title: Whole exome sequencing of distant relatives in multiplex families implicates rare variants in candidate genes for oral clefts.
abstract: A dozen genes/regions have been confirmed as genetic risk factors for oral clefts in human association and linkage studies, and animal models argue even more genes may be involved. Genomic sequencing studies should identify specific causal variants and may reveal additional genes as influencing risk to oral clefts, which have a complex and heterogeneous etiology. We conducted a whole exome sequencing (WES) study to search for potentially causal variants using affected relatives drawn from multiplex cleft families. Two or three affected second, third, and higher degree relatives from 55 multiplex families were sequenced. We examined rare single nucleotide variants (SNVs) shared by affected relatives in 348 recognized candidate genes. Exact probabilities that affected relatives would share these rare variants were calculated, given pedigree structures, and corrected for the number of variants tested. Five novel and potentially damaging SNVs shared by affected distant relatives were found and confirmed by Sanger sequencing. One damaging SNV in CDH1, shared by three affected second cousins from a single family, attained statistical significance (P = 0.02 after correcting for multiple tests). Family-based designs such as the one used in this WES study offer important advantages for identifying genes likely to be causing complex and heterogeneous disorders.
authors.affiliation: Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec and Département de Médecine Sociale et Préventive, Université Laval, Québec, QC G1V 0A6, Canada.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Bureau
authors.affiliation: Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205.
authors.forename: Margaret M
authors.initials: MM
authors.lastname: Parker
authors.affiliation: Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205.
authors.forename: Ingo
authors.initials: I
authors.lastname: Ruczinski
authors.affiliation: Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205.
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Taub
authors.affiliation: Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219.
authors.forename: Mary L
authors.initials: ML
authors.lastname: Marazita
authors.affiliation: Department of Pediatrics, School of Medicine, University of Iowa, Iowa City, Iowa 52242.
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Murray
authors.affiliation: Institute of Human Genetics, University of Bonn, Bonn, Germany D-53111.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Mangold
authors.affiliation: Institute of Human Genetics, University of Bonn, Bonn, Germany D-53111.
authors.forename: Markus M
authors.initials: MM
authors.lastname: Noethen
authors.affiliation: Institute of Human Genetics, University of Bonn, Bonn, Germany D-53111.
authors.forename: Kirsten U
authors.initials: KU
authors.lastname: Ludwig
authors.affiliation: Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205.
authors.forename: Jacqueline B
authors.initials: JB
authors.lastname: Hetmanski
authors.affiliation: Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121.
authors.forename: Joan E
authors.initials: JE
authors.lastname: Bailey-Wilson
authors.affiliation: Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121.
authors.forename: Cheryl D
authors.initials: CD
authors.lastname: Cropp
authors.affiliation: Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121.
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.affiliation: Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121.
authors.forename: Silke
authors.initials: S
authors.lastname: Szymczak
authors.affiliation: Hejazi Clinic, Clinic, Riyadh, Saudia Arabia 11461.
authors.forename: Hasan
authors.initials: H
authors.lastname: Albacha-Hejazi
authors.affiliation: Prime Health Clinic, Jeddah, Saudi Arabia 21511.
authors.forename: Khalid
authors.initials: K
authors.lastname: Alqosayer
authors.affiliation: Department of Human Genetics, University of British Columbia, Vancouver, Canada V6T1Z3.
authors.forename: L Leigh
authors.initials: LL
authors.lastname: Field
authors.affiliation: Laboratory of Human Molecular Genetics, Chang Gung Memorial Hospital, Taipei, Taiwan 333.
authors.forename: Yah-Huei
authors.initials: YH
authors.lastname: Wu-Chou
authors.affiliation: Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore Maryland 21224.
authors.forename: Kimberly F
authors.initials: KF
authors.lastname: Doheny
authors.affiliation: Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore Maryland 21224.
authors.forename: Hua
authors.initials: H
authors.lastname: Ling
authors.affiliation: Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21224.
authors.forename: Alan F
authors.initials: AF
authors.lastname: Scott
authors.affiliation: Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205 tbeaty1@jhu.edu.
authors.forename: Terri H
authors.initials: TH
authors.lastname: Beaty
mesh_terms: D015703:Antigens, CD; D015820:Cadherins / Q000235:genetics; D002972:Cleft Palate / Q000235:genetics*; D005006:Ethnicity / Q000235:genetics; D059472:Exome / Q000235:genetics*; D005190:Family; D005260:Female; D056726:Genetic Association Studies; D006801:Humans; D008297:Male; D009154:Mutation / Q000235:genetics*; D010375:Pedigree; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D015703:Antigens, CD; C513384:CDH1 protein, human; D015820:Cadherins
keywords: oral clefts; pedigree studies; rare variants; whole exome sequencing