Investigating the missing heritability for nonsyndromic orofacial clefts in an African population

Nonsyndromic orofacial clefts (NSOFCs) are the most common birth defects affecting the head and neck. These defects have significant medical, psychological, and financial implications. Genetic alterations are important factors contributing to the development of these defects. Previous genetic studies on NSOFCs were largely among individuals of European descent and have led to the identification of over 60 genetic risk loci, explaining 20-30 % of the estimated heritability for NSOFCs. Therefore, to identify the missing heritability, we investigated the genetic causes of NSOFCs in an African population - the most genetically diverse population. Our study replicated and meta-analyzed suggestive genome-wide significant signals from the first African genome-wide association study on NSOFCs. Through this approach, we identified additional novel genome-wide significant loci (10q24 and 2q22) and replicated some of the previously reported ones (MTHFD1, PTCH1, and 8q24) contributing to the risk of NSOFCs. Pathway-based analysis revealed that cell adhesion and neurogenesis were highly associated with NSOFCs. In addition, we evaluated the contributions of rare genetic variations by analyzing rare coding variants. We identified 18 genes, including both novel and known genes, harboring rare variants associated with NSOFCs. Subsequently, we prioritized 11 genes with robust expression in relevant craniofacial structures during human face development of which five (PRDM16, MASP2, ALKBH8, CENPF, and PDZD8 genes) have been previously implicated in vertebrate craniofacial development and diseases. Furthermore, we checked for genetic overlap between the two major NSOFC phenotypes (NSCL/P and NSCPO) and identified three genetic variations that influence the risk for both phenotypes in opposite directions. Using mouse transcriptomics data, we identified consistently expressed and enriched genes in relevant craniofacial structures within the same TAD (1MB) as the variants. Subsequently, we prioritized MDN1, MAP3k7, KMT2A, ARCN1, and VDAC2 genes as top candidates for their potential roles in NSOFCs pathogenesis. Overall, our studies demonstrated the uniqueness of the African population in uncovering novel loci associated with NSOFCs. We replicated some of the previously reported loci and discovered novel loci. Insights from mouse and human transcriptomics data provided valuable evidence underpinning these associations and the plausible mechanisms. Thus, our findings can lay the foundation for novel therapeutic interventions and prevention strategies for NSOFCs.