Identification of causal genes for nonsyndromic cleft palate only using whole exome sequencing
Final Report Abstract
Cleft palate only (CPO) is the second most common form of orofacial clefting. About half of the affected persons have a syndrome. Affected persons without further abnormalities are referred to individuals with a "non-syndromic cleft palate" (nsCPO). Epidemiologic data indicate that nsCPO has a multifactorial etiology. Population-based studies have found high recurrence risks in first-degree relatives of affected individuals compared with the incidence in the general population. The heritability of nsCPO is estimated to be approximately 90%. Genome-wide association studies have so far identified only ten genome-wide significant risk loci for nsCPO, significantly more limited findings than have thus been obtained for the non-syndromic cleft lip with/without cleft palate. It is reasonable to assume that rare genetic variants with a high effect size play a stronger role in the development of nsCPO than in cleft lip with/without cleft palate. Reports of families in which nsCPO occurs in several successive generations, as well as a stable incidence in areas with high infant mortality and correspondingly low reproductive rates of affecteds, suggest dominant heritable mutations or dominant de novo mutations. The aim of the project was an exome-wide sequencing in nsCPO trios (trio = affected person and their two parents). In a follow-up project, dominant de novo mutations in particular will be identified. The genes in which such variants are localized are potential candidate genes for nsCPO. In the course of the project, 342 individuals were sequenced exome-wide, 124 with nsCPO and 218 non-affected relatives. The studied individuals can be classified according to family structure into 84 trios and 18 families with two or more affected individuals (so-called multiplex families). The analysis of the data set is not part of the proposed project and is ongoing. A preliminary bioinformatic analysis of the data of 43 nsCPO trios revealed 461 potential de novo mutations. After stringent quality control and prioritization of mutations, 46 mutations remained in 46 potential candidate genes, including genes already associated with embryonic development or orofacial clefts in animal models. Protein-protein interaction analysis revealed a statistically significant enrichment of interactions between candidate genes, which may indicate common biological pathways. The preliminary analysis of the partial dataset already shows the great value of the dataset generated here, which can be used to identify further candidate genes, and thus new risk factors and signaling pathways for nsCPO. A follow-up application, in which the generated candidate genes will be processed in a resequencing study and in the animal model, is already in progress.
