Objectives: This study aims to explore the association between single nucleotide polymorphisms (SNPs) loci near the haplotype region hg19 chr9:100560865-100660865 of the forkhead box E1 (FOXE1) gene and the occurrence of non-syndromic cleft lip with or without cleft palate (NSCL/P) in western Han Chinese population.
Methods: In the first stage, our study recruited 159 NSCL/P patients and performed targeted region sequencing to screen SNPs loci near the haplotype region of the FOXE1 gene associated with NSCL/P. In the second stage, we selected 21 common SNPs and re-enrolled 1 000 non-syndromic cleft lip only (NSCLO) patients, 1 000 non-syndromic cleft palate only (NSCPO) patients, and 1 000 normal controls to verify the association. PLINK software was used to perform Hardy-Weinberg equilibrium (HWE) test. Association analysis for common variants, gene burden analysis for rare mutations, and function prediction of SNPs with non-synonymous mutations were performed using Mutation Taster and other software programs.
Results: In the first stage, 126 variants, including 76 single nucleotide variants and 50 insertion-deletions were identified. All the included SNPs confirmed to HWE, and the results of gene burden analysis and prediction of functional harmfulness for rare variants were not statistically significant. Association analysis showed that rs13292899 of the FOXE1 gene was significantly associated with NSCL/P (P=1.85E-27) and was also correlated with NSCLO (P=6.41E-23) and non-syndromic cleft lip with cleft palate (NSCLP) (P=2.36E-15) subtypes. In the validation phase, rs79268293 (P=0.013, P=0.022), rs10983951 (P=0.009 2, P=0.007 6), rs117227387 (P=0.009 2, P=0.007 6), rs3758250 (P=0.009 2, P=0.007 6), and rs116899397 (P=0.009 2, P=0.007 6) were significantly associated with NSCLO and NSCPO; rs13292899 (P=0.008 5), rs74606599 (P=0.008 3), rs143226042 (P=0.008 3), and rs117236550 (P=0.01) were associated with the occurrence of NSCLO; and rs12343182 (P=0.008 7), rs10119760 (P=0.012), rs10113907 (P=0.012), and rs13299924 (P=0.012) were associated with the occurrence of NSCPO.
Conclusions: This study found a new susceptible SNP rs13292899 of the FOXE1 gene that is closely associated with NSCL/P and NSCLO subtype and 13 other SNPs associated with NSCLO or NSCPO.
目的: 探究叉头盒E1（FOXE1）基因所在单倍型区域hg19 chr9:100560865-100660865附近的单核苷酸多态性（SNPs）位点与中国西部汉族人群非综合征型唇腭裂（NSCL/P）发生的相关性。方法: 第一阶段纳入159名NSCL/P患者，采用目标区域捕获测序的方法，拟筛查FOXE1基因所在单倍型区域附近与NSCL/P发生相关的SNPs位点。第二阶段，选择21个常见SNPs位点，在1 000名非综合征型单纯唇裂（NSCLO）患者，1 000名非综合征型单纯腭裂（NSCPO）患者和1 000名正常对照样本中进行验证。使用PLINK软件对研究人群进行哈迪-温伯格平衡（HWE）分析，对常见变异进行关联分析，对罕见变异进行基因负荷分析并使用Mutation Taster等软件对非同义突变的SNPs进行功能预测。结果: 第一阶段，共筛选出126个变异位点，包括76个SNPs变异位点和50个插入/缺失。纳入的所有SNPs在研究人群中遵循HWE。对筛选出的罕见变异进行功能有害性预测和基因负荷分析，差异均无统计学意义；对常见变异的关联分析表明，FOXE1基因的rs13292899位点与NSCL/P发生显著相关（P=1.85E-27），并且该位点与NSCLO（P=6.41E-23）、NSCLP（P=2.36E-15）发生也有相关性。随后在验证阶段，发现rs79268293（P=0.013，P=0.022）、rs10983951（P=0.009 2，P=0.007 6）、rs117227387（P=0.009 2，P=0.007 6）、rs3758250（P=0.009 2，P=0.007 6）和rs116899397（P=0.009 2，P=0.007 6），这5个SNPs位点与NSCLO和NSCPO均有显著关联性；另外，rs13292899（P=0.008 5）、rs74606599（P=0.008 3）、rs143226042（P=0.008 3）和rs117236550（P=0.01），这4个SNPs位点与NSCLO发生相关；rs12343182（P=0.008 7）、rs10119760（P=0.012）、rs10113907（P=0.012）和rs13299924（P=0.012），这4个SNPs位点与NSCPO发生相关。结论: 本研究在FOXE1基因上发现了一个新的易感SNPs位点rs13292899与NSCL/P及NSCLO发生密切相关，以及其他13个SNPs位点与NSCLO或NSCPO发生相关。.
Keywords: association analysis; forkhead box E1 gene; non-syndromic cleft lip with or without cleft palate; single nucleotide polymorphisms; target region sequen-cing.