SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) GENOTYPIC PROFILING OF MALAY PATIENTS WITH AND WITHOUT Helicobacter pylori INFECTION IN KELANTAN
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Date
2012-04
Authors
SATHIYA, MARAN
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Publisher
Pusat Pengajian Sains Perubatan Universiti Sains Malaysia
Abstract
Since first reported in 1986 in Malaysia by the Malaysian Pathology Society, differences in the Helicobacter pylori (H. pylori) prevalence among the three major ethnics has been much characterized. The state of Kelantan, situated at the northeastern region of Peninsular Malaysia is unique with Malays comprising 90% of its population. There is an exceptionally low prevalence rate of H. pylori reported from this region, in the range of 4-5%. The exact reasons for the low prevalence rate of H. pylori infection are unknown. Environmental factors, genetic factors or a combination of both are possible explanation. The current study sets out to determine which of the genetic variant in the form of Single Nucleotide Polymorphisms (SNPs)
using the genome wide association, may play a role in protecting the Malays against H. pylori infection. A total of 23 cases (H. pylori positive) and 37 controls (H. pylori negative) were genotyped in this case-control study. High-throughput downstream analysis was conducted using the Affymetrix Genotyping Console (GTC), SVS
Golden Helix Bioinformatics Software, DAVID Bioinformatics software, FAMHAP programme and F-SNP tool. Phenotype-Genotype analysis was done in resolving the causative genetic variants causing phenotypic alterations that are manifested during H. pylori infection. We found a significant association between SNPs rs678264, rs10505799 and rs9315542 and intestinal metaplasia, dysplasia, and intestinal metaplasia with atrophic gastritis respectively. In addition we also found that the SNPs rs10502974 located within the DCC gene was associated with an increased risk of H. pylori infection among Malays in Kelantan. Finally, our study also suggested that the SNPs rs29886, rs3750370, rs3768591, rs3176670 and rs3176673 as potential
genetic variants which may protect the Malays against H. pylori infection. Hence, this study concludes the determination of candidate genetic variants associated with H. pylori infection in Malays in Kelantan for the first time using the genome wide association approach.
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Internal Medicine