Association studies and direct DNA sequencing implicate some known genetic susceptibility loci in the etiology of nonsyndromic orofacial clefts in sub-Saharan African populations

Orofacial clefts (OFCs) are congenital dysmorphologies of the human face and oral cavity, with a global incidence of 1 per 700 live births. These anomalies exhibit multifactorial pattern of inheritance, with both genetic and environmental factors playing crucial roles. Many loci have been implicated in the aetiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) in populations of Asian and European ancestries through genome-wide association studies (GWAS) and candidate gene studies. However, few populations of African descent have been studied to date. Here, we show evidence of association of some loci with NSCL/P and nonsyndromic cleft palate only (NSCPO) in cohorts from Africa (Ghana, Ethiopia and Nigeria). We genotyped 48 SNPs that were selected from previous GWAS and candidate gene studies. These markers were successfully genotyped on 701 NSCL/P and 163 NSCPO cases, 1070 unaffected relatives and 1078 unrelated controls. We also directly sequenced 7 genes in 184 nonsyndromic OFC (NSOFC) cases and 96 controls from Ghana. Population-specific associations were observed in the case-control analyses of the sub-populations, with West African subpopulations (Ghana and Nigeria) showing similar pattern of associations. In meta-analyses of the case-control cohort, PAX7 (rs742071, p=5.10×10-03), 8q24 (rs987525, p=1.22×10-03) and VAX1 (rs7078160, p=0.04) were nominally associated with NSCL/P; MSX1 (rs115200552, p=0.01), TULP4 (rs651333, p=0.04), CRISPLD2 (rs4783099, p=0.02) and NOG1 (rs17760296, p=0.04) were nominally associated with NSCPO. Moreover, 7 loci exhibited evidence of threshold over-transmission in NSOFC cases in both transmission disequilibrium test (TDT) and family-based association for disease traits (DFAM) analyses. Through DNA sequencing, we also identified two novel, rare, potentially pathogenic variants (p.Asn323Asp and p.Lys426IlefsTer6) in ARHGAP29. In conclusion, we have shown evidence of association of many loci with NSCL/P and NSCPO. To the best of our knowledge, our study is the first to demonstrate any of these association signals in any African population.