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北京大学学报（医学版） ›› 2020, Vol. 52 ›› Issue (5): 809-814. doi: 10.19723/j.issn.1671-167X.2020.05.003

• 论著 • 上一篇    下一篇

中国人群Hedgehog通路基因与非综合征型唇腭裂的亲源效应

李文咏1,王梦莹1,周仁1,王斯悦1,郑鸿尘1,朱洪平2,周治波2,吴涛1,3,∆(),王红1,石冰4   

  1. 1.北京大学公共卫生学院流行病与卫生统计学系,北京 100191
    2.北京大学口腔医学院·口腔医院,口腔颌面外科 国家口腔疾病临床医学研究中心 口腔数字化医疗技术和材料国家工程实验室 口腔数字医学北京市重点实验室,北京 100081
    3.卫生部生育健康重点实验室,北京 100191
    4.四川大学华西口腔医学院口腔颌面外科,口腔疾病研究国家重点实验室,成都 610041
  • 收稿日期:2018-04-26 出版日期:2020-10-18 发布日期:2020-10-15
  • 通讯作者: 吴涛 E-mail:twu@bjmu.edu.cn
  • 基金资助:
    国家自然科学基金(81102178);国家自然科学基金(81573225);北京市自然科学基金(7172115);北京大学医学交叉研究基金(BMU2017MX018)

Exploring parent-of-origin effects for non-syndromic cleft lip with or without cleft palate on PTCH1, PTCH2, SHH, SMO genes in Chinese case-parent trios

Wen-yong LI1,Meng-ying WANG1,Ren ZHOU1,Si-yue WANG1,Hong-chen ZHENG1,Hong-ping ZHU2,Zhi-bo ZHOU2,Tao WU1,3,∆(),Hong WANG1,Bing SHI4   

  1. 1. Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
    2. Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
    3. Key Laboratory of Reproductive Health, Ministry of Health, Beijing 100191, China
    4. Department of Oral and Maxillofacial Surgery, State Key Laboratory of Oral Disease, West China College of Stomatology, Sichuan University, Chengdu 610041, China
  • Received:2018-04-26 Online:2020-10-18 Published:2020-10-15
  • Contact: Tao WU E-mail:twu@bjmu.edu.cn
  • Supported by:
    National Natural Science Foundation of China(81102178);National Natural Science Foundation of China(81573225);Beijing Municipal Natural Science Foundation(7172115);Peking University Health Science Center Interdisciplinary Research Fund(BMU2017MX018)

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摘要：

目的:探索非综合征型唇腭裂(non-syndromic cleft lip with or without cleft palate,NSCL/P)这一类常见出生缺陷的可能致病机制,在Hedgehog(HH)通路基因中(PTCH1、PTCH2、SHH、SMO)探索基因多态性对NSCL/P的关联关系以及亲源效应(parent-of-origin effects,PoO)对NSCL/P发病风险的影响。方法:纳入806个中国非综合征型唇腭裂核心家系,对HH通路基因(PTCH1、PTCH2、SHH、SMO)的83个单核苷酸多态性位点(single nucleotide polymorphisms,SNPs)进行传递不平衡检验(transmission disequilibrium test,TDT), 并采用对数线性模型进行亲源效应分析。家系样本来自“唇腭裂基因和交互作用的国际合作研究”项目。采用Plink进行TDT检验;通过R软件中的Haplin v6.2.1软件包开展亲源效应分析。采用Bonferroni法进行多重检验校正。结果:经过质量控制,共纳入65个SNPs进行分析,Bonferroni显著性水平为7.7×10 -4(0.05/65)。未校正P值前,关联分析发现rs4448343与NSCL/P存在关联(P=0.023), 6个单体型(rs10512249-rs4448343、rs1461208-rs7786445、rs10512249-rs4448343、rs16909865-rs10512249-rs4448343、rs1461208-rs7786445-rs12698335、rs288756-rs288758-rs1151790)与NSCL/P存在关联(P<0.05);6个单体型(rs288765-rs1233563、rs12537550-rs11765352、rs872723-rs288765-rs1233563、rs288765-rs1233563-rs288756、rs6459952-rs12537550-rs11765352、rs12537550-rs11765352-rs6971211)具有潜在的PoO效应(P<0.05)。以上结果经过多重检验校正,均无统计学意义(P>7.7×10 -4)。结论:未发现HH通路基因多态性与NSCL/P的关联,未发现HH通路基因通过PoO效应影响NSCL/P发病风险。

关键词: 亲源效应, 非综合征型唇腭裂, HH通路基因

Abstract:

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). Conclusion: Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.

Key words: Parent-of-origin effects, Non-syndromic cleft lip with or without cleft palate, Hedgehog pathway

中图分类号: 

  • R394

图1

HH通路基因分布情况"

表1

806个中国NSCL/P核心家系分布情况"

Site Male Female Total
Taiwan 139 94 233
Shandong 193 81 274
Hubei 132 55 187
Sichuan 75 37 112
Total 539 267 806

表2

806个中国NSCL/P核心家系传递不平衡检验结果"

Type Gene Haplotype SNP ID P value
SNP PTCH1 - rs4448343 0.023
Haplotype PTCH1 AG rs10512249-rs4448343 0.025
Haplotype SHH GC rs1461208-rs7786445 0.026
Haplotype PTCH1 GA rs10512249-rs4448343 0.031
Haplotype PTCH1 CGA rs16909865-rs10512249-rs4448343 0.036
Haplotype SHH GCG rs1461208-rs7786445-rs12698335 0.036
Haplotype SHH GGC rs288756-rs288758-rs1151790 0.047

表3

806个中国NSCL/P核心家系PoO效应结果"

Gene SNP ID RRm
(95%CI)		 RRm
P value		 RRf
(95%CI)		 RRf P value RRR
(95%CI)		 RRR
P value
SHH rs288765-rs1233563 0.43
(0.15-1.29)		 0.134 1.04
(0.41-2.75)		 0.919 0.41
(0.20-0.86)		 0.018
SHH rs12537550-rs11765352 1.22
(0.87-1.71)		 0.239 0.90
(0.64-0.24)		 0.518 1.36
(1.01-1.82)		 0.036
SHH rs872723-rs288765-rs1233563 0.54
(0.23-1.29)		 0.161 1.33
(0.66-2.69)		 0.427 0.41
(0.20-0.86)		 0.017
SHH rs288765-rs1233563-rs288756 0.58
(0.28-1.20)		 0.153 1.29
(0.72-2.31)		 0.386 0.45
(0.21-0.95)		 0.035
SHH rs6459952-rs12537550-rs11765352 1.16
(0.84-1.61)		 0.366 0.81
(0.59-1.11)		 0.192 1.44
(1.06-1.95)		 0.021
SHH rs12537550-rs11765352-rs6971211 1.13
(0.83-1.56)		 0.433 0.81
(0.59-1.11)		 0.180 1.40
(1.04-1.90)		 0.025
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ISSN 1671-167X
CN 11-4691/R
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