Whole Genome Sequencing of Discordant Monozygotic Twins Reveals Regulatory Variants Associated With Nonsyndromic Orofacial Clefts.

Monozygotic (MZ) twins are expected to share nearly identical genomes, yet a substantial proportion is discordant for complex diseases like nonsyndromic orofacial clefts (nsOFC). This suggests a role for postzygotic discordant genetic variations and other developmental mechanisms. In this study, we performed whole genome sequencing of two MZ twin pairs of African ancestry who were discordant for nsOFC to identify genetic variants that may contribute to phenotypic discordance. Following quality control and genotype-level filtering, we identified 37,271 variants that were present exclusively in the affected twins. Of these, 431 variants were predicted by CADD to have deleterious effects. Among these, 66 were in protein-coding regions, including 2 predicted protein-altering missense variants and splice-site variants. The remaining 365 variants were in noncoding regions including putative craniofacial enhancers. Some of these variants are rare (MAF < 0.01) and were predicted to alter transcription factor binding or disrupt local chromatin architecture within putative craniofacial enhancers located near genes with established roles in craniofacial development, including COL27A1, MPHOSPH8, and SPTBN1. In addition, some common variants previously associated with noncraniofacial traits were also predicted to affect regulatory activity of putative craniofacial enhancers near craniofacial genes. This raises the possibility of pleiotropic regulatory effects that warrant further investigation. Overall, this study identified a set of candidate coding and regulatory variants in MZ twins discordant for nsOFC,providing targets for future functional investigations. We also proposed an overarching genetic mechanism for the prioritized discordant variants.