Identification of functional non-coding variants associated with orofacial cleft [RNA-Seq]
Oral facial cleft (OFC) is a multifactorial disorder that can present as a cleft lip with or without cleft palate (CL/P) or a cleft palate only. Genome wide association studies (GWAS) of isolated OFC have identified common single nucleotide polymorphisms (SNPs) at the 1q32/IRF6 locus and many other loci where, like IRF6, the gene presumed to be relevant to OFC risk is expressed in embryonic oral epithelium. To identify the functional subset of SNPs at eight such loci we conducted a massively parallel reporter assay in a cell line derived from fetal oral epithelium, revealing SNPs with allele-specific effects on enhancer activity. Overall design: RNA-sequencing of a fetal oral epithelial cell line (GMSM-K) to characterize its epithelial features.