目的:非综合征性唇裂伴或不伴腭裂(NSCL/P)是一种常见的出生缺陷,影响每1000名活产儿1.4名,以及影响其风险的多种遗传和环境风险因素。一切已知的遗传风险身分所占的遗传力比例较小。几位作者认为,亲源效应(PoO)可能在这种复杂和异质畸形的病因中起重要作用。为了阐明刺猬(HH)通路中PTCH1,PTCH2,SHH和SMO与NSCL/P之间的遗传关联,以及在中国案例家长三重奏中测试潜在的PoO效应。
方法:我们使用来自806个NSCL/P病例-亲本三重奏的HH途径基因的83个常见单核苷酸多态性(SNP)标记测试了传播不平衡测试(TDT)和PoO效应。这些三重奏来自一个国际财团,该财团是为多种族的非综合征性口腔裂隙的全基因组关联研究(GWAS)而建立的。从每个三重奏收集DNA样品。在TDT测试和PoO效应中都进行了基于单标记和单倍型的分析。如果SNPs(Ⅰ)的呼叫率<95%,则将其排除在外,(2)具有<0.05的次要等位基因频率(MAF),(3)在所有三元组中具有>5%的孟德尔错误,(iv)在父母中的基因型分布偏离了Hardy-Weinberg平衡(HWE)(P<0.0001)。该过程是使用Plink(版本1.07,
http://pngu。mgh.哈佛。edu/~purcell/plink/data.shtml)。TDT测试在Plinkv1.07中进行。使用R包v3.4.2中实现的Haplinv6.2.1,使用对数线性模型来探索PoO效应。使用Bonferroni校正评估显著性水平。
结果:由于MAF低,共有18个SNP下降,因此留下65个SNP可用于分析。因此,Bonferroni阈值为7.7×10-4(0.05/65)。在SNP(PTCH1中的rs4448343,P=0.023)和六个单倍型(rs10512249-rs4448343,rs1461208-rs7786445,rs10512249-rs4448343,rs16909865-r10512s87r814s77343,rs28r8115s208-8r64358<,共有六个单倍型(rs288765-rs1233563,rs12537550-rs11765352,rs872723-rs288765-rs1233563,rs288765-rs1233563-rs288756,rs6459952-rs12537550-rs11765352和rs693550.05-Posr65Bonferroni校正后,结果均无统计学意义(P>7.7×10-4)。
结论:在这项研究中,HH通路内的SNP与NSCL/P或PoO效应的风险之间没有显著关联。
OBJECTIVE: Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect, affecting 1.4 per 1 000 live births, and multiple genetic and environmental risk factors influencing its risk. All the known genetic risk factors accounted for a small proportion of the heritability. Several authors have suggested parent-of-origin effects (PoO) may play an important role in the etiology of this complex and heterogeneous malformation. To clarify the genetic association between PTCH1, PTCH2, SHH and SMO in hedgehog (HH) pathway and NSCL/P, as well as testing for potential PoO effects in Chinese
case-parent trios.
METHODS: We tested for transmission disequilibrium tests (TDT) and PoO effects using 83 common single nucleotide polymorphic (SNP) markers of HH pathway genes from 806 NSCL/P
case-parent trios. These trios were drawn from an international consortium established for a genome-wide association studies (GWAS) of non-syndromic oral clefts of multiple ethnicities. DNA samples were collected from each trio. Single marker and haplotype based analysis were performed both in TDT tests and PoO effects. SNPs were excluded if they (ⅰ) had a call rate of < 95%, (ⅱ) had a minor allele frequency (MAF) of < 0.05, (ⅲ) had Mendelian errors over all trios of >5%, (ⅳ) had a genotype distribution in the parents that deviated from the Hardy-Weinberg equilibrium (HWE) (P < 0.000 1). The process was done using Plink (version 1.07,
http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml). TDT test was performed in Plink v1.07. A log-linear model was used to explore PoO effects using Haplin v6.2.1 as implemented in R package v3.4.2. Significance level was assessed using the Bonferroni correction.
RESULTS: A total of 18 SNPs were dropped due to low MAF, thus leaving 65 SNPs available for the analysis. Thus the Bonferroni threshold was 7.7×10-4 (0.05/65). Nominal significant association with NSCL/P was found at a SNP (rs4448343 in PTCH1, P=0.023) and six haplotypes (rs10512249-rs4448343, rs1461208-rs7786445, rs10512249-rs4448343, rs16909865-rs10512249-rs4448343, rs1461208-rs7786445-rs12698335, and rs288756-rs288758-rs1151790, P < 0.05). A total of six haplotypes (rs288765-rs1233563, rs12537550-rs11765352, rs872723-rs288765-rs1233563, rs288765-rs1233563-rs288756, rs6459952-rs12537550-rs11765352, and rs12537550-rs11765352-rs6971211) showed PoO effect (P < 0.05). None of the results remained significant after the Bonferroni correction (P>7.7×10-4).
CONCLUSIONS: Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.