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Towards understanding the low prevalence of H elicobacter pylori in M alays: Genetic variants among Helicobacter pylori ‐negative ethnic M alays in the north‐eastern region of Peninsular M alaysia and H an C hinese and S outh I ndians
Author(s) -
Maran Sathiya,
Lee Yeong Yeh,
Xu Shu Hua,
Raj Mahendra Sundramoorthy,
Abdul Majid Noorizan,
Choo Keng Ee,
Zilfalil Bin Alwi,
Graham David Y.
Publication year - 2013
Publication title -
journal of digestive diseases
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.684
H-Index - 51
eISSN - 1751-2980
pISSN - 1751-2972
DOI - 10.1111/1751-2980.12023
Subject(s) - single nucleotide polymorphism , snp , genotyping , medicine , genotype , helicobacter pylori , genetics , allele , snp genotyping , allele frequency , gene , biology
Objectives To identify gene polymorphisms that differ between M alays, H an C hinese and S outh I ndians, and to identify candidate genes for the investigation of their role in protecting M alays from H elicobacter pylori ( H. pylori ) infection. Methods M alay participants born and residing in K elantan with a documented absence of H . pylori infection were studied. Venous blood was used for genotyping using the A ffymetrix 50K Xba I kit. CEL files from 141 H an C hinese and 76 S outh I ndians were analyzed to compare their allele frequency with that of the M alays using fixation index ( F ST ) calculation. The single nucleotide polymorphisms ( SNP s) with the highest allele frequency (outliers) were then examined for their functional characteristics using F ‐ SNP software and the E ntrez G ene database. Results: In all, 37 M alays were enrolled in the study; of whom 7 were excluded for low genotyping call rates. The average F ST estimated from the genome‐wide data were 0.038 (Malays in Kelantan vs the South Indians), 0.015 (Malays in Kelantan vs Han Chinese) and 0.066 (Han Chinese vs South Indians), respectively. The outlier gene variants present in M alays with functional characteristics were C7orf10 ( F ST 0.29988), TSTD2 ( F ST 0.43278), SMG 7 ( F ST 0.29877) and XPA ( F ST 0.43393 and 0.43644). Conclusion Genetic variants possibly related to protection against H . pylori infection in ethnic M alays from the north‐eastern region of Peninsular M alaysia were identified for testing in subsequent trials among infected and uninfected M alays.