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

Abstract

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 (χ2=6.25, P=0.012). Conclusion shroom2 gene is closely related to CHPS in Chinese Han population. Key words: Gene, Shroom2; Oligonucleotide array sequence analysis; Pyloric stenosis, hypertrophic