Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes

• Published in: American journal of human genetics Vol. 110; no. 1; pp. 71 - 91
• Main Authors: Lansdon, Lisa A., Dickinson, Amanda, Arlis, Sydney, Liu, Huan, Hlas, Arman, Hahn, Alyssa, Bonde, Greg, Long, Abby, Standley, Jennifer, Tyryshkina, Anastasia, Wehby, George, Lee, Nanette R., Daack-Hirsch, Sandra, Mohlke, Karen, Girirajan, Santhosh, Darbro, Benjamin W., Cornell, Robert A., Houston, Douglas W., Murray, Jeffrey C., Manak, J. Robert
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05.01.2023; Elsevier
• Subjects: ARHGEF38; Cleft Lip - genetics; cleft lip and palate; Cleft Palate - genetics; COBLL1; congenital anomalies; copy number variants; craniofacial; Danio rerio; DNA Copy Number Variations; Genome-Wide Association Study; Guanine Nucleotide Exchange Factors - genetics; Humans; Phenotype; RIC1; Transcription Factors - genetics; Xenopus laevis; RIC1; cleft lip and palate; Xenopus laevis; COBLL1; Danio rerio; ARHGEF38; craniofacial; copy number variants; congenital anomalies
• ISSN: 0002-9297; 1537-6605; 1537-6605
• DOI: 10.1016/j.ajhg.2022.11.012

Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders. The contribution of copy-number variants to cleft lip with or without cleft palate (CL/P) has been relatively understudied. Using a strategy to identify likely higher effect size microdeletions, we identify COBLL1, RIC1, and ARHGEF38 as genes associated with CL/P that play important roles in vertebrate craniofacial development.