Association analysis of SNPs in GRHL3, FAF1, and KCNJ2 with NSCPO sub‐phenotypes in Han Chinese

Abstract

Objectives Non‐syndromic cleft palate only (NSCPO) is a common congenital deformity with complex etiologies. GRHL3, FAF1, and KCNJ2 have been reported to be involved in the pathogenesis of NSCPO. Up till now, there have been no replication studies based on large Han Chinese. Therefore, this study aimed to investigate associations between GRHL3, FAF1, KCNJ2, and NSCPO sub‐phenotypes patients in Han Chinese. Materials and Methods Firstly, we selected 2 SNPs based on previous literatures: FAF1 (rs3827730) and GRHL3 (rs41268753). Also, we selected 8 tagSNPs in GRHL3 (rs557811, rs609352, rs10903078, rs6659209, rs12401714, rs12568599, rs3887581, rs12024148) and 2 tagSNPs in KCNJ2 (rs75855040 and rs236514). Afterward, we evaluated these SNPs among 1668 NSCPO patients and 1811 normal controls from Han Chinese. Following data were analyzed by PLINK and Haploview program. Results Association analysis under additive model showed that allele A at rs12568599 in GRHL3 gene is significantly associated with NSCPO (p = 0.0034, OR = 1.38 and 95%CI: 1.11–1.72) and its sub‐phenotype incomplete cleft palate (ICP) (p = 0.0039, OR = 1.4 and 95%CI: 1.11–1.75), and it could increase the risk of both NSCPO and ICP. Conclusions This study firstly found that rs12568599 in GRHL3 is associated with NSCPO and ICP in Han Chinese, indicating that sub‐phenotypes of NSCPO have different etiologies.

Integrated Analysis of the Association Between Variants at PAX7 and NSCL/P in the Han Population

“…Sliding window-based haplotype association tested with Generalized Linear Models (GLMs) were performed using a logistic regression model to examine the effect of a haplotype of various lengths on the risk of NSCL/P and its subtypes. 17 Interactions between SNPs were analyzed to explore whether the SNPs functioned independently using the MB-MDR package for R.…”