada
| | - Jon R Davids
- Shriners Children's Northern California, Sacramento, CA, USA
| | - Maud de Dieuleveult
- Département I&D, AP-HP, Banque Nationale de Données Maladies Rares, Paris, France
| | - Vinicius de Souza
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - J Raymond DePaulo
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Beata Derfalvi
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Ferdinand Dhombres
- Fetal Medicine Department, Armand Trousseau Hospital, Sorbonne University, GRC26, INSERM, Limics, Paris, France
| | - Claudia Diaz-Byrd
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bruno Donadille
- St Antoine Hospital, Reference Center for Rare Growth Endocrine Disorders, Sorbonne University, AP-HP, INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | | | - Reem Elfeky
- Department of Immunology, GOS Hospital for Children NHS Foundation Trust, University College London, London, UK
| | - Shahim Essaid
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Giovanna Fico
- Bipolar and Depressive Disorders Unit, Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Catalonia, Spain
| | - Helen V Firth
- Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Yun Freudenberg-Hua
- Department of Psychiatry, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | | | - Davera L Gabriel
- School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | - Jessica Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel Gore Moses
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian Green
- SNOMED International, London W2 6BD, UK
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - Tudor Groza
- Rare Care Centre, Perth Children's Hospital, Perth, Australia
| | | | - Julia Guthrie
- Department of Structural and Computational Biology, University of Vienna; Max Perutz Labs, Vienna, Austria
| | - Benjamin Gyori
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marc Hanauer
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Kateřina Hanušová
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | | | - Harshad Hegde
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingo Helbig
- Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kateřina Holasová
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Charles Tapley Hoyt
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Eric Hurwitz
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Lisa Joseph
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD, USA
| | - Kamyar Keramatian
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Bryan King
- Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience, San Francisco, CA, USA
| | - Katrin Knoflach
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Megan L Kraus
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Carlo Kroll
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Maaike Kusters
- Immunology, NIHR Great Ormond Street Hospital BRC, London, UK
| | - Markus S Ladewig
- Department of Ophthalmology, University Clinic Marburg - Campus Fulda, Fulda, Germany
| | - David Lagorce
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Pablo Lapunzina
- Institute of Medical and Molecular Genetics, Hospital Univ. La Paz, Madrid, Spain
| | - Bryan Laraway
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David Lewis-Smith
- Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University, Newcastle-Upon-Tyne NE14LP, UK
| | | | - Caterina Lucano
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Marzieh Majd
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Victor Martinez-Glez
- Center for Genomic Medicine, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Sabadell, Spain
| | - Toby H McHenry
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Julie A McMurry
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela Mihulová
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Caitlin E Millett
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Philip B Mitchell
- Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW, Australia
| | - Veronika Moslerová
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Kenji Narutomi
- Okinawa Prefectural Nanbu Medical Center & Children's Medical Center
| | - Shahrzad Nematollahi
- School of Physical and Occupational Therapy, McGill University, Montreal, Quebec, Canada
| | - Julian Nevado
- Institute of Medical and Molecular Genetics, Hospital Univ. La Paz, Madrid, Spain
| | - Andrew A Nierenberg
- Dauten Family Center for Bipolar Treatment Innovation, Massachusetts General Hospital, Boston, MA, USA
| | - Nikola Novák Čajbiková
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - John I Nurnberger
- Stark Neurosciences Research Institute, Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Daniel Olson
- Data Collaboration Center, Data Science, Critical Path Institute, Tucson, AZ, USA
| | - Abigail Ortiz
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Harry Pachajoa
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad Icesi, Cali, Colombia
| | - Guiomar Perez de Nanclares
- Molecular (epi) genetics lab, Bioaraba Health Research Institute, Araba University Hospital, Vitoria-Gasteiz, Spain
| | - Amy Peters
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Tim Putman
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christina K Rapp
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - Ana Rath
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Justin Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lauren Rekerle
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London W12 0HS, UK
| | - Suzy Roy
- SNOMED International, London W2 6BD, UK
| | - Stephan J Sanders
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Catharina Schuetz
- Universitätsklinikum Carl Gustav Carus, Medizinische Fakultät, TU, Dresden, Germany
| | - Eva C Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, Germany
| | - Thomas G Schulze
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Martin Schwarz
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Katie Scott
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Dominik Seelow
- Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité, Berlin, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center UKS, Homburg/Saar, Germany
| | | | - Morgan N Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric S Simon
- Eisenberg Family Depression Center, University of Michigan, Ann Arbor, MI, USA
| | - Balwinder Singh
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Jake T Smolinsky
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Sarah Sperry
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | | | - Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Robin Steinhaus
- Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité, Berlin, Germany
| | - Rebecca Strawbridge
- Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | | | - Polina Talapova
- Institute for Research and Health Policy Studies, Tufts Medicine, Boston, MA 2111, USA
| | | | - Pavel Tesner
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Rhys H Thomas
- Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University, Newcastle-Upon-Tyne NE14LP, UK
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD, USA
| | - Marek Turnovec
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
| | | | - Markéta Vlčková
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Anita Walden
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kai Wang
- Chinese HPO Consortium, Beijing, China
| | - Ron Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London W12 0HS, UK
| | | | | | - Lisa D Wiggins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Andrew E Williams
- Institute for Research and Health Policy Studies, Tufts Medicine, Boston, MA 2111, USA
| | - Chen Wu
- Chinese HPO Consortium, Beijing, China
| | - Margot J Wyrwoll
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Hui Xiong
- Chinese HPO Consortium, Beijing, China
| | - Nefize Yalin
- Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Yasunori Yamamoto
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Japan
| | - Lakshmi N Yatham
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Anastasia K Yocum
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Allan H Young
- Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham, Kent, London SE5 8AF, UK
| | - Zafer Yüksel
- Department of Human Genetics, Bioscientia Healthcare GmbH, Ingelheim, Germany
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andreas Zankl
- Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Ignacio Zarante
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Miroslav Zvolský
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Sabrina Toro
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Leigh C Carmody
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Nomi L Harris
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Melissa A Haendel
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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4
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Forsyth R, Peretz RH, Dempsey A, Britton J, Kratz L, Hamosh A, Vernon H, Batshaw ML, Valle D. The remarkable journey of one female individual with ornithine transcarbamylase deficiency diagnosed post-mortem. JIMD Rep 2023; 64:233-237. [PMID: 37151362 PMCID: PMC10159862 DOI: 10.1002/jmd2.12361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Urea cycle disorders (UCDs) comprise a group of inborn errors of metabolism with impaired ammonia clearance and an incidence of ~1:35 000 individuals. First described in the 1970s, the diagnosis and management of these disorders has evolved dramatically. We report on a 59-year-old woman with a UCD who contributed to advances in the understanding and treatment of this group of disorders. This individual was diagnosed with carbamoyl phosphate synthetase 1 deficiency based on a biochemical assay under a research context predating genetic sequencing, treated longitudinally as having this metabolic disorder, and was among the first participants to trial UCD pharmaceutical therapies. She ultimately succumbed to a SARS-CoV-2 infection while maintaining unexpectedly normal ammonium levels. Postmortem genetic testing revealed ornithine transcarbamylase deficiency. This individual's contributions to the field of UCDs is discussed herein.
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Affiliation(s)
- RaeLynn Forsyth
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Ryan H. Peretz
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Angela Dempsey
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jacquelyn Britton
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Lisa Kratz
- Biochemical Genetics LaboratoryKennedy Krieger InstituteBaltimoreMarylandUSA
| | - Ada Hamosh
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Hilary Vernon
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Mark L. Batshaw
- Center for Genetic Medicine ResearchChildren's National HospitalWashingtonDCUSA
| | - David Valle
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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5
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, van Sant D, Stark Z, Whiffin N, Rehm HL, Ware JS. Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms. medRxiv 2023:2023.03.30.23287948. [PMID: 37066232 PMCID: PMC10104222 DOI: 10.1101/2023.03.30.23287948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation, and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition (GenCC) members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both sequence ontology (SO) and human phenotype ontology (HPO) ontologies. GenCC member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Rooney Riggs
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Katherine S Josephs
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, 27599
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Ada Hamosh
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
- Open Targets, Cambridge, UK
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA
| | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David van Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia
- University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
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Abstract
Structural variation in genomes, such as copy number variants (CNVs), is under scrutiny for its contribution to phenotypic expression and evolution. Regions of homozygosity (ROH) are ripe for phenotype-gene discovery. Determining the genes and related phenotypes within genomic regions is key to studying potential functional and phenotypic consequences. Because individuals have multiple CNVs and ROHs in their genome, identifying genomic regions that are phenotypically significant is challenging. GeneScout is a web-based tool that can be used to search genomic regions to display and filter the genes and their associated phenotypes within regions of interest. Phenotypes and their associated gene(s) can then be filtered to show only the genes with phenotypes that have a particular inheritance pattern and/or specific clinical feature(s). Phenotypes can then be selected to compare the clinical synopses side-by-side in Online Mendelian Inheritance in Man (OMIM® ). Additionally, two coordinate sets can be compared to determine either the regions of overlap or the unique regions (subtraction). The resulting coordinate ranges are displayed on the results page, and the results table displays only the genes and phenotypes present within the coordinate ranges. The interactive table includes gene-specific links to external resources such as ClinVar, ClinGen validity, ClinGen dosage, and gnomAD, and a diamond symbol next to the gene name indicates a gene that spans the start or end of a coordinate range. Searches and comparisons may be performed for coordinates in assemblies GRCh37 (hg19) and GRCh38 (hg38). The results page offers the option to liftover coordinates entered in GRCh37 to GRCh38 and updates the results table to display the gene content based on assembly GRCh38. The search coordinates and results table can be downloaded in a tab-delimited or Excel file. © 2022 Wiley Periodicals LLC. Basic Protocol: Searching GeneScout.
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Affiliation(s)
- Carolyn D Applegate
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ada Hamosh
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joanna S Amberger
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
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DiStefano MT, Goehringer S, Babb L, Alkuraya FS, Amberger J, Amin M, Austin-Tse C, Balzotti M, Berg JS, Birney E, Bocchini C, Bruford EA, Coffey AJ, Collins H, Cunningham F, Daugherty LC, Einhorn Y, Firth HV, Fitzpatrick DR, Foulger RE, Goldstein J, Hamosh A, Hurles MR, Leigh SE, Leong IUS, Maddirevula S, Martin CL, McDonagh EM, Olry A, Puzriakova A, Radtke K, Ramos EM, Rath A, Riggs ER, Roberts AM, Rodwell C, Snow C, Stark Z, Tahiliani J, Tweedie S, Ware JS, Weller P, Williams E, Wright CF, Yates TM, Rehm HL. The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources. Genet Med 2022; 24:1732-1742. [PMID: 35507016 PMCID: PMC7613247 DOI: 10.1016/j.gim.2022.04.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Several groups and resources provide information that pertains to the validity of gene-disease relationships used in genomic medicine and research; however, universal standards and terminologies to define the evidence base for the role of a gene in disease and a single harmonized resource were lacking. To tackle this issue, the Gene Curation Coalition (GenCC) was formed. METHODS The GenCC drafted harmonized definitions for differing levels of gene-disease validity on the basis of existing resources, and performed a modified Delphi survey with 3 rounds to narrow the list of terms. The GenCC also developed a unified database to display curated gene-disease validity assertions from its members. RESULTS On the basis of 241 survey responses from the genetics community, a consensus term set was chosen for grading gene-disease validity and database submissions. As of December 2021, the database contained 15,241 gene-disease assertions on 4569 unique genes from 12 submitters. When comparing submissions to the database from distinct sources, conflicts in assertions of gene-disease validity ranged from 5.3% to 13.4%. CONCLUSION Terminology standardization, sharing of gene-disease validity classifications, and resolution of curation conflicts will facilitate collaborations across international curation efforts and in turn, improve consistency in genetic testing and variant interpretation.
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Affiliation(s)
- Marina T DiStefano
- Geisinger Health System, Danville, PA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Lawrence Babb
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Online Mendelian Inheritance in Man (OMIM), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Boston, MA; Mass General Brigham Laboratory for Molecular Medicine, Cambridge, MA
| | | | - Jonathan S Berg
- Department of Genetics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carol Bocchini
- Online Mendelian Inheritance in Man (OMIM), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alison J Coffey
- Illumina Clinical Services Laboratory, Illumina Inc, San Diego, CA
| | - Heather Collins
- National Library of Medicine, Bethesda, MD; ICF International Inc, Fairfax, VA
| | - Fiona Cunningham
- Genome Interpretation, Genome Assembly and Annotation (GAA), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Louise C Daugherty
- Genomics England, Queen Mary University of London, London, United Kingdom; Healx Ltd, Cambridge, United Kingdom
| | | | - Helen V Firth
- Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Rebecca E Foulger
- Genomics England, Queen Mary University of London, London, United Kingdom; SciBite Limited, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jennifer Goldstein
- Department of Genetics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC
| | - Ada Hamosh
- Online Mendelian Inheritance in Man (OMIM), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Sarah E Leigh
- Genomics England, Queen Mary University of London, London, United Kingdom
| | - Ivone U S Leong
- Genomics England, Queen Mary University of London, London, United Kingdom
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Ellen M McDonagh
- Genomics England, Queen Mary University of London, London, United Kingdom; Open Targets, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | | | - Arina Puzriakova
- Genomics England, Queen Mary University of London, London, United Kingdom
| | | | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health Bethesda, MD
| | - Ana Rath
- INSERM, US14 - Orphanet, Paris, France
| | | | - Angharad M Roberts
- National Heart and Lung Institute & MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Great Ormond Street Hospital, London, United Kingdom
| | | | - Catherine Snow
- Genomics England, Queen Mary University of London, London, United Kingdom
| | | | | | - Susan Tweedie
- HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - James S Ware
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; National Heart and Lung Institute & MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Phillip Weller
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Eleanor Williams
- Genomics England, Queen Mary University of London, London, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - Thabo Michael Yates
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.
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8
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Kannan S, Bodurtha JN, Hamosh A, Jordan C. Monochorionic twins with 15q26.3 duplication presenting with selective intrauterine growth restriction and discordant cardiac anomalies: A case report. Mol Genet Genomic Med 2022; 10:e1947. [PMID: 35795918 PMCID: PMC9356548 DOI: 10.1002/mgg3.1947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/25/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Duplication of the distal end of chromosome 15q has been previously implicated in a characteristic overgrowth syndrome. Additionally, many patients have other congenital malformations, including cardiac, renal, genital, and musculoskeletal anomalies. However, some patients may present with intrauterine growth restriction and short stature. Different breakpoints within 15q, as well as different environmental factors, may underlie these varied presentations. CASE PRESENTATION We discuss monochorionic-diamniotic twins with a ~345 kb maternally inherited duplication in 15q26.3. The twins presented with discordant pathology-one twin with a single umbilical artery, selective intrauterine growth restriction, and multiple cardiac defects including aortic coarctation, aortic valve stenosis, and ventricular septal defect, whereas the other twin was unaffected. To our knowledge, this case represents the smallest reported duplication of distal 15q. CONCLUSION The discordant phenotype seen in the twins is likely due to a complex interplay between genetic and environmental causes. The affected infant presented prenatally with growth restriction and a single umbilical artery rather than overgrowth, potentially due to a unique breakpoint within 15q. This, in turn, may have produced hemodynamic perturbations between the twins, leading to discordant cardiac disease. Our report thus highlights the importance of genetic and nongenetic mechanisms underlying discordant anomalies in monochorionic twins.
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Affiliation(s)
- Suraj Kannan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joann N Bodurtha
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher Jordan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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9
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Rodrigues EDS, Griffith S, Martin R, Antonescu C, Posey JE, Coban‐Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Sheffer A, Chong JX, Einhorn Y, Cupak M, Sobreira N. Variant-level matching for diagnosis and discovery: Challenges and opportunities. Hum Mutat 2022; 43:782-790. [PMID: 35191117 PMCID: PMC9133151 DOI: 10.1002/humu.24359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/30/2022]
Abstract
Here we describe MyGene2, Geno2MP, VariantMatcher, and Franklin; databases that provide variant-level information and phenotypic features to researchers, clinicians, healthcare providers and patients. Following the footsteps of the Matchmaker Exchange project that connects exome, genome, and phenotype databases at the gene level, these databases have as one goal to facilitate connection to one another using Data Connect, a standard for discovery and search of biomedical data from the Global Alliance for Genomics and Health (GA4GH).
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Affiliation(s)
- Eliete da S. Rodrigues
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Sean Griffith
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Renan Martin
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Corina Antonescu
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Zeynep Coban‐Akdemir
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Shalini N. Jhangiani
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexasUSA
| | - Kimberly F. Doheny
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - James R. Lupski
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexasUSA
- Department of PediatricsBaylor College of MedicineHoustonTexasUSA
- Texas Children's HospitalHoustonTexasUSA
| | - David Valle
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Michael J. Bamshad
- Division of Genetic Medicine, Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Ada Hamosh
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | | | - Jessica X. Chong
- Division of Genetic Medicine, Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | | | | | - Nara Sobreira
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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Boycott KM, Azzariti DR, Hamosh A, Rehm HL. Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking. Hum Mutat 2022; 43:659-667. [PMID: 35537081 PMCID: PMC9133175 DOI: 10.1002/humu.24373] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
The Matchmaker Exchange (MME) was launched in 2015 to provide a robust mechanism to discover novel disease-gene relationships. It operates as a federated network connecting databases holding relevant data using a common application programming interface, where two or more users are looking for a match for the same gene (two-sided matchmaking). Seven years from its launch, it is clear that the MME is making outstanding contributions to understanding the morbid anatomy of the genome. The number of unique genes present across the MME has steadily increased over time; there are currently >13,520 unique genes (~68% of all protein-coding genes) connected across the MME's eight genomic matchmaking nodes, GeneMatcher, DECIPHER, PhenomeCentral, MyGene2, seqr, Initiative on Rare and Undiagnosed Disease, PatientMatcher, and the RD-Connect Genome-Phenome Analysis Platform. The collective data set accessible across the MME currently includes more than 120,000 cases from over 12,000 contributors in 98 countries. The discovery of potential new disease-gene relationships is happening daily and international collaborative teams are moving these advances forward to publication, now numbering well over 500. Expansion of data sharing into routine clinical practice by clinicians, genetic counselors, and clinical laboratories has ensured access to discovery for even more individuals with undiagnosed rare genetic diseases. Tens of thousands of patients and their family members have been directly or indirectly impacted by the discoveries facilitated by two-sided genomic matchmaking. MME supports further connections to the literature (PubCaseFinder) and to human and model organism resources (Monarch Initiative) and scientists (ModelMatcher). Efforts are now underway to explore additional approaches to matchmaking at the gene or variant level where there is only one querier (one-sided matchmaking). Genomic matchmaking has proven its utility over the past 7 years and will continue to facilitate discoveries in the years to come.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Danielle R. Azzariti
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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11
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Thaxton C, Goldstein J, DiStefano M, Wallace K, Witmer PD, Haendel MA, Hamosh A, Rehm HL, Berg JS. Lumping versus splitting: How to approach defining a disease to enable accurate genomic curation. Cell Genom 2022; 2:100131. [PMID: 35754516 PMCID: PMC9221396 DOI: 10.1016/j.xgen.2022.100131] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The dilemma of how to categorize and classify diseases has been debated for centuries. The field of medical genetics has historically approached nosology based on clinical phenotypes observed in patients and families. Advances in genomic sequencing and understanding of genetic contributions to disease often provoke a need to reassess these classifications. The Clinical Genome Resource (ClinGen) has developed frameworks to classify the strength of evidence underlying monogenic gene-disease relationships, variant pathogenicity, and clinical actionability. It is therefore necessary to define the disease entity being evaluated, which can be challenging for genes associated with multiple conditions and/or a broad phenotypic spectrum. We therefore developed criteria to guide "lumping and splitting" decisions and improve consistency in defining monogenic gene-disease relationships. Here, we outline the precuration process, the lumping and splitting guidelines with examples, and describe the implications for clinical diagnosis, informatics, and care management.
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Affiliation(s)
- Courtney Thaxton
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA,Lead contact,Correspondence:
| | - Jennifer Goldstein
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Kathleen Wallace
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - P. Dane Witmer
- Johns Hopkins Genomics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Melissa A. Haendel
- Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Heidi L. Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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12
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Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med 2022; 24:784-797. [PMID: 35148959 PMCID: PMC9119004 DOI: 10.1016/j.gim.2021.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.
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Affiliation(s)
- Samantha M Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ; Department of Genetics, Rutgers University, Piscataway, NJ
| | - Elizabeth E Blue
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Lisa H Chadwick
- Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Kimberly F Doheny
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Colleen P Davis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Genetics, Yale School of Medicine, New Haven, CT
| | | | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA.
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA.
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13
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Hamosh A, Wohler E, Martin R, Griffith S, da S Rodrigues E, Antonescu C, Doheny KF, Valle D, Sobreira N. The impact of GeneMatcher on international data sharing and collaboration. Hum Mutat 2022; 43:668-673. [PMID: 35170833 PMCID: PMC9133194 DOI: 10.1002/humu.24350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
GeneMatcher (genematcher.org) is a tool designed to connect individuals with an interest in the same gene. Now used around the world to create collaborations and generate the evidence needed to support novel disease gene identification, GeneMatcher is a founding member of the Matchmaker Exchange (MME; matchmakerexchange.org) and strongest possible advocate for global data sharing including those in resource‐limited environments. As of October 1, 2021, there are 12,531 submitters from 94 countries who have submitted 58,134 submissions with 13,498 unique genes in the database. Among these genes, 8970 (64%) have matched at least once and the total number of matches is 378,806, growing by about 10,000 per month. GeneMatcher submitters increase by 80–120 each month and submissions grow by >800 per month, while unique genes and gene matches continue to grow steadily at rate of about 80 per month. The number of genes without a match peaked at 4371 in February of 2019 and despite the increase in the number of new submissions, the number of unique genes without a match continues to slowly decline, currently standing at 4,016. All submissions in GeneMatcher are available for matching across the MME.
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Affiliation(s)
- Ada Hamosh
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Elizabeth Wohler
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Renan Martin
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Sean Griffith
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Eliete da S Rodrigues
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Corina Antonescu
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Kimberly F Doheny
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - David Valle
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
| | - Nara Sobreira
- McKusick‐Nathans Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD
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14
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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15
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Rasmussen SA, Hamosh A. Festschrift for Victor A. McKusick on the Centenary of his Birth: Introduction. Am J Med Genet A 2021; 185:3189-3192. [PMID: 34338430 PMCID: PMC8530865 DOI: 10.1002/ajmg.a.62441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Sonja A. Rasmussen
- Departments of Pediatrics and Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, USA
- Department of Epidemiology, University of Florida College of Public Health and Health Professions and College of Medicine, Gainesville, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
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16
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Lee C, Antonarakis SE, Hamosh A, Burn J. Three decades of the Human Genome Organization. Am J Med Genet A 2021; 185:3314-3321. [PMID: 34581472 PMCID: PMC9293206 DOI: 10.1002/ajmg.a.62512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/03/2021] [Accepted: 09/11/2021] [Indexed: 11/07/2022]
Abstract
The Human Genome Organization (HUGO) was initially established in 1988 to help integrate international scientific genomic activity and to accelerate the diffusion of knowledge from the efforts of the human genome project. Its founding President was Victor McKusick. During the late 1980s and 1990s, HUGO organized lively gene mapping meetings to accurately place genes on the genome as chromosomes were being sequenced. With the completion of the Human Genome Project, HUGO went through some transitions and self-reflection. In 2020, HUGO (which hosts a large annual scientific meeting and comprises the renowned HUGO Gene Nomenclature Committee [HGNC], responsible for naming genes, and an outstanding Ethics Committee) was merged with the Human Genome Variation Society (HGVS; which defines the correct nomenclature for variation description) and the Human Variome Project (HVP; championed by the late Richard Cotton) into a single organization that is committed to assembling human genomic variation from all over the world. This consolidated effort, under a new Executive Board and seven focused committees, will facilitate efficient and effective communication and action to bring the benefits of increasing knowledge of genome diversity and biology to people all over the world.
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Affiliation(s)
- Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John Burn
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
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17
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Wohler E, Martin R, Griffith S, Rodrigues EDS, Antonescu C, Posey JE, Coban-Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Hamosh A, Sobreira N. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis 2021; 16:365. [PMID: 34407837 PMCID: PMC8371856 DOI: 10.1186/s13023-021-01916-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/13/2021] [Indexed: 12/02/2022] Open
Abstract
Background With the advent of whole exome (ES) and genome sequencing (GS) as tools for disease gene discovery, rare variant filtering, prioritization and data sharing have become essential components of the search for disease genes and variants potentially contributing to disease phenotypes. The computational storage, data manipulation, and bioinformatic interpretation of thousands to millions of variants identified in ES and GS, respectively, is a challenging task. To aid in that endeavor, we constructed PhenoDB, GeneMatcher and VariantMatcher. Results PhenoDB is an accessible, freely available, web-based platform that allows users to store, share, analyze and interpret their patients’ phenotypes and variants from ES/GS data. GeneMatcher is accessible to all stakeholders as a web-based tool developed to connect individuals (researchers, clinicians, health care providers and patients) around the globe with interest in the same gene(s), variant(s) or phenotype(s). Finally, VariantMatcher was developed to enable public sharing of variant-level data and phenotypic information from individuals sequenced as part of multiple disease gene discovery projects. Here we provide updates on PhenoDB and GeneMatcher applications and implementation and introduce VariantMatcher. Conclusion Each of these tools has facilitated worldwide data sharing and data analysis and improved our ability to connect genes to phenotypic traits. Further development of these platforms will expand variant analysis, interpretation, novel disease-gene discovery and facilitate functional annotation of the human genome for clinical genomics implementation and the precision medicine initiative. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01916-z.
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Affiliation(s)
- Elizabeth Wohler
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Renan Martin
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sean Griffith
- Center for Inherited Disease Research - CIDR, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eliete da S Rodrigues
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corina Antonescu
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Center for Inherited Disease Research - CIDR, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - David Valle
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nara Sobreira
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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18
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Rasmussen SA, Hamosh A. Memories of Victor A. McKusick. Am J Med Genet A 2021; 185:3377-3383. [PMID: 34313375 DOI: 10.1002/ajmg.a.62431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Sonja A Rasmussen
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Epidemiology, University of Florida College of Public Health and Health Professions and College of Medicine, Gainesville, Florida, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Prasad N, Hamosh A, Sponseller P. Orthopaedic Manifestations of Inborn Errors of Metabolism. JBJS Rev 2021; 9:01874474-202107000-00003. [PMID: 34257233 DOI: 10.2106/jbjs.rvw.20.00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
» Inborn errors of metabolism are disorders of carbohydrate, amino acid, organic acid, or purine and pyrimidine metabolism; disorders of fatty acid oxidation; disorders of metal metabolism; and lysosomal storage defects that can cause metabolic derangements that have secondary musculoskeletal effects. » Orthopaedic surgeons should be aware that patients with inborn errors of metabolism may be at high risk for spasticity, which may cause joint subluxations, scoliosis, and contractures, as well as poor bone quality, which is caused by malnutrition or disordered bone growth. » Multidisciplinary care and follow-up are important to identify musculoskeletal problems in a timely manner in order to provide effective treatment.
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Affiliation(s)
- Niyathi Prasad
- Departments of Orthopaedic Surgery and Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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20
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Hamosh A, Amberger JS, Bocchini C, Scott AF, Rasmussen SA. Online Mendelian Inheritance in Man (OMIM®): Victor McKusick's magnum opus. Am J Med Genet A 2021; 185:3259-3265. [PMID: 34169650 PMCID: PMC8596664 DOI: 10.1002/ajmg.a.62407] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/05/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022]
Abstract
Victor McKusick's many contributions to medicine are legendary, but his magnum opus is Mendelian Inheritance in Man (MIM), his catalog of Mendelian phenotypes and their associated genes. The catalog, originally published in 1966 in book form, became available on the internet as Online Mendelian Inheritance in Man (OMIM®) in 1987. The first of 12 editions of MIM included 1486 entries; this number has increased to over 25,000 entries in OMIM as of April 2021, which demonstrates the growth of knowledge about Mendelian phenotypes and their genes through the years. OMIM now has over 20,000 unique users a day, including users from every country in the world. Many of the early decisions made by McKusick, such as to maintain MIM data in a computer‐readable format, to separate phenotype entries from those for genes, and to give phenotypes and genes MIM numbers, have proved essential to the long‐term utility and flexibility of his catalog. Based on his extensive knowledge of genetics and vision of its future in the field of medicine, he developed a framework for the capture and summary of information from the published literature on phenotypes and their associated genes; this catalog continues to serve as an indispensable resource to the genetics community.
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Affiliation(s)
- Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joanna S Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carol Bocchini
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alan F Scott
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sonja A Rasmussen
- Departments of Pediatrics and Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Epidemiology, University of Florida College of Public Health and Health Professions and College of Medicine, Gainesville, Florida, USA
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21
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Rasmussen SA, Pomputius A, Amberger JS, Hamosh A. Viewing Victor McKusick's legacy through the lens of his bibliography. Am J Med Genet A 2021; 185:3212-3223. [PMID: 34159717 DOI: 10.1002/ajmg.a.62394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/13/2021] [Accepted: 05/22/2021] [Indexed: 11/09/2022]
Abstract
Victor McKusick's contributions to the field of medical genetics are legendary and include his contributions as a mentor, as creator of Mendelian Inheritance in Man (now Online Mendelian Inheritance in Man [OMIM®]), and as a leader in the field of medical genetics. McKusick's full bibliography includes 772 publications. Here we review the 453 papers authored by McKusick and indexed in PubMed, from his earliest paper published in the New England Journal of Medicine in 1949 to his last paper published in American Journal of Medical Genetics Part A in 2008. This review of his bibliography chronicles McKusick's evolution from an internist and cardiologist with an interest in genetics to an esteemed leader in the growing field of medical genetics. Review of his bibliography also provides a historical perspective of the development of the discipline of medical genetics. This field came into its own during his lifetime, transitioning from the study of interesting cases and families used to codify basic medical genetics principles to an accredited medical specialty that is expected to transform healthcare. Along the way, he helped to unite the fields of medical and human genetics to focus on mapping the human genome, culminating in completion of the Human Genome Project. This review confirms the critical role played by Victor McKusick as the founding father of medical genetics.
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Affiliation(s)
- Sonja A Rasmussen
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Epidemiology, University of Florida, College of Public Health and Health Professions and College of Medicine, Gainesville, Florida, USA
| | - Ariel Pomputius
- Health Science Center Libraries, University of Florida, Gainesville, Florida, USA
| | - Joanna S Amberger
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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22
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de Macena Sobreira NL, Hamosh A. Next-generation sequencing and the evolution of data sharing. Am J Med Genet A 2021; 185:2633-2635. [PMID: 33960641 DOI: 10.1002/ajmg.a.62239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/26/2021] [Accepted: 04/10/2021] [Indexed: 12/17/2022]
Abstract
Disease gene identification often relies on identifying multiple affected individuals with similar phenotypes and candidate variants in the same gene. Phenotypic and genomic data sharing tools have facilitated connections that led to novel disease gene discoveries and better characterization and recognition of rare diseases. Additionally, data sharing has evolved. From gene-based matches to variant-level information with increasing use of phenotypic information. We expect that these initiatives will continue to expand in the future affording clinicians, researchers, and most importantly, patients and their families faster and more comprehensive answers.
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Affiliation(s)
- Nara Lygia de Macena Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Cif L, Demailly D, Lin JP, Barwick KE, Sa M, Abela L, Malhotra S, Chong WK, Steel D, Sanchis-Juan A, Ngoh A, Trump N, Meyer E, Vasques X, Rankin J, Allain MW, Applegate CD, Attaripour Isfahani S, Baleine J, Balint B, Bassetti JA, Baple EL, Bhatia KP, Blanchet C, Burglen L, Cambonie G, Seng EC, Bastaraud SC, Cyprien F, Coubes C, d'Hardemare V, Doja A, Dorison N, Doummar D, Dy-Hollins ME, Farrelly E, Fitzpatrick DR, Fearon C, Fieg EL, Fogel BL, Forman EB, Fox RG, Gahl WA, Galosi S, Gonzalez V, Graves TD, Gregory A, Hallett M, Hasegawa H, Hayflick SJ, Hamosh A, Hully M, Jansen S, Jeong SY, Krier JB, Krystal S, Kumar KR, Laurencin C, Lee H, Lesca G, François LL, Lynch T, Mahant N, Martinez-Agosto JA, Milesi C, Mills KA, Mondain M, Morales-Briceno H, Ostergaard JR, Pal S, Pallais JC, Pavillard F, Perrigault PF, Petersen AK, Polo G, Poulen G, Rinne T, Roujeau T, Rogers C, Roubertie A, Sahagian M, Schaefer E, Selim L, Selway R, Sharma N, Signer R, Soldatos AG, Stevenson DA, Stewart F, Tchan M, Verma IC, de Vries BBA, Wilson JL, Wong DA, Zaitoun R, Zhen D, Znaczko A, Dale RC, de Gusmão CM, Friedman J, Fung VSC, King MD, Mohammad SS, Rohena L, Waugh JL, Toro C, Raymond FL, Topf M, Coubes P, Gorman KM, Kurian MA. KMT2B-related disorders: expansion of the phenotypic spectrum and long-term efficacy of deep brain stimulation. Brain 2021; 143:3242-3261. [PMID: 33150406 DOI: 10.1093/brain/awaa304] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/28/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022] Open
Abstract
Heterozygous mutations in KMT2B are associated with an early-onset, progressive and often complex dystonia (DYT28). Key characteristics of typical disease include focal motor features at disease presentation, evolving through a caudocranial pattern into generalized dystonia, with prominent oromandibular, laryngeal and cervical involvement. Although KMT2B-related disease is emerging as one of the most common causes of early-onset genetic dystonia, much remains to be understood about the full spectrum of the disease. We describe a cohort of 53 patients with KMT2B mutations, with detailed delineation of their clinical phenotype and molecular genetic features. We report new disease presentations, including atypical patterns of dystonia evolution and a subgroup of patients with a non-dystonic neurodevelopmental phenotype. In addition to the previously reported systemic features, our study has identified co-morbidities, including the risk of status dystonicus, intrauterine growth retardation, and endocrinopathies. Analysis of this study cohort (n = 53) in tandem with published cases (n = 80) revealed that patients with chromosomal deletions and protein truncating variants had a significantly higher burden of systemic disease (with earlier onset of dystonia) than those with missense variants. Eighteen individuals had detailed longitudinal data available after insertion of deep brain stimulation for medically refractory dystonia. Median age at deep brain stimulation was 11.5 years (range: 4.5-37.0 years). Follow-up after deep brain stimulation ranged from 0.25 to 22 years. Significant improvement of motor function and disability (as assessed by the Burke Fahn Marsden's Dystonia Rating Scales, BFMDRS-M and BFMDRS-D) was evident at 6 months, 1 year and last follow-up (motor, P = 0.001, P = 0.004, and P = 0.012; disability, P = 0.009, P = 0.002 and P = 0.012). At 1 year post-deep brain stimulation, >50% of subjects showed BFMDRS-M and BFMDRS-D improvements of >30%. In the long-term deep brain stimulation cohort (deep brain stimulation inserted for >5 years, n = 8), improvement of >30% was maintained in 5/8 and 3/8 subjects for the BFMDRS-M and BFMDRS-D, respectively. The greatest BFMDRS-M improvements were observed for trunk (53.2%) and cervical (50.5%) dystonia, with less clinical impact on laryngeal dystonia. Improvements in gait dystonia decreased from 20.9% at 1 year to 16.2% at last assessment; no patient maintained a fully independent gait. Reduction of BFMDRS-D was maintained for swallowing (52.9%). Five patients developed mild parkinsonism following deep brain stimulation. KMT2B-related disease comprises an expanding continuum from infancy to adulthood, with early evidence of genotype-phenotype correlations. Except for laryngeal dysphonia, deep brain stimulation provides a significant improvement in quality of life and function with sustained clinical benefit depending on symptoms distribution.
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Affiliation(s)
- Laura Cif
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Diane Demailly
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Jean-Pierre Lin
- Complex Motor Disorder Service, Children's Neurosciences Department, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK.,Children's Neuromodulation Group, Women and Children's Health Institute, Faculty of life Sciences and Medicine (FOLSM), King's Health Partners, London, UK
| | - Katy E Barwick
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mario Sa
- Complex Motor Disorder Service, Children's Neurosciences Department, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Lucia Abela
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Wui K Chong
- Developmental Imaging and Biophysics, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Dora Steel
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, UK
| | - Adeline Ngoh
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Natalie Trump
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Esther Meyer
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - Julia Rankin
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Meredith W Allain
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Carolyn D Applegate
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sanaz Attaripour Isfahani
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julien Baleine
- Unité de Soins Intensifs et Réanimation Pédiatrique et Néonatale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Bettina Balint
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jennifer A Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medical College, New York, NY, USA
| | - Emma L Baple
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Catherine Blanchet
- Département d'Oto-Rhino-Laryngologie et Chirurgie Cervico-Faciale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Lydie Burglen
- Département de génétique médicale, APHP Hôpital Armand Trousseau, Paris, France
| | - Gilles Cambonie
- Unité de Soins Intensifs et Réanimation Pédiatrique et Néonatale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Emilie Chan Seng
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | | | - Fabienne Cyprien
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Christine Coubes
- Département de Génétique médicale, Maladies rares et médecine personnalisée, CHU Montpellier, Montpellier, France
| | - Vincent d'Hardemare
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | | | - Asif Doja
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nathalie Dorison
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | - Diane Doummar
- Neuropédiatrie, Centre de référence neurogénétique mouvement anormaux de l'enfant, Hôpital Armand Trousseau, AP-HP, Sorbonne Université, France
| | - Marisela E Dy-Hollins
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ellyn Farrelly
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Palo Alto, CA, USA.,Department of Pediatrics, Lucile Packard Children's Hospital at Stanford, CA, USA
| | - David R Fitzpatrick
- Human Genetics Unit, Medical and Developmental Genetics, University of Edinburgh Western General Hospital, Edinburgh, Scotland, UK
| | - Conor Fearon
- Department of Neurology, The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin, Ireland
| | - Elizabeth L Fieg
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brent L Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Eva B Forman
- Department of Paediatric Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland
| | - Rachel G Fox
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | | | - William A Gahl
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Serena Galosi
- Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Victoria Gonzalez
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Tracey D Graves
- Department of Neurology, Hinchingbrooke Hospital, North West Anglia NHS Foundation Trust, Huntingdon, UK
| | - Allison Gregory
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Mark Hallett
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Harutomo Hasegawa
- Complex Motor Disorder Service, Children's Neurosciences Department, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK.,Children's Neuromodulation Group, Women and Children's Health Institute, Faculty of life Sciences and Medicine (FOLSM), King's Health Partners, London, UK
| | - Susan J Hayflick
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.,Department of Paediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marie Hully
- Département de Neurologie, APHP-Necker-Enfants Malades, Paris, France
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Suh Young Jeong
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Joel B Krier
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sidney Krystal
- Département de Neuroradiologie, Hôpital Fondation Rothschild, Paris
| | - Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Sydney, NSW, Australia
| | - Chloé Laurencin
- Département de Neurologie, Hôpital Neurologique Pierre Wertheimer, Lyon, France
| | - Hane Lee
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Gaetan Lesca
- Département de Génétique, Hôpital Universitaire de Lyon, Lyon, France
| | | | - Timothy Lynch
- Department of Neurology, The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin, Ireland.,UCD School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Neil Mahant
- Movement Disorders Unit, Department of Neurology, Westmead Hospital, Westmead, NSW, Australia
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Christophe Milesi
- Unité de Soins Intensifs et Réanimation Pédiatrique et Néonatale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Kelly A Mills
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michel Mondain
- Département d'Oto-Rhino-Laryngologie et Chirurgie Cervico-Faciale, Hôpital Universitaire de Montpellier, Montpellier, France
| | - Hugo Morales-Briceno
- Movement Disorders Unit, Department of Neurology, Westmead Hospital, Westmead, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | - John R Ostergaard
- Centre for Rare Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Swasti Pal
- Institute of Genetics and Genomics, Sir Ganga Ram Hospital, Rajender Nagar, New Delhi, India
| | - Juan C Pallais
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frédérique Pavillard
- Département d'Anesthésie-Réanimation Gui de Chauliac, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Pierre-Francois Perrigault
- Département d'Anesthésie-Réanimation Gui de Chauliac, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | | | - Gustavo Polo
- Département de Neurochirurgie Fonctionnelle, Hôpital Neurologique et Neurochirurgical, Pierre Wertheimer, Lyon, France
| | - Gaetan Poulen
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Roujeau
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France
| | - Caleb Rogers
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Agathe Roubertie
- Département de Neuropédiatrie, Hôpital Universitaire de Montpellier, Montpellier, France.,INSERM U1051, Institut des Neurosciences de Montpellier, Montpellier, France
| | - Michelle Sahagian
- Division of Neurology, Rady Children's Hospital San Diego, CA, USA.,Department of Neuroscience, University of California San Diego, CA, USA
| | - Elise Schaefer
- Medical Genetics, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Laila Selim
- Cairo University Children Hospital, Pediatric Neurology and Metabolic division, Cairo, Egypt
| | - Richard Selway
- Department of Neurosurgery, King's College Hospital, London, UK
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Rebecca Signer
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ariane G Soldatos
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David A Stevenson
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Fiona Stewart
- Department of Genetic Medicine, Belfast Health and Social Care Trust, Belfast, UK
| | - Michel Tchan
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Department of Genetics, Westmead Hospital, Westmead, NSW, Australia
| | | | - Ishwar C Verma
- Institute of Genetics and Genomics, Sir Ganga Ram Hospital, Rajender Nagar, New Delhi, India
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jenny L Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Derek A Wong
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Raghda Zaitoun
- Department of Paediatrics, Neurology Division, Ain Shams University Hospital, Cairo, Egypt
| | - Dolly Zhen
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Anna Znaczko
- Department of Genetic Medicine, Belfast Health and Social Care Trust, Belfast, UK
| | - Russell C Dale
- Department of Paediatric Neurology, The Children's Hospital at Westmead, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Claudio M de Gusmão
- Department of Neurology, Harvard Medical School, Boston, MA, USA.,Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Jennifer Friedman
- Division of Neurology, Rady Children's Hospital San Diego, CA, USA.,Department of Neuroscience, University of California San Diego, CA, USA.,Departments of Paediatrics, University of California, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Victor S C Fung
- Movement Disorders Unit, Department of Neurology, Westmead Hospital, Westmead, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Mary D King
- Department of Paediatric Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland.,UCD School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Shekeeb S Mohammad
- Department of Paediatric Neurology, The Children's Hospital at Westmead, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, TX, USA.,Department of Pediatrics, Long School of Medicine, UT Health, San Antonio, TX, USA
| | - Jeff L Waugh
- Division of Pediatric Neurology, Department of Pediatrics, University of Texas Southwestern, Dallas, TX, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Philippe Coubes
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Kathleen M Gorman
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
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Dyment DA, O'Donnell-Luria A, Agrawal PB, Coban Akdemir Z, Aleck KA, Antaki D, Al Sharhan H, Au PYB, Aydin H, Beggs AH, Bilguvar K, Boerwinkle E, Brand H, Brownstein CA, Buyske S, Chodirker B, Choi J, Chudley AE, Clericuzio CL, Cox GF, Curry C, de Boer E, de Vries BBA, Dunn K, Dutmer CM, England EM, Fahrner JA, Geckinli BB, Genetti CA, Gezdirici A, Gibson WT, Gleeson JG, Greenberg CR, Hall A, Hamosh A, Hartley T, Jhangiani SN, Karaca E, Kernohan K, Lauzon JL, Lewis MES, Lowry RB, López-Giráldez F, Matise TC, McEvoy-Venneri J, McInnes B, Mhanni A, Garcia Minaur S, Moilanen J, Nguyen A, Nowaczyk MJM, Posey JE, Õunap K, Pehlivan D, Pajusalu S, Penney LS, Poterba T, Prontera P, Doriqui MJR, Sawyer SL, Sobreira N, Stanley V, Torun D, Wargowski D, Witmer PD, Wong I, Xing J, Zaki MS, Zhang Y, Boycott KM, Bamshad MJ, Nickerson DA, Blue EE, Innes AM. Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome. Am J Med Genet A 2021; 185:119-133. [PMID: 33098347 PMCID: PMC8197629 DOI: 10.1002/ajmg.a.61926] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/09/2020] [Accepted: 09/19/2020] [Indexed: 01/19/2023]
Abstract
Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a "Dubowitz-like" condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.
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Affiliation(s)
- David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Anne O'Donnell-Luria
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kyrieckos A Aleck
- Department of Genetics and Metabolism, Phoenix Children's Medical Group, Phoenix, Arizona, USA
| | - Danny Antaki
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Hind Al Sharhan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Ping-Yee B Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Waco, Texas, USA
| | - Harrison Brand
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Steve Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, USA
| | - Bernard Chodirker
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Albert E Chudley
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carol L Clericuzio
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Gerald F Cox
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Cynthia Curry
- University of California, San Francisco, California, USA
- Genetic Medicine, University Pediatric Specialists, Fresno, California, USA
| | - Elke de Boer
- Department of Human Genetics, Raboud University Medical Centre, Nijmegen, Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Raboud University Medical Centre, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Raboud University Medical Centre, Nijmegen, Netherlands
| | - Kathryn Dunn
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Cullen M Dutmer
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eleina M England
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
| | - Jill A Fahrner
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bilgen B Geckinli
- Department of Medical Genetics, School of Medicine, Marmara University, Istanbul, Turkey
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - William T Gibson
- Department of Medical Genetics and British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Cheryl R Greenberg
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - April Hall
- Waisman Center Clinical Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Julie L Lauzon
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics and British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - R Brian Lowry
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Francesc López-Giráldez
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Tara C Matise
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Jennifer McEvoy-Venneri
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Brenda McInnes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Aziz Mhanni
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sixto Garcia Minaur
- Sección de Genética Clínica, INGEMM (Instituto de Genética Médica y Molecular), Madrid, Spain
| | - Jukka Moilanen
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - An Nguyen
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Malgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Katrin Õunap
- United Laboratories, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Sander Pajusalu
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- United Laboratories, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Lynette S Penney
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Timothy Poterba
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia and University of Perugia, Perugia, Italy
| | | | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Deniz Torun
- Department of Medical Genetics, Gulhane Military Medical Academy, Ankara, Turkey
| | - David Wargowski
- Division of Genetics, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Isaac Wong
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Yeting Zhang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman-Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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25
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Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res 2020; 48:D704-D715. [PMID: 31701156 PMCID: PMC7056945 DOI: 10.1093/nar/gkz997] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022] Open
Abstract
In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.
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Affiliation(s)
- Kent A Shefchek
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Michael Gargano
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Nicolas Matentzoglu
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Deepak Unni
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Matthew Brush
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel Keith
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Tom Conlin
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Nicole Vasilevsky
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - James P Balhoff
- Renaissance Computing Institute at UNC, Chapel Hill, NC 27517, USA
| | - Larry Babb
- Broad Institute, Cambridge, MA 02142, USA
| | | | - Hannah Blau
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Yvonne Bradford
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Leigh Carmody
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Valentina Cipriani
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Maria Della Rocca
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Nathan Dunn
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Shahim Essaid
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Petra Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chris Grove
- California Institute of Technology, Pasadena, CA 91125, USA
| | - Jean-Phillipe Gourdine
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.,Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maureen Hoatlin
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marcin Joachimiak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Simon Jupp
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kenneth B Lett
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Suzanna E Lewis
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | | | - Zoë M Pendlington
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Tim Putman
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Vida Ravanmehr
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Erin Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA 17837, USA
| | - Sofia Robb
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Erik Segerdell
- Xenbase, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Morgan Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea L Storm
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Courtney Thaxon
- University of North Carolina Medical School, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Anne Thessen
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Julie A McMurry
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | | | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Peter N Robinson
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Melissa A Haendel
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.,Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Monica C Munoz-Torres
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Abstract
In the last decade, exome and/or genome sequencing has become a common test in the diagnosis of individuals with features of a rare Mendelian disorder. Despite its success, this test leaves the majority of tested individuals undiagnosed. This review describes the Matchmaker Exchange (MME), a federated network established to facilitate the solving of undiagnosed rare-disease cases through data sharing. MME supports genomic matchmaking, the act of connecting two or more parties looking for cases with similar phenotypes and variants in the same candidate genes. An application programming interface currently connects six matchmaker nodes-the Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER), GeneMatcher, PhenomeCentral, seqr, MyGene2, and the Initiative on Rare and Undiagnosed Diseases (IRUD) Exchange-resulting in a collective data set spanning more than 150,000 cases from more than 11,000 contributors in 88 countries. Here, we describe the successes and challenges of MME, its individual matchmaking nodes, plans for growing the network, and considerations for future directions.
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Affiliation(s)
- Danielle R Azzariti
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA;
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Jelin AC, Sobreira N, Wohler E, Solomon B, Sparks T, Sagaser KG, Forster KR, Miller J, Witmer PD, Hamosh A, Valle D, Blakemore K. The utility of exome sequencing for fetal pleural effusions. Prenat Diagn 2020; 40:590-595. [PMID: 31994743 DOI: 10.1002/pd.5650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 01/23/2023]
Abstract
OBJECTIVE We sought to evaluate the performance of exome sequencing (ES) in determining an underlying genetic etiology for cases of fetal pleural effusions. STUDY DESIGN We examined a prospective cohort series of fetal pleural effusions visualized sonographically between 1 April 2016 and 31 August 2017. Fetal pleural effusions attributed to twin sharing, anemia, or structural anomalies were excluded, as were all cases with a genetic diagnosis established by karyotype or chromosomal microarray analysis. The remaining cases with pleural effusions of unclear etiology were offered ES. ES was performed by clinical sequencing and/or sequencing under the Baylor-Hopkins Center for Mendelian Genomics' (BHCMG) research platform. All cases were evaluated for novel genes or phenotypic expansion of disease-causing genes. RESULTS ES was performed on six probands affected by pleural effusions. A pathogenic variant was identified in one case (16.7%). Four additional cases had variants of uncertain significance (VUS) in candidate genes of pathological interest. Neither clinical nor candidate genes were evident in the final case. CONCLUSION ES should be considered in the evaluation of prenatally detected idiopathic pleural effusions when other diagnostic workup for a genetic etiology has failed.
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Affiliation(s)
- Angie C Jelin
- Department of Gynecology and Obstetrics, Division of Maternal Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Elizabeth Wohler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | | | - Teresa Sparks
- Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Maternal Fetal Medicine, University of California, San Francisco, CA, USA
| | - Katelynn G Sagaser
- Department of Gynecology and Obstetrics, Division of Maternal Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Katherine R Forster
- Department of Gynecology and Obstetrics, Center for Fetal Therapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jena Miller
- Department of Gynecology and Obstetrics, Center for Fetal Therapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Karin Blakemore
- Department of Gynecology and Obstetrics, Division of Maternal Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
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28
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Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxon C, Bocci G, Joachimiak MP, Köhler S, Robinson PN, Mungall C, Oprea TI. How many rare diseases are there? Nat Rev Drug Discov 2020; 19:77-78. [PMID: 32020066 PMCID: PMC7771654 DOI: 10.1038/d41573-019-00180-y] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A lack of robust knowledge of the number of rare diseases and the number of people affected by them limits the development of approaches to ameliorate the substantial cumulative burden of rare diseases. Here, we call for coordinated efforts to more precisely define rare diseases.
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Affiliation(s)
- Melissa Haendel
- Oregon Clinical & Translational Science Institute, Oregon Health & Science University, Portland, OR, USA
| | - Nicole Vasilevsky
- Oregon Clinical & Translational Science Institute, Oregon Health & Science University, Portland, OR, USA
| | - Deepak Unni
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cristian Bologa
- Department of Internal Medicine and UNM Comprehensive Cancer Center, UNM School of Medicine, Albuquerque, NM, USA
| | - Nomi Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, WA Department of Health, Perth, Australia
| | | | - Julie McMurry
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - Courtney Thaxon
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Giovanni Bocci
- Department of Internal Medicine and UNM Comprehensive Cancer Center, UNM School of Medicine, Albuquerque, NM, USA
| | - Marcin P. Joachimiak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sebastian Köhler
- Charité Centrum für Therapieforschung, Charité— Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Berlin, Germany
| | | | - Chris Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tudor I. Oprea
- Department of Internal Medicine and UNM Comprehensive Cancer Center, UNM School of Medicine, Albuquerque, NM, USA
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29
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Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FP, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJ, deVries BB, Douzgou S, Dudding-Byth T, Eichler EE, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MR, Robinson PN, Romano C, Rose CM, Sainsbury DC, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AO. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Front Genet 2019; 10:611. [PMID: 31417602 PMCID: PMC6681681 DOI: 10.3389/fgene.2019.00611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/12/2019] [Indexed: 01/25/2023] Open
Abstract
The clinical utility of computational phenotyping for both genetic and rare diseases is increasingly appreciated; however, its true potential is yet to be fully realized. Alongside the growing clinical and research availability of sequencing technologies, precise deep and scalable phenotyping is required to serve unmet need in genetic and rare diseases. To improve the lives of individuals affected with rare diseases through deep phenotyping, global big data interrogation is necessary to aid our understanding of disease biology, assist diagnosis, and develop targeted treatment strategies. This includes the application of cutting-edge machine learning methods to image data. As with most digital tools employed in health care, there are ethical and data governance challenges associated with using identifiable personal image data. There are also risks with failing to deliver on the patient benefits of these new technologies, the biggest of which is posed by data siloing. The Minerva Initiative has been designed to enable the public good of deep phenotyping while mitigating these ethical risks. Its open structure, enabling collaboration and data sharing between individuals, clinicians, researchers and private enterprise, is key for delivering precision public health.
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Affiliation(s)
- Christoffer Nellåker
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Institute for Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, and Genetic Services of Western Australia, King Edward Memorial, Subiaco, WA, Australia
- Telethon Kids Institute and School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
- Spatial Sciences, Science and Engineering, Curtin University, Perth, WA, Australia
| | - Raphael A. Bernier
- Department of Psychiatry & Behavioral Science, University of Washington School of Medicine, Seattle, WA, United States
| | | | - Vanessa Boulanger
- National Organization for Rare Disorders, Danbury, CT, United States
| | - Michael Brudno
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Hugh J.S. Dawkins
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health Government of Western Australia, Perth, WA, Australia
- Sir Walter Murdoch School of Policy and International Affairs, Murdoch University
- Centre for Population Health Research, Curtin University of Technology, Perth, WA, Australia
| | - Bert B.A. deVries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | | | - Evan E. Eichler
- Department of Genome Science, University of Washington School of Medicine, Seattle, WA, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States
| | - Michael Ferlaino
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Karen Fieggen
- Division of Human Genetics, Level 3, Wernher and Beit North, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Helen V. Firth
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Dylan Gration
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Tudor Groza
- The Garvan Institute, Sydney, NSW, Australia
| | - Melissa Haendel
- Oregon Health & Science University, Portland, OR, United States
| | - Nina Hallowell
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, United Kingdom
- Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jayne Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein–Campus Kiel, Kiel, Germany
| | - Mark Hughes
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, United Kingdom
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford, United Kingdom
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Peter Krawitz
- Institut für Genomische Statistik und Bioinformatik, Universitätsklinikum Bonn, Rheinische-Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Melissa Lees
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Gholson J. Lyon
- George A. Jervis Clinic and Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, United States
| | | | | | - Stephen Meyn
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Veronika Moslerová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Juan M. Politei
- Laboratorio Chamoles, Errores Congénitos del Metabolismo, Buenos Aires, Argentina
| | - Cathryn C. Poulton
- Department of Paediatrics and Neonates, Fiona Stanley Hospital, Perth, WA, Australia
| | - F Lucy Raymond
- CIMR (Wellcome Trust/MRC Building), Cambridge, United Kingdom
| | - Margot R.F. Reijnders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | | | - Catherine M. Rose
- Victorian Clinical Genetics Service and Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
| | - David C.G. Sainsbury
- Northern & Yorkshire Cleft Lip and Palate Service, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Lyn Schofield
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Vernon R. Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Marek Turnovec
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Andrew O.M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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30
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Fichtman B, Harel T, Biran N, Zagairy F, Applegate CD, Salzberg Y, Gilboa T, Salah S, Shaag A, Simanovsky N, Ayoubieh H, Sobreira N, Punzi G, Pierri CL, Hamosh A, Elpeleg O, Harel A, Edvardson S. Pathogenic Variants in NUP214 Cause "Plugged" Nuclear Pore Channels and Acute Febrile Encephalopathy. Am J Hum Genet 2019; 105:48-64. [PMID: 31178128 DOI: 10.1016/j.ajhg.2019.05.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/06/2019] [Indexed: 12/15/2022] Open
Abstract
We report biallelic missense and frameshift pathogenic variants in the gene encoding human nucleoporin NUP214 causing acute febrile encephalopathy. Clinical symptoms include neurodevelopmental regression, seizures, myoclonic jerks, progressive microcephaly, and cerebellar atrophy. NUP214 and NUP88 protein levels were reduced in primary skin fibroblasts derived from affected individuals, while the total number and density of nuclear pore complexes remained normal. Nuclear transport assays exhibited defects in the classical protein import and mRNA export pathways in affected cells. Direct surface imaging of fibroblast nuclei by scanning electron microscopy revealed a large increase in the presence of central particles (known as "plugs") in the nuclear pore channels of affected cells. This observation suggests that large transport cargoes may be delayed in passage through the nuclear pore channel, affecting its selective barrier function. Exposure of fibroblasts from affected individuals to heat shock resulted in a marked delay in their stress response, followed by a surge in apoptotic cell death. This suggests a mechanistic link between decreased cell survival in cell culture and severe fever-induced brain damage in affected individuals. Our study provides evidence by direct imaging at the single nuclear pore level of functional changes linked to a human disease.
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Affiliation(s)
- Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Nitzan Biran
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Fadia Zagairy
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Carolyn D Applegate
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yuval Salzberg
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Tal Gilboa
- Pediatric Neurology Unit, Hadassah-Hebrew University Medical Center, Jerusalem 91240, Israel
| | - Somaya Salah
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Avraham Shaag
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel; Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Natalia Simanovsky
- Department of Medical Imaging, Hadassah Medical Center, Jerusalem 91240, Israel
| | - Houriya Ayoubieh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Baylor-Hopkins Center for Mendelian Genomics, Jerusalem 91240, Israel, Jerusalem 91240, Israel
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Baylor-Hopkins Center for Mendelian Genomics, Jerusalem 91240, Israel, Jerusalem 91240, Israel
| | - Giuseppe Punzi
- Laboratory of Biochemistry, Molecular and Computational Biology; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Computational Biology; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Baylor-Hopkins Center for Mendelian Genomics, Jerusalem 91240, Israel, Jerusalem 91240, Israel
| | - Orly Elpeleg
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel; Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah-Hebrew University Medical Center, Jerusalem 91240, Israel; Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
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Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 2019; 21:798-812. [PMID: 30655598 PMCID: PMC6691975 DOI: 10.1038/s41436-018-0408-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Kumar
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corinne Boehm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Shrikant Mane
- Yale Center for Genome Analysis, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Richard P Lifton
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
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Amberger JS, Bocchini CA, Scott AF, Hamosh A. OMIM.org: leveraging knowledge across phenotype-gene relationships. Nucleic Acids Res 2019; 47:D1038-D1043. [PMID: 30445645 PMCID: PMC6323937 DOI: 10.1093/nar/gky1151] [Citation(s) in RCA: 436] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 01/28/2023] Open
Abstract
For over 50 years Mendelian Inheritance in Man has chronicled the collective knowledge of the field of medical genetics. It initially cataloged the known X-linked, autosomal recessive and autosomal dominant inherited disorders, but grew to be the primary repository of curated information on both genes and genetic phenotypes and the relationships between them. Each phenotype and gene is given a separate entry assigned a stable, unique identifier. The entries contain structured summaries of new and important information based on expert review of the biomedical literature. OMIM.org provides interactive access to the knowledge repository, including genomic coordinate searches of the gene map, views of genetic heterogeneity of phenotypes in Phenotypic Series, and side-by-side comparisons of clinical synopses. OMIM.org also supports computational queries via a robust API. All entries have extensive targeted links to other genomic resources and additional references. Updates to OMIM can be found on the update list or followed through the MIMmatch service. Updated user guides and tutorials are available on the website. As of September 2018, OMIM had over 24,600 entries, and the OMIM Morbid Map Scorecard had 6,259 molecularized phenotypes connected to 3,961 genes.
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Affiliation(s)
- Joanna S Amberger
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Carol A Bocchini
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alan F Scott
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA,To whom correspondence should be addressed. Tel: +1 410 614 3313; Fax: +1 410 955 4999;
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Straub V, Murphy A, Udd B, Corrado A, Aymé S, Bönneman C, de Visser M, Hamosh A, Jacobs L, Khizanishvili N, Kroneman M, Laflorêt P, Murphy A, Nigro V, Rufibach L, Sarkozy A, Swanepoel S, Torrente I, Udd B, Urtizberea A, Vissing J, Walter M. 229th ENMC international workshop: Limb girdle muscular dystrophies – Nomenclature and reformed classification Naarden, the Netherlands, 17–19 March 2017. Neuromuscul Disord 2018; 28:702-710. [DOI: 10.1016/j.nmd.2018.05.007] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 11/26/2022]
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Bush LW, Beck AE, Biesecker LG, Evans JP, Hamosh A, Holm IA, Martin CL, Richards CS, Rehm HL. Professional responsibilities regarding the provision, publication, and dissemination of patient phenotypes in the context of clinical genetic and genomic testing: points to consider-a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2018; 20:169-171. [PMID: 29323668 PMCID: PMC5931217 DOI: 10.1038/gim.2017.242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 01/25/2023] Open
Affiliation(s)
- Lynn W Bush
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Medical Center, New York, New York, USA
| | - Anita E Beck
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, Washington, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christa L Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - C Sue Richards
- Knight Diagnostic Laboratories, Oregon Health and Science University, Portland, Oregon, USA
| | - Heidi L Rehm
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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35
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Sobreira NLM, Arachchi H, Buske OJ, Chong JX, Hutton B, Foreman J, Schiettecatte F, Groza T, Jacobsen JOB, Haendel MA, Boycott KM, Hamosh A, Rehm HL. Matchmaker Exchange. ACTA ACUST UNITED AC 2017; 95:9.31.1-9.31.15. [PMID: 29044468 DOI: 10.1002/cphg.50] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In well over half of the individuals with rare disease who undergo clinical or research next-generation sequencing, the responsible gene cannot be determined. Some reasons for this relatively low yield include unappreciated phenotypic heterogeneity; locus heterogeneity; somatic and germline mosaicism; variants of uncertain functional significance; technically inaccessible areas of the genome; incorrect mode of inheritance investigated; and inadequate communication between clinicians and basic scientists with knowledge of particular genes, proteins, or biological systems. To facilitate such communication and improve the search for patients or model organisms with similar phenotypes and variants in specific candidate genes, we have developed the Matchmaker Exchange (MME). MME was created to establish a federated network connecting databases of genomic and phenotypic data using a common application programming interface (API). To date, seven databases can exchange data using the API (GeneMatcher, PhenomeCentral, DECIPHER, MyGene2, matchbox, Australian Genomics Health Alliance Patient Archive, and Monarch Initiative; the latter included for model organism matching). This article guides usage of the MME for rare disease gene discovery. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | - Orion J Buske
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Julia Foreman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | | | - Tudor Groza
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine (IGM), Clinical Director, IGM. Scientific Director, OMIM. Johns Hopkins University. Baltimore, Maryland
| | - Heidi L Rehm
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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36
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Dyke SOM, Knoppers BM, Hamosh A, Firth HV, Hurles M, Brudno M, Boycott KM, Philippakis AA, Rehm HL. "Matching" consent to purpose: The example of the Matchmaker Exchange. Hum Mutat 2017; 38:1281-1285. [PMID: 28699299 DOI: 10.1002/humu.23278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 01/11/2023]
Abstract
The Matchmaker Exchange (MME) connects rare disease clinicians and researchers to facilitate the sharing of data from undiagnosed patients for the purpose of novel gene discovery. Such sharing raises the odds that two or more similar patients with candidate genes in common may be found, thereby allowing their condition to be more readily studied and understood. Consent considerations for data sharing in MME included both the ethical and legal differences between clinical and research settings and the level of privacy risk involved in sharing varying amounts of rare disease patient data to enable patient matches. In this commentary, we discuss these consent considerations and the resulting MME Consent Policy as they may be relevant to other international data sharing initiatives.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario, Canada
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
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37
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Amberger JS, Hamosh A. Searching Online Mendelian Inheritance in Man (OMIM): A Knowledgebase of Human Genes and Genetic Phenotypes. ACTA ACUST UNITED AC 2017; 58:1.2.1-1.2.12. [PMID: 28654725 DOI: 10.1002/cpbi.27] [Citation(s) in RCA: 302] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Online Mendelian Inheritance in Man (OMIM) at OMIM.org is the primary repository of comprehensive, curated information on genes and genetic phenotypes and the relationships between them. This unit provides an overview of the types of information in OMIM and optimal strategies for searching and retrieving the information. OMIM.org has links to many related and complementary databases, providing easy access to more information on a topic. The relationship between genes and genetic disorders is highlighted in this unit. The basic protocol explains searching OMIM both from a gene perspective and a clinical features perspective. Two alternate protocols provide strategies for viewing gene-phenotype relationships: a gene map table and Quick View or Side-by-Side format for clinical features. OMIM.org is updated nightly, and the MIMmatch service, described in the support protocol, provides a convenient way to follow updates to entries, gene-phenotype relationships, and collaborate with other researchers. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joanna S Amberger
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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38
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Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet 2017; 100:695-705. [PMID: 28475856 PMCID: PMC5420351 DOI: 10.1016/j.ajhg.2017.04.003] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.
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Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Ana Rath
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Research Center, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Gareth Baynam
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto M5S 1A1, Canada
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine and University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Johan T den Dunnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Xavier Estivill
- Experimental Division, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar; Genetics Unit, Dexeus Woman's Health, 08028 Barcelona, Spain
| | - Jack Goldblatt
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Catherine Gonthier
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Ivo Gut
- Centre Nacional d'Anàlisi Genòmica, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21286, USA
| | - Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sophie Höhn
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Petra Kaufmann
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Jeffrey P Krischer
- University of South Florida Health Informatics Institute, Tampa, FL 33620, USA
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, 150 06 Prague 5, Czech Republic
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Annie Olry
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | | | - Justin Paschall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité Universitätsmdizin Berlin, 13353 Berlin, Germany; Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, China
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv 4002, Bulgaria
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome 299-00161, Italy
| | - Divya Unni
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Megan R Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Feng Zhang
- WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China; WuXi NextCODE, Cambridge, MA 02142, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, 6229 GT Maastricht, the Netherlands
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJS, DeMare LE, Devereau AD, de Vries BBA, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MWM, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res 2016; 45:D865-D876. [PMID: 27899602 PMCID: PMC5210535 DOI: 10.1093/nar/gkw1039] [Citation(s) in RCA: 494] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nicole A Vasilevsky
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark Engelstad
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erin Foster
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julie McMurry
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ségolène Aymé
- Institut du Cerveau et de la Moelle épinière-ICM, CNRS UMR 7225-Inserm U 1127-UPMC-P6 UMR S 1127, Hôpital Pitié-Salpêtrière, 47, bd de l'Hôpital, 75013 Paris, France
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital Department of Health, Government of Western Australia, Perth, WA 6008, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia
| | - Susan M Bello
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Cornelius F Boerkoel
- Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.,NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia
| | - Laura E DeMare
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Andrew D Devereau
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Daniel Greene
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Courtney Hum
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada
| | - Johanna A Jähn
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Roger James
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Roland Krause
- LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA
| | - Soichi Ogishima
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Tohoku Medical Megabank Organization Bldg 7F room #741,736, Seiryo 2-1, Aoba-ku, Sendai Miyagi 980-8573 Japan
| | - Annie Olry
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Willem H Ouwehand
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ana Rath
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Franz Schaefer
- Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Segal
- SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA
| | | | - Richard Sever
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Cynthia L Smith
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Catherine Turner
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Marijcke W M Veltman
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Tom Vulliamy
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Julie von Ziegenweidt
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK
| | - Andreas Zankl
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.,Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia
| | - Stephan Züchner
- JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Julius O B Jacobsen
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Tudor Groza
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Australia
| | - Damian Smedley
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa Haendel
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA .,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
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Bradburne C, Hamosh A. Integrating the microbiome into precision medicine. Expert Review of Precision Medicine and Drug Development 2016. [DOI: 10.1080/23808993.2016.1259562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Christopher Bradburne
- National Security Systems Biology Center, Asymmetric Operations Sector, Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ada Hamosh
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
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41
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Duis J, Dean S, Applegate C, Harper A, Xiao R, He W, Dollar JD, Sun LR, Waberski MB, Crawford TO, Hamosh A, Stafstrom CE. KIF5A mutations cause an infantile onset phenotype including severe myoclonus with evidence of mitochondrial dysfunction. Ann Neurol 2016; 80:633-7. [PMID: 27463701 DOI: 10.1002/ana.24744] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/13/2016] [Accepted: 07/24/2016] [Indexed: 01/17/2023]
Abstract
Missense mutations in kinesin family member 5A (KIF5A) cause spastic paraplegia 10. We report on 2 patients with de novo stop-loss frameshift variants in KIF5A resulting in a novel phenotype that includes severe infantile onset myoclonus, hypotonia, optic nerve abnormalities, dysphagia, apnea, and early developmental arrest. We propose that alteration and elongation of the carboxy-terminus of the protein has a dominant-negative effect, causing mitochondrial dysfunction in the setting of an abnormal kinesin "motor." These results highlight the role of expanded testing and whole-exome sequencing in critically ill infants and emphasize the importance of accurate test interpretation. Ann Neurol 2016;80:633-637.
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Affiliation(s)
- Jessica Duis
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD.
| | - Shannon Dean
- Pediatric Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Carolyn Applegate
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Amy Harper
- Carolinas Pediatric Neurology Care, Charlotte, NC
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Weimin He
- Department of Molecular and Human Genetics, Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | | | - Lisa R Sun
- Pediatric Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Marta Biderman Waberski
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Thomas O Crawford
- Pediatric Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Carl E Stafstrom
- Pediatric Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
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42
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Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SOM, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat 2016; 36:915-21. [PMID: 26295439 DOI: 10.1002/humu.22858] [Citation(s) in RCA: 340] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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Affiliation(s)
- Anthony A Philippakis
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cardiology, Brigham & Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | | | - Catherine A Brownstein
- Harvard Medical School, Boston, Massachusetts.,Division of Genetics and Genomics and the Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Han G Brunner
- Radboud University Medical Center, Department of Human Genetics, Nijmegen 6500 HB, The Netherlands.,Maastricht University Medical Center, Department of Clinical Genetics, Maastricht 6202AZ, The Netherlands
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Quebec, Canada
| | - Johan T den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Helen V Firth
- East Anglian Medical Genetics Service, Box 134, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Ingrid A Holm
- Harvard Medical School, Boston, Massachusetts.,Division of Genetics and Genomics and the Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts
| | - Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Joel B Krier
- Harvard Medical School, Boston, Massachusetts.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, 02115
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Justin Paschall
- European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, Santa Cruz, California
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany.,Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.,Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany.,Berlin Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | | | - Nara L Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Ganesh J Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Peter E Taschner
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Generade Center of Expertise Genomics, University of Applied Sciences Leiden, Leiden, The Netherlands
| | | | | | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Heidi L Rehm
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
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Srivastava AK, Wang Y, Huang R, Skinner C, Thompson T, Pollard L, Wood T, Luo F, Stevenson R, Polimanti R, Gelernter J, Lin X, Lim IY, Wu Y, Teh AL, Chen L, Aris IM, Soh SE, Tint MT, MacIsaac JL, Yap F, Kwek K, Saw SM, Kobor MS, Meaney MJ, Godfrey KM, Chong YS, Holbrook JD, Lee YS, Gluckman PD, Karnani N, Kapoor A, Lee D, Chakravarti A, Maercker C, Graf F, Boutros M, Stamoulis G, Santoni F, Makrythanasis P, Letourneau A, Guipponi M, Panousis N, Garieri M, Ribaux P, Falconnet E, Borel C, Antonarakis SE, Kumar S, Curran J, Blangero J, Chatterjee S, Kapoor A, Akiyama J, Auer D, Berrios C, Pennacchio L, Chakravarti A, Donti TR, Cappuccio G, Miller M, Atwal P, Kennedy A, Cardon A, Bacino C, Emrick L, Hertecant J, Baumer F, Porter B, Bainbridge M, Bonnen P, Graham B, Sutton R, Sun Q, Elsea S, Hu Z, Wang P, Zhu Y, Zhao J, Xiong M, Bennett DA, Hidalgo-Miranda A, Romero-Cordoba S, Rodriguez-Cuevas S, Rebollar-Vega R, Tagliabue E, Iorio M, D’Ippolito E, Baroni S, Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Semple CA, Rosenthal EA, Shirts B, Amendola L, Gallego C, Horike-Pyne M, Burt A, Robertson P, Beyers P, Nefcy C, Veenstra D, Hisama F, Bennett R, Dorschner M, Nickerson D, Smith J, Patterson K, Crosslin D, Nassir R, Zubair N, Harrison T, Peters U, Jarvik G, Menghi F, Inaki K, Woo X, Kumar P, Grzeda K, Malhotra A, Kim H, Ucar D, Shreckengast P, Karuturi K, Keck J, Chuang J, Liu ET, Ji B, Tyler A, Ananda G, Carter G, Nikbakht H, Montagne M, Zeinieh M, Harutyunyan A, Mcconechy M, Jabado N, Lavigne P, Majewski J, Goldstein JB, Overman M, Varadhachary G, Shroff R, Wolff R, Javle M, Futreal A, Fogelman D, Bravo L, Fajardo W, Gomez H, Castaneda C, Rolfo C, Pinto JA, Akdemir KC, Chin L, Futreal A, Patterson S, Statz C, Mockus S, Nikolaev SN, Bonilla XI, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy V, Sharpe H, McKee T, Letourneau A, Ribaux P, Popadin K, Basset-Seguin N, Chaabene RB, Santoni F, Andrianova M, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage F, Antonarakis S, Likhitrattanapisal S, Lincoln S, Kurian A, Desmond A, Yang S, Kobayashi Y, Ford J, Ellisen L, Peters TL, Alvarez KR, Hollingsworth EF, Lopez-Terrada DH, Hastie A, Dzakula Z, Pang AW, Lam ET, Anantharaman T, Saghbini M, Cao H, Gonzaga-Jauregui C, Ma L, King A, Rosenzweig EB, Krishnan U, Reid JG, Overton JD, Dewey F, Chung WK, Small K, DeLuca A, Cremers F, Lewis RA, Puech V, Bakall B, Silva-Garcia R, Rohrschneider K, Leys M, Shaya FS, Stone E, Sobreira NL, Schiettecatte F, Ling H, Pugh E, Witmer D, Hetrick K, Zhang P, Doheny K, Valle D, Hamosh A, Jhangiani SN, Akdemir ZC, Bainbridge MN, Charng W, Wiszniewski W, Gambin T, Karaca E, Bayram Y, Eldomery MK, Posey J, Doddapaneni H, Hu J, Sutton VR, Muzny DM, Boerwinkle EA, Valle D, Lupski JR, Gibbs RA, Shekar S, Salerno W, English A, Mangubat A, Bruestle J, Thorogood A, Knoppers BM, Takahashi H, Nitta KR, Kozhuharova A, Suzuki AM, Sharma H, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P, Mulvihill JJ, Baynam G, Gahl W, Groft SC, Kosaki K, Lasko P, Melegh B, Taruscio D, Ghosh R, Plon S, Scherer S, Qin X, Sanghvi R, Walker K, Chiang T, Muzny D, Wang L, Black J, Boerwinkle E, Weinshilboum R, Gibbs R, Karpinets T, Calderone T, Wani K, Yu X, Creasy C, Haymaker C, Forget M, Nanda V, Roszik J, Wargo J, Haydu L, Song X, Lazar A, Gershenwald J, Davies M, Bernatchez C, Zhang J, Futreal A, Woodman S, Chesler EJ, Reynolds T, Bubier JA, Phillips C, Langston MA, Baker EJ, Xiong M, Ma L, Lin N, Amos C, Lin N, Wang P, Zhu Y, Zhao J, Calhoun V, Xiong M, Dobretsberger O, Egger M, Leimgruber F, Sadedin S, Oshlack A, Antonio VAA, Ono N, Ahmed Z, Bolisetty M, Zeeshan S, Anguiano E, Ucar D, Sarkar A, Nandineni MR, Zeng C, Shao J, Cao H, Hastie A, Pang AW, Lam ET, Liang T, Pham K, Saghbini M, Dzakula Z, Chee-Wei Y, Dongsheng L, Lai-Ping W, Lian D, Hee ROT, Yunus Y, Aghakhanian F, Mokhtar SS, Lok-Yung CV, Bhak J, Phipps M, Shuhua X, Yik-Ying T, Kumar V, Boon-Peng H, Campbell I, Young MA, James P, Rain M, Mohammad G, Kukreti R, Pasha Q, Akilzhanova AR, Guelly C, Abilova Z, Rakhimova S, Akhmetova A, Kairov U, Trajanoski S, Zhumadilov Z, Bekbossynova M, Schumacher C, Sandhu S, Harkins T, Makarov V, Doddapaneni H, Glenn R, Momin Z, Dilrukshi B, Chao H, Meng Q, Gudenkauf B, Kshitij R, Jayaseelan J, Nessner C, Lee S, Blankenberg K, Lewis L, Hu J, Han Y, Dinh H, Jireh S, Walker K, Boerwinkle E, Muzny D, Gibbs R, Hu J, Walker K, Buhay C, Liu X, Wang Q, Sanghvi R, Doddapaneni H, Ding Y, Veeraraghavan N, Yang Y, Boerwinkle E, Beaudet AL, Eng CM, Muzny DM, Gibbs RA, Worley KCC, Liu Y, Hughes DST, Murali SC, Harris RA, English AC, Qin X, Hampton OA, Larsen P, Beck C, Han Y, Wang M, Doddapaneni H, Kovar CL, Salerno WJ, Yoder A, Richards S, Rogers J, Lupski JR, Muzny DM, Gibbs RA, Meng Q, Bainbridge M, Wang M, Doddapaneni H, Han Y, Muzny D, Gibbs R, Harris RA, Raveenedran M, Xue C, Dahdouli M, Cox L, Fan G, Ferguson B, Hovarth J, Johnson Z, Kanthaswamy S, Kubisch M, Platt M, Smith D, Vallender E, Wiseman R, Liu X, Below J, Muzny D, Gibbs R, Yu F, Rogers J, Lin J, Zhang Y, Ouyang Z, Moore A, Wang Z, Hofmann J, Purdue M, Stolzenberg-Solomon R, Weinstein S, Albanes D, Liu CS, Cheng WL, Lin TT, Lan Q, Rothman N, Berndt S, Chen ES, Bahrami H, Khoshzaban A, Keshal SH, Bahrami H, Khoshzaban A, Keshal SH, Alharbi KKR, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Matar M, Mili N, Molinari R, Ma Y, Guerrier S, Elhawary N, Tayeb M, Bogari N, Qotb N, McClymont SA, Hook PW, Goff LA, McCallion A, Kong Y, Charette JR, Hicks WL, Naggert JK, Zhao L, Nishina PM, Edrees BM, Athar M, Al-Allaf FA, Taher MM, Khan W, Bouazzaoui A, Harbi NA, Safar R, Al-Edressi H, Anazi A, Altayeb N, Ahmed MA, Alansary K, Abduljaleel Z, Kratz A, Beguin P, Poulain S, Kaneko M, Takahiko C, Matsunaga A, Kato S, Suzuki AM, Bertin N, Lassmann T, Vigot R, Carninci P, Plessy C, Launey T, Graur D, Lee D, Kapoor A, Chakravarti A, Friis-Nielsen J, Izarzugaza JM, Brunak S, Chakraborty A, Basak J, Mukhopadhyay A, Soibam BS, Das D, Biswas N, Das S, Sarkar S, Maitra A, Panda C, Majumder P, Morsy H, Gaballah A, Samir M, Shamseya M, Mahrous H, Ghazal A, Arafat W, Hashish M, Gruber JJ, Jaeger N, Snyder M, Patel K, Bowman S, Davis T, Kraushaar D, Emerman A, Russello S, Henig N, Hendrickson C, Zhang K, Rodriguez-Dorantes M, Cruz-Hernandez CD, Garcia-Tobilla CDP, Solorzano-Rosales S, Jäger N, Chen J, Haile R, Hitchins M, Brooks JD, Snyder M, Jiménez-Morales S, Ramírez M, Nuñez J, Bekker V, Leal Y, Jiménez E, Medina A, Hidalgo A, Mejía J, Halytskiy V, Naggert J, Collin GB, DeMauro K, Hanusek R, Nishina PM, Belhassa K, Belhassan K, Bouguenouch L, Samri I, Sayel H, moufid FZ, El Bouchikhi I, Trhanint S, Hamdaoui H, Elotmani I, Khtiri I, Kettani O, Quibibo L, Ahagoud M, Abbassi M, Ouldim K, Marusin AV, Kornetov AN, Swarovskaya M, Vagaiceva K, Stepanov V, De La Paz EMC, Sy R, Nevado J, Reganit P, Santos L, Magno JD, Punzalan FE, Ona D, Llanes E, Santos-Cortes RL, Tiongco R, Aherrera J, Abrahan L, Pagauitan-Alan P, Morelli KH, Domire JS, Pyne N, Harper S, Burgess R, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Gari MA, Dallol A, Alsehli H, Gari A, Gari M, Abuzenadah A, Thomas M, Sukhai M, Garg S, Misyura M, Zhang T, Schuh A, Stockley T, Kamel-Reid S, Sherry S, Xiao C, Slotta D, Rodarmer K, Feolo M, Kimelman M, Godynskiy G, O’Sullivan C, Yaschenko E, Xiao C, Yaschenko E, Sherry S, Rangel-Escareño C, Rueda-Zarate H, Tayubi IA, Mohammed R, Ahmed I, Ahmed T, Seth S, Amin S, Song X, Mao X, Sun H, Verhaak RG, Futreal A, Zhang J, Whiite SJ, Chiang T, English A, Farek J, Kahn Z, Salerno W, Veeraraghavan N, Boerwinkle E, Gibbs R, Kasukawa T, Lizio M, Harshbarger J, Hisashi S, Severin J, Imad A, Sahin S, Freeman TC, Baillie K, Sandelin A, Carninci P, Forrest ARR, Kawaji H, Salerno W, English A, Shekar SN, Mangubat A, Bruestle J, Boerwinkle E, Gibbs RA, Salem AH, Ali M, Ibrahim A, Ibrahim M, Barrera HA, Garza L, Torres JA, Barajas V, Ulloa-Aguirre A, Kershenobich D, Mortaji S, Guizar P, Loera E, Moreno K, De León A, Monsiváis D, Gómez J, Cardiel R, Fernandez-Lopez JC, Bonifaz-Peña V, Rangel-Escareño C, Hidalgo-Miranda A, Contreras AV, Polfus L, Wang X, Philip V, Carter G, Abuzenadah AA, Gari M, Turki R, Dallol A, Uyar A, Kaygun A, Zaman S, Marquez E, George J, Ucar D, Hendrickson CL, Emerman A, Kraushaar D, Bowman S, Henig N, Davis T, Russello S, Patel K, Starr DB, Baird M, Kirkpatrick B, Sheets K, Nitsche R, Prieto-Lafuente L, Landrum M, Lee J, Rubinstein W, Maglott D, Thavanati PKR, de Dios AE, Hernandez REN, Aldrate MEA, Mejia MRR, Kanala KRR, Abduljaleel Z, Khan W, Al-Allaf FA, Athar M, Taher MM, Shahzad N, Bouazzaoui A, Huber E, Dan A, Al-Allaf FA, Herr W, Sprotte G, Köstler J, Hiergeist A, Gessner A, Andreesen R, Holler E, Al-Allaf F, Alashwal A, Abduljaleel Z, Taher M, Bouazzaoui A, Abalkhail H, Al-Allaf A, Bamardadh R, Athar M, Filiptsova O, Kobets M, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Al-allaf FA, Mohiuddin MT, Zainularifeen A, Mohammed A, Abalkhail H, Owaidah T, Bouazzaoui A. Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016. Hum Genomics 2016; 10 Suppl 1:12. [PMID: 27294413 PMCID: PMC4896275 DOI: 10.1186/s40246-016-0063-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar
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Affiliation(s)
| | - Y. Wang
- School of Computing, Clemson University, Clemson, SC USA
| | - R. Huang
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - C. Skinner
- JCSRI, Greenwood Genetic Center, Greenwood, SC USA
| | - T. Thompson
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - L. Pollard
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - T. Wood
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - F. Luo
- School of Computing, Clemson University, Clemson, SC USA
| | - R. Stevenson
- JCSRI, Greenwood Genetic Center, Greenwood, SC USA
| | - R. Polimanti
- Department Psychiatry, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
| | - J. Gelernter
- Department Psychiatry, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
- Department Genetics, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
- Department Neurobiology, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
| | - X. Lin
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - I. Y. Lim
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Y. Wu
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - A. L. Teh
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - L. Chen
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - I. M. Aris
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - S. E. Soh
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - M. T. Tint
- National University of Singapore, Singapore, Singapore
| | - J. L. MacIsaac
- University of British Columbia, Vancouver, British Columbia Canada
| | - F. Yap
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | - K. Kwek
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | - S. M. Saw
- National University of Singapore, Singapore, Singapore
| | - M. S. Kobor
- University of British Columbia, Vancouver, British Columbia Canada
| | - M. J. Meaney
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - K. M. Godfrey
- University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Y. S. Chong
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - J. D. Holbrook
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Y. S. Lee
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - P. D. Gluckman
- Singapore Institute for Clinical Sciences, Singapore, Singapore
- University of Auckland, Auckland, New Zealand
| | - N. Karnani
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | | | - A. Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - D. Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - A. Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - C. Maercker
- Esslingen University of Applied Sciences, Esslingen, Germany
| | - F. Graf
- German Cancer Research Center, Heidelberg, Germany
| | - M. Boutros
- German Cancer Research Center, Heidelberg, Germany
| | - G. Stamoulis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - F. Santoni
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - P. Makrythanasis
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - A. Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Guipponi
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - N. Panousis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - P. Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - E. Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - C. Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - S. E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, University of Geneva Medical School, Geneva, Switzerland
| | - S. Kumar
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Edinburg, TX USA
| | - J. Curran
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Brownsville, TX USA
| | - J. Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Brownsville, TX USA
| | - S. Chatterjee
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - A. Kapoor
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - J. Akiyama
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - D. Auer
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - C. Berrios
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - L. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - A. Chakravarti
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - T. R. Donti
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - G. Cappuccio
- Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - M. Miller
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Atwal
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | | | - A. Cardon
- Section of Pediatric Neurology and Neuroscience, Baylor College of Medicine, Houston, TX USA
| | - C. Bacino
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - L. Emrick
- Section of Pediatric Neurology and Neuroscience, Baylor College of Medicine, Houston, TX USA
| | | | - F. Baumer
- Stanford Medical School, Stanford, CA USA
| | - B. Porter
- Stanford Medical School, Stanford, CA USA
| | - M. Bainbridge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Bonnen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - B. Graham
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. Sutton
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Q. Sun
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - S. Elsea
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Z. Hu
- School of Public Health, Houston Health Science Center, Houston, TX USA
| | - P. Wang
- University of Texas, Houston Health Science Center, Houston, TX USA
| | - Y. Zhu
- Tulane University, New Orleans, LO USA
| | - J. Zhao
- Tulane University, New Orleans, LO USA
| | - M. Xiong
- University of Texas, Houston Health Science Center, Houston, TX USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University, Chicago, IL USA
| | - A. Hidalgo-Miranda
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - S. Romero-Cordoba
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - R. Rebollar-Vega
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - M. Iorio
- National Tumor Institute, Milan, Italy
| | | | - S. Baroni
- National Tumor Institute, Milan, Italy
| | - B. Kaczkowski
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Y. Tanaka
- Preventive Medicine and Applied Genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - H. Kawaji
- Preventive Medicine and Applied Genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - A. Sandelin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - R. Andersson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - T. Lassmann
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | | | - Y. Hayashizaki
- RIKEN Preventive Medicine & Diagnosis Innovation Program, Wako, Japan
| | - P. Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - A. R. R. Forrest
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Australia
| | - C. A. Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | | | | | | | - C. Gallego
- University of Michigan, Ann Arbor, MI USA
| | | | - A. Burt
- Univ of Washington, Seattle, WA USA
| | | | | | - C. Nefcy
- Univ of Washington, Seattle, WA USA
| | | | | | | | | | | | - J. Smith
- Univ of Washington, Seattle, WA USA
| | | | | | - R. Nassir
- University California, Davis, CA USA
| | | | | | - U. Peters
- Univ of Washington, Seattle, WA USA
- Fred Hutch, Seattle, WA USA
| | | | | | - F. Menghi
- The Jackson Laboratory, Farmington, CT USA
| | - K. Inaki
- The Jackson Laboratory, Farmington, CT USA
| | - X. Woo
- The Jackson Laboratory, Farmington, CT USA
| | - P. Kumar
- The Jackson Laboratory, Farmington, CT USA
| | - K. Grzeda
- The Jackson Laboratory, Farmington, CT USA
| | | | - H. Kim
- The Jackson Laboratory, Farmington, CT USA
| | - D. Ucar
- The Jackson Laboratory, Farmington, CT USA
| | | | | | - J. Keck
- The Jackson Laboratory, Sacramento, CA USA
| | - J. Chuang
- The Jackson Laboratory, Farmington, CT USA
| | - E. T. Liu
- The Jackson Laboratory, Farmington, CT USA
| | - B. Ji
- The Jackson Laboratory, Bar Harbor, ME USA
| | - A. Tyler
- The Jackson Laboratory, Bar Harbor, ME USA
| | - G. Ananda
- The Jackson Laboratory, Bar Harbor, ME USA
| | - G. Carter
- The Jackson Laboratory, Bar Harbor, ME USA
| | - H. Nikbakht
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - M. Montagne
- Biochemistry, Sherbrooke University, Sherbrooke, Quebec Canada
| | - M. Zeinieh
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - A. Harutyunyan
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - M. Mcconechy
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - N. Jabado
- Pediatrics, McGill University, Montreal, Quebec Canada
| | - P. Lavigne
- Biochemistry, Sherbrooke University, Sherbrooke, Quebec Canada
| | - J. Majewski
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - J. B. Goldstein
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - M. Overman
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - G. Varadhachary
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - R. Shroff
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - R. Wolff
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - M. Javle
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - A. Futreal
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - D. Fogelman
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - L. Bravo
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - W. Fajardo
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - H. Gomez
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - C. Castaneda
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - C. Rolfo
- Oncology Department, University Hospital Antwerp, Antwerp, Belgium
| | - J. A. Pinto
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - K. C. Akdemir
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - L. Chin
- University of Texas System, Houston, TX USA
| | - A. Futreal
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | | | - S. Patterson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - C. Statz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. Mockus
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. N. Nikolaev
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - X. I. Bonilla
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - L. Parmentier
- Department of Dermatology, Hospital of Valais, Sion, Switzerland
| | - B. King
- Department of Pathology, NYU School of Medicine, New York, NY USA
| | - F. Bezrukov
- Department of Physics, University of Connecticut, Connecticut, USA
| | - G. Kaya
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - V. Zoete
- Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - V. Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - H. Sharpe
- Department of Molecular Oncology, Genentech Inc, San Francisco, CA USA
| | - T. McKee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - A. Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - P. Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - K. Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - R. Ben Chaabene
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - F. Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Andrianova
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - M. Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - M. Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - C. Verdan
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - K. Grosdemange
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - O. Sumara
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - M. Eilers
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - I. Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY USA
| | - O. Michielin
- Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - F. de Sauvage
- Department of Molecular Oncology, Genentech Inc, San Francisco, CA USA
| | - S. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | | | | | - A. Kurian
- Stanford Medical Center, Palo Alto, CA USA
| | - A. Desmond
- Massachusetts General Hospital, Boston, MA USA
| | - S. Yang
- Invitae, San Francisco, CA USA
| | | | - J. Ford
- Stanford Medical Center, San Francisco, CA USA
| | - L. Ellisen
- Massachusetts General Hospital, Boston, MA USA
| | - T. L. Peters
- Pathology & Immunology, Baylor College of Medicine, Houston, TX USA
| | - K. R. Alvarez
- Pathology, Texas Children’s Hospital, Houston, TX USA
| | | | - D. H. Lopez-Terrada
- Pathology & Immunology, Baylor College of Medicine, Houston, TX USA
- Pathology, Texas Children’s Hospital, Houston, TX USA
| | - A. Hastie
- BioNano Genomics, Inc, San Diego, CA USA
| | - Z. Dzakula
- BioNano Genomics, Inc, San Diego, CA USA
| | - A. W. Pang
- BioNano Genomics, Inc, San Diego, CA USA
| | - E. T. Lam
- BioNano Genomics, Inc, San Diego, CA USA
| | | | | | - H. Cao
- BioNano Genomics, Inc, San Diego, CA USA
| | | | - C. Gonzaga-Jauregui
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - L. Ma
- Department of Pediatrics, New York, NY USA
| | - A. King
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - E. Berman Rosenzweig
- Department of Pediatrics, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
| | | | - J. G. Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - J. D. Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - F. Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - W. K. Chung
- Department of Pediatrics, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - K. Small
- Molecular Insight Research Foundation, Glendale, ᅟ
| | - A. DeLuca
- Ophthalmology, University of Iowa, Iowa City, IA USA
| | - F. Cremers
- Biology, Raboud University Medical Center, Nijmegen, Netherlands
| | - R. A. Lewis
- Ophthalmology, Baylor College of Medicine, Houston, TX USA
| | - V. Puech
- Service d’Exploration de la vision et Neuro-ophtalmologie CHRU, Service d’Exploration de la vision et Neuro-ophtalmologie CHRU, Lille, France
| | - B. Bakall
- Associated Retina Consultants, University of Arizona College of Medicine, Phoenix, TX USA
| | | | | | - M. Leys
- WVU Eye Institute, Morgantown, WV USA
| | - F. S. Shaya
- Molecular Insight Research Foundation, Glendale, ᅟ
| | - E. Stone
- University of Iowa, Iowa City, IA USA
| | - N. L. Sobreira
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | | | - H. Ling
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - E. Pugh
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - D. Witmer
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - K. Hetrick
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - P. Zhang
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - K. Doheny
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - D. Valle
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - A. Hamosh
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - S. N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Z. Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. N. Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - W. Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - W. Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - T. Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - E. Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - V. R. Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - E. A. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - J. R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | | | - A. Thorogood
- Centre of Genomics and Policy, McGill University, Montreal, Quebec Canada
| | - B. M. Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Quebec Canada
| | | | - H. Takahashi
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - K. R. Nitta
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - A. Kozhuharova
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - A. M. Suzuki
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - H. Sharma
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - D. Cotella
- Dipartimento di Scienze della Salute, Universita’ del Piemonte Orientale, Novara, Italy
| | - C. Santoro
- Dipartimento di Scienze della Salute, Universita’ del Piemonte Orientale, Novara, Italy
| | - S. Zucchelli
- Area of Neuroscience, SISSA, International School for Advanced Studies, Trieste, Italy
| | - S. Gustincich
- Area of Neuroscience, SISSA, International School for Advanced Studies, Trieste, Italy
| | - P. Carninci
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - J. J. Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD USA
| | - G. Baynam
- Office of Population Health, Department of Health, Perth, Australia
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- Undiagnosed Diseases Program, National Human Genome Research Institute, Bethesda, MD USA
| | - S. C. Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD USA
| | - K. Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - P. Lasko
- Department of Biology, McGill University, Montreal, Quebec Canada
| | - B. Melegh
- Department of Medical Genetics, University of Pecs, Pecs, Hungary
| | - D. Taruscio
- National Center for Rare Diseases, Istituto Superiore di Sanita, Rome, Italy
| | - R. Ghosh
- Pediatrics-Oncology, Baylor College of Medicine, Houston, TX USA
| | - S. Plon
- Pediatrics-Oncology, Baylor College of Medicine, Houston, TX USA
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- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
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- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Sanghvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
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- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
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- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
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- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, NY USA
| | - J. Black
- Department of Psychiatry, Mayo Clinic, Rochester, NY USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | | | - K. Wani
- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
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- MD Anderson Cancer Center, Houston, USA
| | | | - M. Davies
- MD Anderson Cancer Center, Houston, USA
| | | | - J. Zhang
- MD Anderson Cancer Center, Houston, USA
| | | | | | | | | | | | | | | | | | - M. Xiong
- University of Texas School of Public Health, Houston, TX USA
| | - L. Ma
- University of Texas School of Public Health, Houston, TX USA
| | - N. Lin
- University of Texas School of Public Health, Houston, TX USA
| | - C. Amos
- Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - N. Lin
- Biostatistics, University of Texas Health Science Center at Houston, Houston, TX USA
| | - P. Wang
- Biostatistics, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Y. Zhu
- Tulane University, New Orleans, LO USA
| | - J. Zhao
- Tulane University, New Orleans, LO USA
| | - V. Calhoun
- University of New Mexico, Albuquerque, NM USA
| | - M. Xiong
- University of Texas Health Science Center at Houston, Houston, TX USA
| | | | - M. Egger
- EPS Software Corp, Spring, TX USA
| | | | - S. Sadedin
- Bioinformatics, Murdoch Childrens Research Institute, Parkville, Australia
| | - A. Oshlack
- Bioinformatics, Murdoch Childrens Research Institute, Parkville, Australia
| | | | - V. A. A. Antonio
- Computational Systems Biology Laboratory, Nara Institute of Science and Technology, Ikoma-cho, Japan
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- Computational Systems Biology Laboratory, Nara Institute of Science and Technology, Ikoma-cho, Japan
| | | | - Z. Ahmed
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - M. Bolisetty
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. Zeeshan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - E. Anguiano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - D. Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - A. Sarkar
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - M. R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - C. Zeng
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - J. Shao
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - H. Cao
- BioNano Genomics, Inc, San Diego, CA USA
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- BioNano Genomics, Inc, San Diego, CA USA
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- BioNano Genomics, Inc, San Diego, CA USA
| | - E. T. Lam
- BioNano Genomics, Inc, San Diego, CA USA
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- BioNano Genomics, Inc, San Diego, CA USA
| | - K. Pham
- BioNano Genomics, Inc, San Diego, CA USA
| | | | - Z. Dzakula
- BioNano Genomics, Inc, San Diego, CA USA
| | - Y. Chee-Wei
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - L. Dongsheng
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - W. Lai-Ping
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - D. Lian
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - R. O. Twee Hee
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Y. Yunus
- Institute of Medical Molecular Biotechnology, Universiti Teknologi MARA, Sungai Buloh, ᅟ
| | - F. Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, Petaling Jaya, Malaysia
| | - S. S. Mokhtar
- Institute of Medical Molecular Biotechnology, Universiti Teknologi MARA, Sungai Buloh, ᅟ
| | - C. V. Lok-Yung
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - J. Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic Of Korea
| | - M. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campu, Petaling Jaya, Malaysia
| | - X. Shuhua
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - T. Yik-Ying
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - V. Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - H. Boon-Peng
- UCSI University, Kuala Lumpur, Kuala Lumpur, Malaysia
| | - I. Campbell
- Research Division, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | - M. -A. Young
- Familial Cancer Centre, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | - P. James
- Familial Cancer Centre, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | | | - M. Rain
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - G. Mohammad
- Department of Medicine, Sonam Norbu Memorial Hospital, Leh, Ladakh India
| | - R. Kukreti
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Q. Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - A. R. Akilzhanova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - C. Guelly
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Z. Abilova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - S. Rakhimova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - A. Akhmetova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - U. Kairov
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - S. Trajanoski
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Z. Zhumadilov
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - M. Bekbossynova
- National Scientific Cardiac Surgery Center, Astana, Kazakhstan
| | | | - S. Sandhu
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - T. Harkins
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - V. Makarov
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Glenn
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Z. Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - B. Dilrukshi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Q. Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - B. Gudenkauf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Kshitij
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Nessner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - S. Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Blankenberg
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - S. Jireh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - X. Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Q. Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Sanghvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - N. Veeraraghavan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX USA
| | - A. L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - C. M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. C. C. Worley
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Liu
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. S. T. Hughes
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - S. C. Murali
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Harris
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - A. C. English
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - X. Qin
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - O. A. Hampton
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Larsen
- Department of Biology, Duke University, Durham, NC USA
| | - C. Beck
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Han
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. Wang
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - C. L. Kovar
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - W. J. Salerno
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - A. Yoder
- Department of Biology, Duke University, Durham, NC USA
| | - S. Richards
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. Rogers
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. R. Lupski
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Q. Meng
- HGSC, Baylor College of Medicine, Houston, TX USA
| | | | - M. Wang
- HGSC, Baylor College of Medicine, Houston, TX USA
| | | | - Y. Han
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - R. A. Harris
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - M. Raveenedran
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Xue
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - M. Dahdouli
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Cox
- Genetics, Southwest National Primate Research Center, San Antonio, TX USA
| | - G. Fan
- Human Genetics, Univeristy of California Los Angeles, Los Angeles, CA USA
| | - B. Ferguson
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR USA
| | - J. Hovarth
- Genomics & Microbiology Research Laboratory, NC Museum of Natural Sciences, Raleigh, NC USA
| | - Z. Johnson
- Yerkes Nonhuman Primate Genomics Core, Yerkes National Primate Research Center, Atlanta, GA USA
| | - S. Kanthaswamy
- Environmental Toxicology, California National Primate Research Center, Davis, CA USA
| | - M. Kubisch
- Physiology, Tulane National Primate Research Center, New Orleans, LO USA
| | - M. Platt
- Neuroscience, University of Pennsylvania, Philadelphia, PA USA
| | - D. Smith
- Anthropology, University of California Davis, Davis, CA USA
| | - E. Vallender
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS USA
| | - R. Wiseman
- Genetics, Wisconsin National Primate Research Center, Madison, WI USA
| | - X. Liu
- Epidemiology, Human Genetics & Environmental Sciences, ᅟ, ᅟ
| | - J. Below
- Epidemiology and Disease Control Human Genetics Center, University of Texas Health Science Center, Houston, TX USA
| | - D. Muzny
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - F. Yu
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Rogers
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Y. Zhang
- Department of Statistics, University of Connecticut, Storrs, CT USA
| | - Z. Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - A. Moore
- National Cancer Institute, Rockville, USA
| | - Z. Wang
- St. Jude Children’s Research Hospital, Memphis, USA
| | - J. Hofmann
- National Cancer Institute, NIH, DHHS, Rockville, USA
| | - M. Purdue
- National Cancer Institute, Rockville, USA
| | | | | | - D. Albanes
- National Cancer Institute, Rockville, USA
| | - C. S. Liu
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - W. L. Cheng
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - T. T. Lin
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - Q. Lan
- National Cancer Institute, Rockville, USA
| | - N. Rothman
- National Cancer Institute, Rockville, USA
| | - S. Berndt
- National Cancer Institute, Rockville, USA
| | - E. S. Chen
- Biochemistry, National University of Singapore, Singapore, Singapore
| | - H. Bahrami
- Proteomics, Faraby Eye Hospital, Tehran, Iran Islamic Republic Of
- R & D, MIB Co., Tehran, Iran Islamic Republic Of
| | | | | | - H. Bahrami
- Proteomics, Faraby Eye Hospital, Tehran, Iran Islamic Republic Of
- R & D, MIB Co., Tehran, Iran Islamic Republic Of
| | | | | | - K. K. R. Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - M. Zhalbinova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - A. Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - S. Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - M. Bekbosynova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National medical holding, Astana, Kazakhstan
| | - S. Myrzakhmetova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National medical holding, Astana, Kazakhstan
| | - M. Matar
- UAE Genetic Diseases Association, Dubai, United Arab Emirates
| | - N. Mili
- Research Center for Statistics, University of Geneva, Switzerland, Geneva Switzerland
| | - R. Molinari
- Research Center for Statistics, University of Geneva, Switzerland, Geneva Switzerland
| | - Y. Ma
- Department of Statistics, University of South Carolina, Columbia, USA
| | - S. Guerrier
- Department of Statistics, University of Illinois at Urbana Champaign, Champaign, USA
| | - N. Elhawary
- Department of Molecular Genetics, Medical Genetics Center, Ain Shams University, Cairo, Egypt
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Tayeb
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - N. Bogari
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - N. Qotb
- Department of Psychology, Umm Al-Qura University, Faculty of Education, Mecca, Saudi Arabia
| | - S. A. McClymont
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - P. W. Hook
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - L. A. Goff
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - A. McCallion
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Y. Kong
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, USA
| | | | | | | | - L. Zhao
- The Jackson Laboratory, Bar Harbor, USA
| | - P. M. Nishina
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, USA
| | - B. M. Edrees
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - F. A. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - W. Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - N. A. Harbi
- Department of Pediatric, King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia
| | - R. Safar
- Department of Pediatric, Madinah Maternity and Children’s Hospital, Madinah, Saudi Arabia
| | - H. Al-Edressi
- Department of Pediatric, Madinah Maternity and Children’s Hospital, Madinah, Saudi Arabia
| | - A. Anazi
- Pediatric, King Fahad Medical City, Riyadh, Saudi Arabia
| | - N. Altayeb
- Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah, Saudi Arabia
| | - M. A. Ahmed
- Medical Genetics, King Salman Armed Forces Hospital, Tabuk, Saudi Arabia
| | - K. Alansary
- Medical Genetics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - A. Kratz
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - P. Beguin
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - S. Poulain
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - M. Kaneko
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - C. Takahiko
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - A. Matsunaga
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - S. Kato
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - A. M. Suzuki
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - N. Bertin
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - T. Lassmann
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - R. Vigot
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - P. Carninci
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - C. Plessy
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - T. Launey
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - D. Graur
- Biology and Biochemistry, University of Houston, Houston, USA
| | - D. Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - A. Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - A. Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J. Friis-Nielsen
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - J. M. Izarzugaza
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - S. Brunak
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - A. Chakraborty
- Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | - J. Basak
- Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | - A. Mukhopadhyay
- Medical Oncology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | | | - D. Das
- National Institute of Biomedical Genomics, Kalyani, India
| | - N. Biswas
- National Institute of Biomedical Genomics, Kalyani, India
| | - S. Das
- National Institute of Biomedical Genomics, Kalyani, India
| | - S. Sarkar
- Chittaranjan National Cancer Institute, Kolkata, India
| | - A. Maitra
- National Institute of Biomedical Genomics, Kalyani, India
| | - C. Panda
- Chittaranjan National Cancer Institute, Kolkata, India
| | - P. Majumder
- National Institute of Biomedical Genomics, Kalyani, India
| | - H. Morsy
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | - A. Gaballah
- Microbiology, Faculty of Medicine, Alexandria, Egypt
| | - M. Samir
- Clinical and Experimental Surgery, Faculty of Medicine, Alexandria, Egypt
| | - M. Shamseya
- Clinical and Experimental Internal Medicine, Medical Research Institute, Faculty of Medicine, Alexandria, Egypt
| | - H. Mahrous
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | - A. Ghazal
- Microbiology, Faculty of Medicine, Alexandria, Egypt
| | - W. Arafat
- Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Alexandria, Egypt
| | - M. Hashish
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | | | - N. Jaeger
- Genetics, Stanford University, Palo Alto, USA
| | - M. Snyder
- Genetics, Stanford University, Palo Alto, USA
| | | | | | - T. Davis
- New England Biolabs, Ipswich, USA
| | | | | | | | | | | | - K. Zhang
- Pathology, University of North Dakota, Grand Forks, USA
| | | | | | | | | | - N. Jäger
- Genetics, Stanford University, Palo Alto, USA
| | - J. Chen
- Genetics, Stanford University, Palo Alto, USA
| | - R. Haile
- Stanford Cancer Institute, Stanford University, Palo Alto, USA
| | - M. Hitchins
- Stanford Cancer Institute, Stanford University, Palo Alto, USA
| | | | - M. Snyder
- Genetics, Stanford University, Palo Alto, USA
| | - S. Jiménez-Morales
- Cancer Genomic Laboratory, National Institute of Genomic Medicine (INMEGEN), ᅟ, Mexico
| | - M. Ramírez
- Biología, FES -Iztacala, UNAM, ᅟ, Mexico
| | - J. Nuñez
- Hospital de Pediatría, CMN SXXI, IMSS, ᅟ, Mexico
| | - V. Bekker
- Investigación Médica en Inmunología, CMN La Raza, IMSS, ᅟ, Mexico
| | - Y. Leal
- Diagnóstico Molecular H1N1-Influenza , UMAE-IMSS, Mérida, Yucatán Mexico
| | - E. Jiménez
- Hematología Pediátrica, CMN La Raza, IMSS, ᅟ, Mexico
| | - A. Medina
- Hemato-Oncología, Hospital Infantil de México, ᅟ, Mexico
| | - A. Hidalgo
- Cancer Genomics Laboratory, INMEGEN, ᅟ, Mexico
| | - J. Mejía
- Coordinación de Investigación en Salud, IMSS, ᅟ, Mexico
| | - V. Halytskiy
- Molecular Immunology Department, Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, Kiev, Ukraine
| | | | | | | | | | | | - K. Belhassa
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - K. Belhassan
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - L. Bouguenouch
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Samri
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - H. Sayel
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - FZ. moufid
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. El Bouchikhi
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - S. Trhanint
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - H. Hamdaoui
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Elotmani
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Khtiri
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - O. Kettani
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - L. Quibibo
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - M. Ahagoud
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - M. Abbassi
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - K. Ouldim
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - A. V. Marusin
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - A. N. Kornetov
- Siberian State Medical University, Tomsk, Russian Federation
| | - M. Swarovskaya
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - K. Vagaiceva
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - V. Stepanov
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - E. M. Cutiongco De La Paz
- National Institutes of Health, University of the Philippines, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | - R. Sy
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. Nevado
- National Institutes of Health, University of the Philippines, Manila, Philippines
| | - P. Reganit
- College of Medicine, University of the Philippines, Manila, Philippines
| | - L. Santos
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. D. Magno
- College of Medicine, University of the Philippines, Manila, Philippines
| | - F. E. Punzalan
- College of Medicine, University of the Philippines, Manila, Philippines
| | - D. Ona
- College of Medicine, University of the Philippines, Manila, Philippines
| | - E. Llanes
- College of Medicine, University of the Philippines, Manila, Philippines
| | - R. L. Santos-Cortes
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX United States
| | - R. Tiongco
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. Aherrera
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - L. Abrahan
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - P. Pagauitan-Alan
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | | | - K. H. Morelli
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Sciences & Engineering, The University of Maine, Orono, USA
| | - J. S. Domire
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - N. Pyne
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - S. Harper
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - R. Burgess
- Graduate School of Biomedical Sciences & Engineering, The University of Maine, Orono, USA
| | - M. Zhalbinova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - A. Akilzhanova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - S. Rakhimova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - M. Bekbosynova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National Medical Holding, Astana, Kazakhstan
| | - S. Myrzakhmetova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National Medical Holding, Astana, Kazakhstan
| | - M. A. Gari
- Medical Laboratory Technology, ᅟ, Saudi Arabia
| | - A. Dallol
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - H. Alsehli
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A. Gari
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M. Gari
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A. Abuzenadah
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M. Thomas
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - M. Sukhai
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - S. Garg
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - M. Misyura
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - T. Zhang
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - A. Schuh
- Princess Margaret Cancer Centre, Toronto, Canada
| | - T. Stockley
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - S. Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | | | | | | | | | | | | | | | | | | | - C. Xiao
- National Institutes of Health, Bethesda, USA
| | | | - S. Sherry
- National Institutes of Health, Bethesda, USA
| | - C. Rangel-Escareño
- Computational Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - H. Rueda-Zarate
- Computational Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - I. A. Tayubi
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - R. Mohammed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | | | - I. Ahmed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - T. Ahmed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - S. Seth
- Institute of Applied Cancer Science, ᅟ, USA
| | - S. Amin
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - X. Song
- Institute of Applied Cancer Science, ᅟ, USA
| | - X. Mao
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - H. Sun
- MD Anderson Cancer Center, Houston, USA
| | | | - A. Futreal
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - J. Zhang
- Institute of Applied Cancer Science, ᅟ, USA
| | - S. J. Whiite
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - T. Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - J. Farek
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - Z. Kahn
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - N. Veeraraghavan
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - E. Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, USA
| | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - T. Kasukawa
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - M. Lizio
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - J. Harshbarger
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - S. Hisashi
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
- Preventive Medicine and Diagnosis Innovation Program, RIKEN, Wako, Japan
| | - J. Severin
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - A. Imad
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - S. Sahin
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - T. C. Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - K. Baillie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - A. Sandelin
- Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - P. Carninci
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | | | - H. Kawaji
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
- Preventive Medicine and Diagnosis Innovation Program, RIKEN, Wako, Japan
- Advanced Center for Computing and Communication, RIKEN, Yokohama, Japan
| | | | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | | | | | | | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
- Human Genetics Center and Department of Epidemiology, UT School of Public Health, Houston, Texas USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | - A. H. Salem
- Anatomy, Arabian Gulf University, Manama, Bahrain
| | - M. Ali
- Biochemistry, Arabian Gulf University, Manama, Bahrain
| | - A. Ibrahim
- Central Laboratory, Ministry of Science and Technology, ᅟ, Sudan
| | - M. Ibrahim
- College of Animal Production Science and Technology, Sudan University of Science and Technology, Khartoum, Sudan
| | - H. A. Barrera
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - L. Garza
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - J. A. Torres
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - V. Barajas
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | | | - D. Kershenobich
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Shahroj Mortaji
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Pedro Guizar
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Eliezer Loera
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Karen Moreno
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Adriana De León
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Daniela Monsiváis
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Jackeline Gómez
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Raquel Cardiel
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | | | - V. Bonifaz-Peña
- Computational Genomics, Nacional de Medicina Genomica, Mexico City, Mexico
| | - C. Rangel-Escareño
- Computational Genomics, Nacional de Medicina Genomica, Mexico City, Mexico
| | - A. Hidalgo-Miranda
- Cancer Genomics Laboratory, Nacional de Medicina Genomica, Mexico City, Mexico
| | - A. V. Contreras
- Nutrigenetics and Nutrigenomics Laboratory, Instituto Nacional de Medicina Genomica, Mexico City, Mexico
| | - L. Polfus
- Human Genetics Center, University of Texas Health Science Center, Houston, USA
| | | | - X. Wang
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - V. Philip
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - G. Carter
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - A. A. Abuzenadah
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - M. Gari
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - R. Turki
- Ob/Gyn, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - A. Dallol
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - A. Uyar
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - A. Kaygun
- Department of Mathematical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - S. Zaman
- Department of Biomedical Engineering, University of Connecticut, Storrs, USA
| | - E. Marquez
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - J. George
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - D. Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | | | | | | | | | | | - T. Davis
- New England Biolabs, Ipswich, USA
| | | | | | - D. B. Starr
- Genetics, Stanford University, Stanford, USA
| | - M. Baird
- DNA Diagnostics Center, Fairfield, USA
| | | | - K. Sheets
- Vibrant Gene Consulting, Cambridge, USA
| | - R. Nitsche
- Agilent Technologies, Agilent Technologies, Waldbronn, Germany
| | - L. Prieto-Lafuente
- Agilent Technologies UK Ltd, Agilent Technologies UK Ltd., Edinburgh, UK
| | | | - J. Lee
- NIH/NLM/NCBI, Bethesda, USA
| | | | | | - P. K. R. Thavanati
- Institute of Human Genetics, Department of Molecular Biology & Genomics, Centre for Health Sciences, ᅟ, Mexico
| | - A. Escoto de Dios
- Institute of Human Genetics, Department of Molecular Biology & Genomics, Centre for Health Sciences, ᅟ, Mexico
| | | | | | - M. R. Ruiz Mejia
- Biochemistry, Centre for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | - K. R. R. Kanala
- Human Genetics Unit, Department Anthropology, Sri Venkateswara University, Tirupati, India
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - W. Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdul Aziz University for Health Sciences, Riyadh, Saudi Arabia
| | - F. A. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - N. Shahzad
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - A. Bouazzaoui
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Department of Medical Genetics, Umm Al Qura University, Mecca, Saudi Arabia
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - E. Huber
- Department of Pathology, University Hospital Regensburg, Regensburg, Germany
| | - A. Dan
- IgNova GmbH, Oberursel, Germany
| | - F. A. Al-Allaf
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
| | - W. Herr
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - G. Sprotte
- Department of Ansethesiologie, University of Würzburg Medical School, Würzburg, Germany
| | - J. Köstler
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - A. Hiergeist
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - A. Gessner
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - R. Andreesen
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - E. Holler
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - F. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
- Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah, Saudi Arabia
| | - A. Alashwal
- King Faisal Specialist Hospital and Research Centre, ᅟ, Saudi Arabia
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - H. Abalkhail
- King Faisal Specialist Hospital and Research Centre, ᅟ, Saudi Arabia
| | - A. Al-Allaf
- Faculty of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - R. Bamardadh
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. N. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. N. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - F. A. Al-allaf
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Molecular Diagnostics Unit Department of Laboratory Medicine and Blood Bank, King Abdullah Medical City, ᅟ, Saudi Arabia
| | - M. T. Mohiuddin
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - A. Zainularifeen
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - A. Mohammed
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - H. Abalkhail
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - T. Owaidah
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
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Pipitone A, Raval DB, Duis J, Vernon H, Martin R, Hamosh A, Valle D, Gunay-Aygun M. The management of pregnancy and delivery in 3-hydroxy-3-methylglutaryl-CoA lyase deficiency. Am J Med Genet A 2016; 170:1600-2. [PMID: 26997609 DOI: 10.1002/ajmg.a.37620] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/29/2016] [Indexed: 11/07/2022]
Abstract
3-hydroxy-3-methylglutaric (HMG)-CoA lyase is required for ketogenesis and leucine degradation. Patients with HMG-CoA lyase deficiency typically present with hypoketotic hypoglycemia and metabolic acidosis, which can be fatal if untreated. The patient is a 28-year-old female with HMG-CoA lyase deficiency who presented at 4 weeks gestation for prenatal care. Protein intake as well as carnitine supplementation were gradually increased to support maternal and fetal demands up to 65 g per day for protein and 80 mg/kg/day for carnitine. Fetal growth was appropriate. At 36 5/7 weeks, she presented with spontaneous rupture of membranes. Twice maintenance 10% glucose-containing intravenous fluids were initiated. During labor, vomiting and metabolic acidosis developed. Delivery was by cesarean. Preeclampsia developed postpartum. The patient recovered well and was discharged home on postpartum day 5. Stress of pregnancy and labor and delivery can lead to metabolic decompensation in HMG-CoA lyase deficiency. Patients should be monitored closely by a biochemical geneticist, dietitian, and high-risk obstetrician at a tertiary care center during their pregnancy. Fasting should be avoided. Intravenous 10% glucose-containing fluids should be provided to prevent catabolism and metabolic decompensation during labor and delivery. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Angela Pipitone
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Donna B Raval
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Jessica Duis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hilary Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Regina Martin
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meral Gunay-Aygun
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Byrne S, Jansen L, U-King-Im JM, Siddiqui A, Lidov HGW, Bodi I, Smith L, Mein R, Cullup T, Dionisi-Vici C, Al-Gazali L, Al-Owain M, Bruwer Z, Al Thihli K, El-Garhy R, Flanigan KM, Manickam K, Zmuda E, Banks W, Gershoni-Baruch R, Mandel H, Dagan E, Raas-Rothschild A, Barash H, Filloux F, Creel D, Harris M, Hamosh A, Kölker S, Ebrahimi-Fakhari D, Hoffmann GF, Manchester D, Boyer PJ, Manzur AY, Lourenco CM, Pilz DT, Kamath A, Prabhakar P, Rao VK, Rogers RC, Ryan MM, Brown NJ, McLean CA, Said E, Schara U, Stein A, Sewry C, Travan L, Wijburg FA, Zenker M, Mohammed S, Fanto M, Gautel M, Jungbluth H. EPG5-related Vici syndrome: a paradigm of neurodevelopmental disorders with defective autophagy. Brain 2016; 139:765-81. [PMID: 26917586 PMCID: PMC4766378 DOI: 10.1093/brain/awv393] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/31/2015] [Accepted: 11/12/2015] [Indexed: 01/07/2023] Open
Abstract
Vici syndrome is a progressive neurodevelopmental multisystem disorder due to recessive mutations in the key autophagy gene EPG5. We report genetic, clinical, neuroradiological, and neuropathological features of 50 children from 30 families, as well as the neuronal phenotype of EPG5 knock-down in Drosophila melanogaster. We identified 39 different EPG5 mutations, most of them truncating and predicted to result in reduced EPG5 protein. Most mutations were private, but three recurrent mutations (p.Met2242Cysfs*5, p.Arg417*, and p.Gln336Arg) indicated possible founder effects. Presentation was mainly neonatal, with marked hypotonia and feeding difficulties. In addition to the five principal features (callosal agenesis, cataracts, hypopigmentation, cardiomyopathy, and immune dysfunction), we identified three equally consistent features (profound developmental delay, progressive microcephaly, and failure to thrive). The manifestation of all eight of these features has a specificity of 97%, and a sensitivity of 89% for the presence of an EPG5 mutation and will allow informed decisions about genetic testing. Clinical progression was relentless and many children died in infancy. Survival analysis demonstrated a median survival time of 24 months (95% confidence interval 0-49 months), with only a 10th of patients surviving to 5 years of age. Survival outcomes were significantly better in patients with compound heterozygous mutations (P = 0.046), as well as in patients with the recurrent p.Gln336Arg mutation. Acquired microcephaly and regression of skills in long-term survivors suggests a neurodegenerative component superimposed on the principal neurodevelopmental defect. Two-thirds of patients had a severe seizure disorder, placing EPG5 within the rapidly expanding group of genes associated with early-onset epileptic encephalopathies. Consistent neuroradiological features comprised structural abnormalities, in particular callosal agenesis and pontine hypoplasia, delayed myelination and, less frequently, thalamic signal intensity changes evolving over time. Typical muscle biopsy features included fibre size variability, central/internal nuclei, abnormal glycogen storage, presence of autophagic vacuoles and secondary mitochondrial abnormalities. Nerve biopsy performed in one case revealed subtotal absence of myelinated axons. Post-mortem examinations in three patients confirmed neurodevelopmental and neurodegenerative features and multisystem involvement. Finally, downregulation of epg5 (CG14299) in Drosophila resulted in autophagic abnormalities and progressive neurodegeneration. We conclude that EPG5-related Vici syndrome defines a novel group of neurodevelopmental disorders that should be considered in patients with suggestive features in whom mitochondrial, glycogen, or lysosomal storage disorders have been excluded. Neurological progression over time indicates an intriguing link between neurodevelopment and neurodegeneration, also supported by neurodegenerative features in epg5-deficient Drosophila, and recent implication of other autophagy regulators in late-onset neurodegenerative disease.
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Affiliation(s)
- Susan Byrne
- 1 Department of Paediatric Neurology, Neuromuscular Service, Evelina's Children Hospital, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Lara Jansen
- 2 Department of Basic and Clinical Neuroscience, IoPPN, King's College London, London, UK
| | - Jean-Marie U-King-Im
- 3 Department of Neuroradiology, Evelina's Children Hospital, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Ata Siddiqui
- 3 Department of Neuroradiology, Evelina's Children Hospital, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Hart G W Lidov
- 4 Department of Pathology, Boston Children's Hospital, Boston MA 02115, USA
| | - Istvan Bodi
- 5 Department of Clinical Neuropathology, King's College Hospital, London, UK
| | - Luke Smith
- 6 Randall Division for Cell and Molecular Biophysics, Muscle Signalling Section, King's College, London, UK
| | | | - Thomas Cullup
- 8 Regional Molecular Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Carlo Dionisi-Vici
- 9 Division of Metabolism, Department of Paediatric Medicine, Bambino Gesù Children's Research Hospital, Rome
| | - Lihadh Al-Gazali
- 10 Departments of Paediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, UAE
| | - Mohammed Al-Owain
- 11 College of Medicine, Alfaisal University, Riyadh, Saudi Arabia 12 Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Zandre Bruwer
- 13 Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Sultanate of Oman
| | - Khalid Al Thihli
- 13 Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Sultanate of Oman
| | | | - Kevin M Flanigan
- 15 Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kandamurugu Manickam
- 16 Center for Human and Molecular Genetics at The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Erik Zmuda
- 16 Center for Human and Molecular Genetics at The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Wesley Banks
- 16 Center for Human and Molecular Genetics at The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ruth Gershoni-Baruch
- 17 Institute of Human Genetics, Rambam Health Care Campus and the Technion Faculty of Medicine, Haifa, Israel
| | - Hanna Mandel
- 18 Metabolic Disease Unit, Meyer Children's Hospital, Rambam Health Care Campus and the Technion Faculty of Medicine, Haifa, Israel
| | - Efrat Dagan
- 19 Department of Nursing, University of Haifa, Haifa, Israel
| | - Annick Raas-Rothschild
- 20 Institute of Rare Diseases, Institute of Genetics; Sheba Medical Centre, Tel Hashomer and the Sackler school of Medicine Tel Aviv University Ramat Aviv, Israel
| | - Hila Barash
- 20 Institute of Rare Diseases, Institute of Genetics; Sheba Medical Centre, Tel Hashomer and the Sackler school of Medicine Tel Aviv University Ramat Aviv, Israel
| | - Francis Filloux
- 21 Division of Pediatric Neurology, University of Utah School of Medicine and Primary Children's Medical Centre, Salt Lake City, Utah, USA
| | - Donnell Creel
- 22 University of Utah School of Medicine, Moran Eye Centre, Salt Lake City, Utah, USA
| | - Michael Harris
- 23 Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington DC, USA
| | - Ada Hamosh
- 24 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Stefan Kölker
- 25 Division of Child Neurology and Metabolic Medicine, University Children's Hospital, Heidelberg, Germany
| | - Darius Ebrahimi-Fakhari
- 25 Division of Child Neurology and Metabolic Medicine, University Children's Hospital, Heidelberg, Germany
| | - Georg F Hoffmann
- 25 Division of Child Neurology and Metabolic Medicine, University Children's Hospital, Heidelberg, Germany
| | - David Manchester
- 26 Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, USA
| | - Philip J Boyer
- 27 Department of Pathology, East Carolina University, Brody School of Medicine, Brody Medical Sciences Building, Greenville, NC 27834, USA
| | | | | | - Daniela T Pilz
- 30 Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Arveen Kamath
- 30 Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Prab Prabhakar
- 31 Department of Paediatric Neurology, Great Ormond Street Children's Hospital, London, UK
| | - Vamshi K Rao
- 32 University of Nebraska Medical Center and Childrens Hospital and Medical Center, Omaha, Nebraska, USA
| | - R Curtis Rogers
- 33 Greenwood Genetic Center, Greenville, South Carolina, USA
| | - Monique M Ryan
- 34 Departments of Neurology, Royal Children's Hospital and Paediatrics, University of Melbourne, and Murdoch Childrens Research Institute, Melbourne Australia
| | - Natasha J Brown
- 35 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute Parkville, Australia 36 Department of Paediatrics, University of Melbourne, Parkville, Australia 37 Department of Clinical Genetics, Austin Health, Australia
| | | | - Edith Said
- 39 Department of Anatomy and Cell Biology, University of Malta, Msida, Malta 40 Section of Medical Genetics, Mater dei Hospital, Msida, Malta
| | - Ulrike Schara
- 41 Pediatric Neurology, University Childrens Hospital, University of Duisburg-Essen University of Duisburg-Essen, Essen, Germany
| | - Anja Stein
- 42 Department of Neonatology, University Childrens Hospital, University of Duisburg-Essen, Essen, Germany
| | - Caroline Sewry
- 43 Dubowitz Neuromuscular Centre, Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Laura Travan
- 44 Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Frits A Wijburg
- 45 Department of Paediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Martin Zenker
- 46 Institute of Human Genetics, University Hospital Magdeburg, Germany
| | - Shehla Mohammed
- 47 Department of Clinical Genetics, Guy's Hospital, London, UK
| | - Manolis Fanto
- 2 Department of Basic and Clinical Neuroscience, IoPPN, King's College London, London, UK
| | - Mathias Gautel
- 6 Randall Division for Cell and Molecular Biophysics, Muscle Signalling Section, King's College, London, UK
| | - Heinz Jungbluth
- 1 Department of Paediatric Neurology, Neuromuscular Service, Evelina's Children Hospital, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK 6 Randall Division for Cell and Molecular Biophysics, Muscle Signalling Section, King's College, London, UK 48 Department of Basic and Clinical Neuroscience, IoPPN, King's College London, London, UK
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46
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Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat 2015; 36:425-31. [PMID: 25684268 DOI: 10.1002/humu.22769] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/09/2015] [Indexed: 01/10/2023]
Abstract
Identifying the causative variant from among the thousands identified by whole-exome sequencing or whole-genome sequencing is a formidable challenge. To make this process as efficient and flexible as possible, we have developed a Variant Analysis Module coupled to our previously described Web-based phenotype intake tool, PhenoDB (http://researchphenodb.net and http://phenodb.org). When a small number of candidate-causative variants have been identified in a study of a particular patient or family, a second, more difficult challenge becomes proof of causality for any given variant. One approach to this problem is to find other cases with a similar phenotype and mutations in the same candidate gene. Alternatively, it may be possible to develop biological evidence for causality, an approach that is assisted by making connections to basic scientists studying the gene of interest, often in the setting of a model organism. Both of these strategies benefit from an open access, online site where individual clinicians and investigators could post genes of interest. To this end, we developed GeneMatcher (http://genematcher.org), a freely accessible Website that enables connections between clinicians and researchers across the world who share an interest in the same gene(s).
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Affiliation(s)
- Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
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47
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Jurgens J, Ling H, Hetrick K, Pugh E, Schiettecatte F, Doheny K, Hamosh A, Avramopoulos D, Valle D, Sobreira N. Assessment of incidental findings in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. Genet Med 2015; 17:782-8. [PMID: 25569433 PMCID: PMC4496331 DOI: 10.1038/gim.2014.196] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/01/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE In March 2013 the American College of Medical Genetics and Genomics published a list of 56 genes with the recommendation that pathogenic and likely pathogenic variants detected incidentally by clinical sequencing be reported to patients. As an initial step in determining the practical consequences of this recommendation in the research setting, we searched for variants in these genes in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. METHODS We identified rare, nonsynonymous, and splicing single-nucleotide variants and insertions/deletions and assessed variant classification using the Human Gene Mutation, Emory, and ClinVar databases. We analyzed the burden of mutation in each of the 56 genes and determined which variants should be reported to patients. RESULTS Our filtering resulted in 249 distinct variants, with a mean of 1.69 variants per individual. Half of these were novel missense mutations not classified by any of the three reference databases. Of 101 variants listed in the Human Gene Mutation Database, 48 were also in ClinVar and 3 were also in Emory; half of these shared variants were classified discordantly between databases. Some genes consistently had greater variation than others. In total, 0.86% of individuals had a reportable incidental variant. CONCLUSION These observations demonstrate some current challenges of assessing phenotypic consequences of incidental variants for counseling patients.
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Affiliation(s)
- Julie Jurgens
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hua Ling
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Kurt Hetrick
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | | | - Kimberly Doheny
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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48
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Fleming L, Lemmon M, Beck N, Johnson M, Mu W, Murdock D, Bodurtha J, Hoover-Fong J, Cohn R, Bosemani T, Barañano K, Hamosh A. Genotype-phenotype correlation of congenital anomalies in multiple congenital anomalies hypotonia seizures syndrome (MCAHS1)/PIGN-related epilepsy. Am J Med Genet A 2015; 170A:77-86. [PMID: 26394714 DOI: 10.1002/ajmg.a.37369] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/24/2015] [Indexed: 01/31/2023]
Abstract
Mutations in PIGN, resulting in multiple congenital anomalies-hypotonia-seizures syndrome, a glycosylphosphatidylinositol anchor deficiency, have been published in four families to date. We report four patients from three unrelated families with epilepsy and hypotonia in whom whole exome sequencing yielded compound heterozygous variants in PIGN. As with previous reports Patients 1 and 2 (full siblings) have severe global developmental delay, gastroesophageal reflux disease, and minor dysmorphic features, including high palate, bitemporal narrowing, depressed nasal bridge, and micrognathia; Patient 3 had early global developmental delay with later progressive spastic quadriparesis, intellectual disability, and intractable generalized epilepsy; Patient 4 had bilateral narrowing as well but differed by the presence of hypertelorism, markedly narrow palpebral fissures, and long philtrum, had small distal phalanges of fingers 2, 3, and 4, absent distal phalanx of finger 5 and similar toe anomalies, underdeveloped nails, unusual brain anomalies, and a more severe early clinical course. These patients expand the known clinical spectrum of the disease. The severity of the presentations in conjunction with the patients' mutations suggest a genotype-phenotype correlation in which congenital anomalies are only seen in patients with biallelic loss-of-function. In addition, PIGN mutations appear to be panethnic and may be an underappreciated cause of epilepsy.
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Affiliation(s)
- Leah Fleming
- NHGRI, Office of the Clinical Director, NIH, Bethesda, Maryland
| | - Monica Lemmon
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Natalie Beck
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland.,Greenberg Center for Skeletal Dysplasia, Johns Hopkins University, Baltimore, Maryland
| | - Maria Johnson
- Department of Neurology, University of Minnesota, Minneapolis, Minnesota
| | - Weiyi Mu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - David Murdock
- NHGRI, Office of the Clinical Director, NIH, Bethesda, Maryland
| | - Joann Bodurtha
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Julie Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland.,Greenberg Center for Skeletal Dysplasia, Johns Hopkins University, Baltimore, Maryland
| | - Ronald Cohn
- The Hospital for Sick Children, Clinical and Metabolic Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Thangamadhan Bosemani
- Section of Pediatric Neuroradiology, Division of Pediatric Radiology, Johns Hopkins University, Baltimore, Maryland
| | - Kristin Barañano
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland.,Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
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Abstract
Here, we describe an overview and update on GeneMatcher (http://www.genematcher.org), a freely accessible Web-based tool developed as part of the Baylor-Hopkins Center for Mendelian Genomics. We created GeneMatcher with the goal of identifying additional individuals with rare phenotypes who had variants in the same candidate disease gene. We also wanted to facilitate connections to basic scientists working on orthologous genes in model systems with the goal of connecting their work to human Mendelian phenotypes. Meeting these goals will enhance the identification of novel Mendelian genes. Launched in September, 2013, GeneMatcher now has 2,178 candidate genes from 486 submitters spread across 38 countries entered in the database (June 1, 2015). GeneMatcher is also part of the Matchmaker Exchange (http://matchmakerexchange.org/) with an Application Programing Interface enabling submitters to query other databases of genetic variants and phenotypes without having to create accounts and data entries in multiple systems.
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Affiliation(s)
- Nara Sobreira
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - David Valle
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ada Hamosh
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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50
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Chong J, Buckingham K, Jhangiani S, Boehm C, Sobreira N, Smith J, Harrell T, McMillin M, Wiszniewski W, Gambin T, Coban Akdemir Z, Doheny K, Scott A, Avramopoulos D, Chakravarti A, Hoover-Fong J, Mathews D, Witmer P, Ling H, Hetrick K, Watkins L, Patterson K, Reinier F, Blue E, Muzny D, Kircher M, Bilguvar K, López-Giráldez F, Sutton V, Tabor H, Leal S, Gunel M, Mane S, Gibbs R, Boerwinkle E, Hamosh A, Shendure J, Lupski J, Lifton R, Valle D, Nickerson D, Bamshad M, Bamshad MJ. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. Am J Hum Genet 2015; 97:199-215. [PMID: 26166479 DOI: 10.1016/j.ajhg.2015.06.009] [Citation(s) in RCA: 445] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 01/06/2023] Open
Abstract
Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA.
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