Genome-Wide Association Studies in Dogs and Humans Identify ADAMTS20 as a Risk Variant for Cleft Lip and Palate

Abstract\ud \ud Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted p= 2.2 x 10-3). Further analysis in NSDTR families and additional full sibling cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 – 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3 CLPS cases and 4 controls at 15X coverage led to the discovery of a frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)), which segregated concordant with the phenotype. In a parallel study in humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420 unaffected relatives, and 392 controls from a Guatemalan cohort, identified a suggestive association (rs10785430; p =2.67 x 10-6) with the same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was unable to identify a causative mutation within the coding region of ADAMTS20, but four coding variants were found in additional cases of CL/P. In summary, this study provides genetic evidence for a role of ADAMTS20 in CL/P development in dogs and as a candidate gene for CL/P development in humans.\ud \ud Author Summary\ud \ud Cleft lip with or without cleft palate (CL/P) is a commonly occurring birth defect that can lead to a lifetime of complications in affected children. To better understand the genetic cause of these disorders, we investigated CL/P in both dogs and humans. Genome-wide association studies in both species independently identify ADAMTS20 as a candidate gene for CL/P development. In dogs, a deletion within a functional domain of ADAMTS20 is responsible for CL/P in the Nova Scotia Duck Tolling Retriever dog breed. In humans, an associated region containing the same gene, ADAMTS20, was identified in a study population of native Guatemalans. Subsequent sequencing in humans was unable to identify a causative mutation within the coding region of ADAMTS20 in the Guatemalan cohort; however, sequencing of ADAMTS20 in additional cases with CL/P identified four novel coding variants. This work provides genetic evidence for a role for ADAMTS20 in CL/P development in both dogs and humans