全基因组芯片扫描研究shroom2基因与先天性肥厚性幽门狭窄的相关性

Correlation between shroom2 gene and congenital hypertrophic pyloric stenosis：a genome-wide association study

目的：全基因组范围探讨先天性肥厚性幽门狭窄（CHPS）发病的相关基因。方法选择2006年8月至2010年10月就诊于广州市第一人民医院的CHPS患儿31例及其父母双亲为研究对象，所有入选者均为汉族。对其中23个CHPS患儿及其父母组成的核心家系采用Affymetrix GencChip-Genome-Wide Human Mapping SNP 6.0芯片进行全基因组芯片扫描，判断每个单核苷酸多态性（SNP）位点及基因型，应用传递不平衡检验（TDT）判断基因型与CHPS发病的关系。选择全基因组芯片扫描发现的有统计学意义的位点，扩大样本（31个CHPS核心家系）进行PCR及测序，进一步验证其基因型与CHPS的相关性。结果共有894135个SNP在所有23个核心家系成员中被扫描出来，总体扫描成功率达98.63%。全基因组芯片扫描结果采用Genotyping Console 4.1.3软件分析每个SNP的基因型。考虑CHPS男性发病远高于女性的特点，通过全基因组扫描结合Hardy-Weinberg平衡及P值大小，选择位于X染色体上的Shroom2基因相关SNP位点进行验证。最终选择rs12012202[c.4423A〉G]扩大样本利用PCR及测序方法进行验证，测序结果TDT分析显示其与CHPS发病密切相关（χ^2=6.25，P=0.012）。结论 shroom2基因与中国汉族人群CHPS发病密切相关。

Objective To investigate the genes related to pathogenesis of congenital hypertrophic pyloric stenosis （CHPS） through genome-wide association study （GWAS）. Methods Thirty-one CHPS children and their parents who visited Guangzhou First Municipal People＇s Hospital between August 2006 and October 2010 were included in this study. All enrolled subjects were of Han ethnicity. Twenty-three trios of CHPS children and their parents received genome-wide scan using Affymetrix GencChip- Genome-Wide Human SNP 6.0 array. Single nucleotide polymorphisms （SNP） locus and genotypes were studied. Transmission disequilibrium test （TDT） was used to determine the association between genotypes and development of CHPS. Gene loci found to be of statistically relevance by genome-wide microarray were subjected to PCR amplification and sequencing in more samples（31 CHPS trios）for further validating the correlation between genotype and CHPS. Results Totally,894 135 SNPs were identified from all 23 trios, yielding an overall success rate of 98.63%. Then the genome-wide microarray results were processed with Genotyping Console 4.1.3 software for genotyping of each SNP. Given CHPS being much more common in males than in females,we focused on SNP loci of Shroom2 gene on X chromosome for correlation validation by using genome-wide microarray in combination with Hardy-Weinberg equilibrium and proper P values. rs12012202[c.4423A〉G]was finally selected for PCR amplification and sequencing in more samples. TDT analysis of the resultant sequencing showed that the tested SNP was closely related to the pathogenesis of CHPS （χ^2=6.25,P=0.012）. Conclusion shroom2 gene is closely related to CHPS in Chinese Han population.