Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease

Gabrielle Lemire; Alba Sanchis-Juan; Kathryn Russell; Samantha Baxter; Katherine R Chao; Moriel Singer-Berk; Emily Groopman; Isaac Wong; Eleina England; Julia Goodrich; Lynn Pais; Christina Austin-Tse; Stephanie DiTroia; Emily O'Heir; Vijay S Ganesh; Monica H Wojcik; Emily Evangelista; Hana Snow; Ikeoluwa Osei-Owusu; Jack Fu; Mugdha Singh; Yulia Mostovoy; Steve Huang; Kiran Garimella; Samantha L Kirkham; Jennifer E Neil; Diane D Shao; Christopher A Walsh; Emanuela Argilli; Carolyn Le; Elliott H Sherr; Joseph G Gleeson; Shirlee Shril; Ronen Schneider; Friedhelm Hildebrandt; Vijay G Sankaran; Jill A Madden; Casie A Genetti; Alan H Beggs; Pankaj B Agrawal; Kinga M Bujakowska; Emily Place; Eric A Pierce; Sandra Donkervoort; Carsten G Bönnemann; Lyndon Gallacher; Zornitza Stark; Tiong Yang Tan; Susan M White; Ana Töpf; Volker Straub; Mark D Fleming; Martin R Pollak; Katrin Õunap; Sander Pajusalu; Kirsten A Donald; Zandre Bruwer; Gianina Ravenscroft; Nigel G Laing; Daniel G MacArthur; Heidi L Rehm; Michael E Talkowski; Harrison Brand; Anne O'Donnell-Luria

doi:10.1016/j.ajhg.2024.03.008

Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease

Am J Hum Genet. 2024 May 2;111(5):863-876. doi: 10.1016/j.ajhg.2024.03.008. Epub 2024 Apr 1.

Authors

Gabrielle Lemire¹, Alba Sanchis-Juan², Kathryn Russell³, Samantha Baxter³, Katherine R Chao⁴, Moriel Singer-Berk⁴, Emily Groopman⁵, Isaac Wong⁴, Eleina England⁵, Julia Goodrich⁴, Lynn Pais⁶, Christina Austin-Tse⁴, Stephanie DiTroia⁶, Emily O'Heir⁶, Vijay S Ganesh⁷, Monica H Wojcik⁸, Emily Evangelista³, Hana Snow³, Ikeoluwa Osei-Owusu⁴, Jack Fu², Mugdha Singh⁹, Yulia Mostovoy⁴, Steve Huang³, Kiran Garimella³, Samantha L Kirkham¹⁰, Jennifer E Neil¹¹, Diane D Shao¹², Christopher A Walsh¹³, Emanuela Argilli¹⁴, Carolyn Le¹⁴, Elliott H Sherr¹⁴, Joseph G Gleeson¹⁵, Shirlee Shril¹⁶, Ronen Schneider¹⁶, Friedhelm Hildebrandt¹⁶, Vijay G Sankaran¹⁷, Jill A Madden¹⁸, Casie A Genetti¹⁸, Alan H Beggs¹⁹, Pankaj B Agrawal¹⁹, Kinga M Bujakowska²⁰, Emily Place²⁰, Eric A Pierce²⁰, Sandra Donkervoort²¹, Carsten G Bönnemann²¹, Lyndon Gallacher²², Zornitza Stark²², Tiong Yang Tan²², Susan M White²², Ana Töpf²³, Volker Straub²³, Mark D Fleming²⁴, Martin R Pollak²⁵, Katrin Õunap²⁶, Sander Pajusalu²⁶, Kirsten A Donald²⁷, Zandre Bruwer²⁷, Gianina Ravenscroft²⁸, Nigel G Laing²⁸, Daniel G MacArthur²⁹, Heidi L Rehm², Michael E Talkowski², Harrison Brand², Anne O'Donnell-Luria³⁰

Affiliations

¹ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. Electronic address: [email protected].
² Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
³ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁴ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
⁵ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
⁶ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
⁷ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.
⁸ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
⁹ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
¹⁰ Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
¹¹ Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
¹² Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Neurology, Boston Children's Hospital, Boston, MA, USA.
¹³ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
¹⁴ Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
¹⁵ Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
¹⁶ Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
¹⁷ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
¹⁸ Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
¹⁹ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
²⁰ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
²¹ Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
²² Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.
²³ John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
²⁴ Harvard Medical School, Boston, MA, USA; Department of Pathology, Boston Children's Hospital, Boston, MA, USA.
²⁵ Harvard Medical School, Boston, MA, USA; Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
²⁶ Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia.
²⁷ Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa.
²⁸ University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.
²⁹ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
³⁰ Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA. Electronic address: [email protected].

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 Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.

Keywords: CNV; GATK-gCNV; copy number variant; diagnostic yield; exome; variant classification.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cohort Studies
DNA Copy Number Variations* / genetics
Exome Sequencing*
Exome* / genetics
Female
Genetic Testing / methods
Humans
Male
Rare Diseases* / diagnosis
Rare Diseases* / genetics

Abstract

Publication types

MeSH terms

Grants and funding