Contribution of genetic variants to orofacial clefts in African populations

Orofacial clefts (OFCs) are the most common craniofacial birth defect and epidemiological studies report their huge burden on public health. Genetic risk factors contributions to the OFCs etiopathogenesis have long been investigated in other populations but the African population is understudied. Findings from these studies could only explain 25% OFCs genetic risk factors. Risk loci which have been associated with OFCs are population specific and the high genetic variation within the African genome provide opportunity for novel discovery. In order to identify new genetic risk factors in OFCs developmental pathogenesis we employed novel analytical approaches. First, using the African nonsyndromic OFCs (nsOFCs) common polymorphisms data we conducted a genome-wide association studies testing the effect of Gene-by-sex (GxSex) interaction on the risk of nsOFCs. We identified a novel risk locus on chromosome 8p22 which is in topologically associating domain (TAD) with craniofacially expressed and enriched genes during embryonic development. Whole-exome sequencing analysis found pathogenic variants of some of these genes in nsOFCs cohort providing further evidence of these genes in cleft pathogenesis. Secondly, we conducted whole-genome sequencing analysis of nsCL/P African case-parent trios in order to identify novel pathogenic mutations. We identified pathogenic de-novo mutations (DNMs) in genes with evidence of their roles in craniofacial development and OFCs pathogenesis. Some of these genes are enriched in neural crest migration, lip, and palate developmental process. In addition to these DNMs, we identified pathogenic mutations in a novel cleft candidate gene, AFDN. Computational analyses suggest that the mutations in Afadin affect its interactions with cleft candidate gene products, notable among them being nectins. Perturbations of these interactions have been reported in syndromic cleft. In summary, we employed several approaches to investigate the African genome for genetic risks to nsOFCs pathogenesis and found novel risk factors and plausible mechanism involved which could serve as bedrock for effective therapeutic intervention targeted at prevention. Additionally, these findings provide further evidence supporting the need to increase genetic studies in the African population.