Association of single nucleotide polymorphisms at 20q12 with nonsyndromic cleft lip with or without cleft palate in a Southern Chinese Han cohort

BACKGROUND: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation in the world. Both environment and genetics are involved with the etiology of the disease. Genome‐wide association studies have identified two single nucleotide polymorphisms (SNPs) at chromosome 20q12 to be associated with NSCL/P. The current study aimed to explore the association of the two SNPs at 20q12 with NSCL/P and different subtypes in a Southern Chinese Han cohort. METHODS: A total of 430 NSCL/P patients and 451 controls were recruited in the current study. Two SNPs including rs17820943 and rs6072081 at 20q12 were genotyped in the study cohort using Taqman SNP genotyping analysis. Chi‐Square test was used to compare allele and genotype frequencies of NSCL/P patients and control group. RESULTS: Case–control analysis showed that the allele and genotype of rs17820943 and rs6072081 were significantly associated with NSCL/P (p < .01). Comparison between subtypes of NSCL/P and controls showed that frequencies of the G allele and GG genotype of rs6072081 (p = 4.52 × 10(−4) and p = .001 respectively), and those of the T allele and TT genotype of rs17820943 (p = 6.7 × 10(−5) and p = 1.71 × 10(–4) respectively) were decreased in cleft lip and palate (CLP). No significant association of the two SNPs with cleft lip only (CLO) and cleft palate only (CPO) was found (p > .05). CONCLUSION: These results showed that rs17820943 and rs6072081 at 20q12 were associated with NSCL/P, especially with the CLP subtype in a Southern Chinese Han cohort.