title: De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects.
abstract: Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD). In a primary analysis, by combining developmental coexpression networks with inheritance modeling, we identify a de novo mutation in the DNA binding domain of NR1D2 (p.R175W). We show that p.R175W changes the transcriptional activity of Nr1d2 using an in vitro transactivation model in HUVEC cells. Finally, we demonstrate previously unrecognized cardiovascular malformations in the Nr1d2tm1-Dgen knockout mouse. In secondary analyses we map genetic variation to protein-interaction networks suggesting a role for two collagen genes in AVSD, which we corroborate by burden testing in a second replication cohort of 100 AVSDs and 533 controls (p = 8.37e-08). Finally, we apply a rare-disease inheritance model to identify variation in genes previously associated with CHD (ZFPM2, NSD1, NOTCH1, VCAN, and MYH6), cardiac malformations in mouse models (ADAM17, CHRD, IFT140, PTPRJ, RYR1 and ATE1), and hypomorphic alleles of genes causing syndromic CHD (EHMT1, SRCAP, BBS2, NOTCH2, and KMT2D) in 14 of 59 trios, greatly exceeding variation in control trios without CHD (p = 9.60e-06). In total, 32% of trios carried at least one putatively disease-associated variant across 19 loci,suggesting that inherited and de novo variation across a heterogeneous group of loci may contribute to disease risk.
authors.affiliation: Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.|Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: James R
authors.initials: JR
authors.lastname: Priest
authors.affiliation: Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Kazutoyo
authors.initials: K
authors.lastname: Osoegawa
authors.affiliation: University of California San Francisco Benioff Children's Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Nebil
authors.initials: N
authors.lastname: Mohammed
authors.affiliation: Department of Vascular Surgery, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Vivek
authors.initials: V
authors.lastname: Nanda
authors.affiliation: Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Ramendra
authors.initials: R
authors.lastname: Kundu
authors.affiliation: University of California San Francisco Benioff Children's Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Schultz
authors.affiliation: University of California San Francisco Benioff Children's Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Lammer
authors.affiliation: Departments of Biochemistry, Molecular Biology, and Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: Santhosh
authors.initials: S
authors.lastname: Girirajan
authors.affiliation: College of Engineering, University of Iowa, Iowa City, Iowa, United States of America.
authors.forename: Todd
authors.initials: T
authors.lastname: Scheetz
authors.affiliation: Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Daryl
authors.initials: D
authors.lastname: Waggott
authors.affiliation: Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.|Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Francois
authors.initials: F
authors.lastname: Haddad
authors.affiliation: Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.|Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Sushma
authors.initials: S
authors.lastname: Reddy
authors.affiliation: Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.|Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Daniel
authors.initials: D
authors.lastname: Bernstein
authors.affiliation: College of Public Health, University of Iowa, Iowa City, Iowa, United States of America.
authors.forename: Trudy
authors.initials: T
authors.lastname: Burns
authors.affiliation: Department of Pathology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Steimle
authors.affiliation: Department of Pathology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Xinan H
authors.initials: XH
authors.lastname: Yang
authors.affiliation: Department of Pathology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Ivan P
authors.initials: IP
authors.lastname: Moskowitz
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hurles
authors.affiliation: Department of Genetics, Yale University, New Haven, Connecticut, United States of America.|Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.
authors.forename: Richard P
authors.initials: RP
authors.lastname: Lifton
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Debbie
authors.initials: D
authors.lastname: Nickerson
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.|Department of Pediatrics, University of Washington, Seattle, Washington, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Bamshad
authors.affiliation: Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.|Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.affiliation: Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Seema
authors.initials: S
authors.lastname: Mital
authors.affiliation: Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.|Division of Medical Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America.
authors.forename: Val
authors.initials: V
authors.lastname: Sheffield
authors.affiliation: Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.|Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Thomas
authors.initials: T
authors.lastname: Quertermous
authors.affiliation: Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, New York, United States of America.
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Gelb
authors.affiliation: Department of Pediatrics, University of Washington, Seattle, Washington, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Portman
authors.affiliation: Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.|Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America.
authors.forename: Euan A
authors.initials: EA
authors.lastname: Ashley
mesh_terms: D000818:Animals; D005260:Female; D006343:Heart Septal Defects / Q000235:genetics*; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D008297:Male; D051379:Mice; D018345:Mice, Knockout; D009154:Mutation; D010375:Pedigree