ArticlemedRxiv : the preprint server for health sciences2023
Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease.
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Article in medRxiv : the preprint server for health sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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64 authors at 11 institutions in 5 countries.
Gabrielle LemireBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Alba Sanchis-JuanBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Kathryn RussellBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Samantha BaxterBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Katherine R ChaoBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Moriel Singer-BerkBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Emily GroopmanBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Isaac WongProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Eleina EnglandBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Julia GoodrichBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Lynn PaisBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Christina Austin-TseBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Stephanie DiTroiaBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Emily O'HeirBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Vijay S GaneshBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Monica H WojcikBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Emily EvangelistaBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Hana SnowBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ikeoluwa Osei-OwusuBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Jack FuProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Mugdha SinghBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Yulia MostovoyBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Steve HuangProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Kiran GarimellaProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Samantha L KirkhamDivision of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
Jennifer E NeilDivision of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
Diane D ShaoDivision of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
Christopher A WalshProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Emanuela ArgiliDepartment of Neurology, University of California, San Francisco, San Francisco, CA, USA.
Carolyn LeDepartment of Neurology, University of California, San Francisco, San Francisco, CA, USA.
Elliott H SherrDepartment of Neurology, University of California, San Francisco, San Francisco, CA, USA.
Joseph GleesonDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.
Shirlee ShrilHarvard Medical School, Boston, MA, USA.
Ronen SchneiderHarvard Medical School, Boston, MA, USA.
Friedhelm HildebrandtHarvard Medical School, Boston, MA, USA.
Vijay G SankaranProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Jill A MaddenDivision of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
Casie A GenettiDivision of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
Alan H BeggsProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Pankaj B AgrawalProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Kinga M BujakowskaProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Emily PlaceProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Eric A PierceProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Sandra DonkervoortNeuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
Carsten G BönnemannNeuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
Lyndon GallacherDepartment of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
Zornitza StarkDepartment of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
Tiong TanDepartment of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
Susan M WhiteDepartment of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
Ana TöpfJohn Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
Volker StraubJohn Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
Mark D FlemingHarvard Medical School, Boston, MA, USA.
Martin R PollakHarvard Medical School, Boston, MA, USA.
Katrin ÕunapDepartment of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia.
Sander PajusaluDepartment of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia.
Kirsten A DonaldDepartment of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.
Zandre BruwerDepartment of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.
Gianina RavenscroftUniversity of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Australia.
Nigel G LaingUniversity of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Australia.
Daniel G MacArthurBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Heidi L RehmBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Michael E TalkowskiBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Harrison BrandBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Anne O'Donnell-LuriaBroad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Broad Institute · USBoston Children's Hospital · USThe University of Melbourne · AUUniversity of California, San Francisco · USNational Institutes of Health · USNewcastle upon Tyne Hospitals NHS Foundation Trust · GBTartu University Hospital · EEThe University of Western Australia · AUUniversity of Cape Town · ZABeth Israel Deaconess Medical Center · USChildren’s Institute · US
Funding
Joint Center for Mendelian GenomicsUM1HG008900 · NHGRI · BROAD INSTITUTE, INC. · PI O'DONNELL-LURIA, ANNE, REHM, HEIDI L · 2016 to 2020
$16.5MBroad Institute Mendelian Genomic Research CenterU01HG011755 · NHGRI · BROAD INSTITUTE, INC. · PI Anne O'Donnell-Luria, MICHAEL E TALKOWSKI · 2021 to 2026
$14.6MCell Identity Determination In Human Brain: Somatic Mutation and Cell LineageR01NS032457 · NINDS · BOSTON CHILDREN'S HOSPITAL · PI Alice Eunjung Lee, Christopher A. Walsh · 1995 to 2026
$12.7MDe novo copy number variation and gene discovery in human brain malformationsR01NS058721 · NINDS · UNIVERSITY OF CHICAGO · PI ARGILLI, EMANUELA · 2008 to 2025
$10.9MGenetic Analysis and Manipulation Core (GAEC)P50HD105351 · NICHD · BOSTON CHILDREN'S HOSPITAL · PI SCOTT Loren POMEROY, MUSTAFA SAHIN · 2021 to 2026
$9.4MThe Massachusetts General Hospital Harvard Center for Reproductive MedicineP50HD104224 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI SEMINARA, STEPHANIE BETH · 2021 to 2025
$7.8MIntegrating large scale genomics and functional studies to accelerate FSGS/NS discoveryRC2DK122397 · NIDDK · BETH ISRAEL DEACONESS MEDICAL CENTER · PI HILDEBRANDT, FRIEDHELM, POLLAK, MARTIN R. · 2020 to 2024
$7.4MClinical Diagnostic Sequencing of Structural VariationR01HD081256 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI TALKOWSKI, MICHAEL E · 2015 to 2025
$7.2MPartners Healthcare Training Program in Precision and Genomic MedicineT32HG010464 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI HEIDI L REHM, JORDAN W SMOLLER · 2019 to 2026
$3.1MA powerful web-based discovery platform for rare disease geneticsR01HG009141 · NHGRI · BROAD INSTITUTE, INC. · PI QUINLAN, AARON R, REHM, HEIDI L · 2017 to 2020
$2.9MThe Burden of Genetic Disorders in Infant MortalityK23HD102589 · NICHD · BOSTON CHILDREN'S HOSPITAL · PI WOJCIK, MONICA HSIUNG · 2020 to 2024
$840kNHGRI NIH HHS R01 HG009141NHGRI NIH HHS T32 HG010464NHGRI NIH HHS U01 HG011755NHGRI NIH HHS UM1 HG008900NICHD NIH HHS K23 HD102589NICHD NIH HHS P50 HD104224NICHD NIH HHS P50 HD105351NICHD NIH HHS R01 HD081256NIDDK NIH HHS RC2 DK122397NINDS NIH HHS R01 NS032457NINDS NIH HHS R01 NS058721
Abstract
Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and with new innovative methods can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the GREGoR consortium. Each family's CNV data was analyzed using the
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