Association of polymorphisms of IRF6 to non-syndromic cleft lip with or without palate in a Guangdong population

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is the most common birth defect. The gene interferon regulatory factor 6 (IRF6) is the most studied candidate-cause of clefts of the lip, palate, or both. Variations of IRF6 are associated with ethnicity. We investigated the presence of 8 tag SNPs of IRF6 in residents of Guangdong province: 126 patients with NSCL/P (29 with cleft lip only [CLO], 45 with cleft palate only [CPO], 52 with cleft lip and palate [CLP]), and 140 healthy individuals. After genotyping, associations between the tag SNPs and NSCL/P were based on results of allele and genotype frequency, multivariate logistic regression, linkage disequilibrium, and haplotype analysis. The IRF6 polymorphisms rs2236909 T/C, rs2236908 C/G, rs2236907 G/T, rs2235375 C/G, and rs2235373 C/T appeared linked and may belong to the same haplotypes. They may increase risk for NSCL/P but are not linked with risk factor rs2235371 G/A. SNPs rs595918 (C > T) and rs861019 (T > C) are protective against NSCL/P. Thus, these SNPs of IRF6 are present in residents of Guangdong province and are associated with risk of CLP, CPO and CLO.