Differences between the sexes among genetic variants affecting orofacial cleft birth defect risk

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PROJECT SUMMARY Orofacial clefts (OFCs) represent the most common group of craniofacial malformations in humans affecting approximately one per 1,000 live births worldwide. OFCs include cleft lip (CL), cleft palate (CP) and cleft lip with cleft palate (CLP), which can occur as isolated malformations, with another malformation or as part of a recognized malformation syndrome (often Mendelian with incomplete penetrance). OFCs are commonly categorized into two anatomically and embryologically distinct entities based on embryologic and epidemiologic patterns: cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP). Among all infants born with an OFC, 70 percent of CL/P cases and 50 percent of CP cases occur as isolated, non-syndromic malformations. Non-syndromic CL/P occurs more frequently in males than females (ratio 2:1) whereas non-syndromic CP occurs more often in females (ratio approximately 1:1.14). Substantial variation in birth prevalence rates of non- syndromic CL/P has been reported across populations, with Asian populations having higher birth prevalence rates compared to European populations, and African populations having the lowest birth prevalence rates. Risk to OFC shows strong evidence of genetic control with estimated heritability up to 90%. Recent genome- wide association studies have clearly shown multiple genes play a role in the etiology of OFCs, but with substantial heterogeneity among families and across populations. To date, approximately 50 different genes have been identified as significant in such genome-wide studies of OFCs, with about two dozen having substantial replication and/or functional studies. However, despite a long history of scientific research into the genetic control of OFC, much of the heritability remains unexplained (which may reflect the genetic heterogeneity influencing risk to OFC, where a number of different genes with both rare and common variants control risk), and it remains difficult to clearly identify underlying causal genes. Moreover, sex differences in risk to OFC and parent-of-origin effects traditionally have not been the focus of genetic studies, and X chromosome variants have largely been ignored. In this application, we are using existing genomic data from family-based studies in different ethnic groups to specifically study the underlying mechanisms for differential risk to OFC between the sexes. Specifically, we will (i) use case-parent trios to detect different genetic OFC risk effect sizes and parent of origin effects, (ii) use a novel method to characterize sex differences in the genetic architecture of OFCs accounting for potential cleft type differences and similarities, and (iii) conduct association tests for variants on the X chromosome. In addition, we will use genomic data from extended multiplex pedigrees to identify highly penetrant genomic X-linked variants. The family-based designs allow us to study common and rare variants, parent-of origin effects, and allow us to assess the impact of de novo variants. In all aims, we will attempt to use functional data from external data bases to conduct an “in silico” validation of our findings.