title: Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate.
abstract: Studies suggest that nonsyndromic cleft lip and palate (NSCLP) is polygenic with variable penetrance, presenting a challenge in identifying all causal genetic variants. Despite relatively high prevalence of NSCLP among Amerindian populations, no large whole exome sequencing (WES) studies have been completed in this population. Our goal was to identify candidate genes with rare genetic variants for NSCLP in a Honduran population using WES. WES was performed on two to four members of 27 multiplex Honduran families. Genetic variants with a minor allele frequency > 1% in reference databases were removed. Heterozygous variants consistent with dominant disease with incomplete penetrance were ascertained, and variants with predicted functional consequence were prioritized for analysis. Pedigree-specific P-values were calculated as the probability of all affected members in the pedigree being carriers, given that at least one is a carrier. Preliminary results identified 3,727 heterozygous rare variants; 1,282 were predicted to be functionally consequential. Twenty-three genes had variants of interest in ≥3 families, where some genes had different variants in each family, giving a total of 50 variants. Variant validation via Sanger sequencing of the families and unrelated unaffected controls excluded variants that were sequencing errors or common variants not in databases, leaving four genes with candidate variants in ≥3 families. Of these, candidate variants in two genes consistently segregate with NSCLP as a dominant variant with incomplete penetrance: ACSS2 and PHYH. Rare variants found at the same gene in all affected individuals in several families are likely to be directly related to NSCLP.
authors.affiliation: Columbia University College of Physicians, Surgeons Otolaryngology Department, New York, New York, United States of America.
authors.forename: Alana
authors.initials: A
authors.lastname: Aylward
authors.affiliation: Columbia University College of Physicians, Surgeons Otolaryngology Department, New York, New York, United States of America.
authors.forename: Yi
authors.initials: Y
authors.lastname: Cai
authors.affiliation: Columbia University College of Physicians, Surgeons Otolaryngology Department, New York, New York, United States of America.
authors.forename: Andrew
authors.initials: A
authors.lastname: Lee
authors.affiliation: University of Washington Department of Medicine, Division of Medical Genetics, Seattle, Washington, United States of America.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Blue
authors.affiliation: Department of Statistics, Columbia University, New York, New York, United States of America.
authors.forename: Daniel
authors.initials: D
authors.lastname: Rabinowitz
authors.affiliation: Columbia University College of Physicians, Surgeons Otolaryngology Department, New York, New York, United States of America.
authors.forename: Joseph
authors.initials: J
authors.lastname: Haddad
mesh_terms: D000106:Acetate-CoA Ligase / Q000235:genetics; D000483:Alleles; D002971:Cleft Lip / Q000235:genetics* / Q000473:pathology; D002972:Cleft Palate / Q000235:genetics* / Q000473:pathology; D005260:Female; D005787:Gene Frequency; D005838:Genotype; D006579:Heterozygote; D006593:Hexokinase / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D006899:Mixed Function Oxygenases / Q000235:genetics; D010375:Pedigree; D019683:Penetrance; D017422:Sequence Analysis, DNA; D014841:von Willebrand Factor / Q000235:genetics
chemical_list: D014841:von Willebrand Factor; D006899:Mixed Function Oxygenases; C102623:PHYH protein, human; C472074:HK1 protein, human; D006593:Hexokinase; C000595379:ACSS2 protein, human; D000106:Acetate-CoA Ligase
keywords: Incomplete penetrance; craniofacial anomaly; nonsyndromic cleft lip and palate; rare genetic variants; whole exome sequencing