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In silico analysis of Single Nucleotide Polymorphisms (SNPs) in the Heparin-Binding EGF-like Growth Factor (HBEGF) gene and their allelic profiles in the Sri Lankan population: a comprehensive approach to prioritise SNPs for candidate gene studies

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Author(s): G.Gayani Harendra | Rohan W. Jayasekara | Vajira H.W. Dissanayake

Journal: Sri Lanka Journal of Bio-Medical Informatics
ISSN 2012-6077

Volume: 2;
Issue: 1;
Start page: 21;
Date: 2011;
Original page

Keywords: In silico analysis | Single Nucleotide Polymorphisms | Heparin-Binding EGF-like growth factor | HBEGF | allelic profiles | Sri Lankan population | candidate gene studies

ABSTRACT
In this paper, using the Heparin-Binding EGF-like growth factor (HBEGF) gene, we illustrate a comprehensive approach to select the most appropriate SNP markers for molecular epidemiological studies. Initially an in silico functional analysis was undertaken to verify the SNPs that regulate HBEGF expression. Thereafter based on predefined criteria (the significance of the function identified, ability to represent other SNPs in the gene (being a tagSNP), presence within an evolutionary conserved region, validation status of the SNP, and the minor allele frequency of the SNP) SNPs with putative functional effects were prioritised to identify the most appropriate HBEGF markers for molecular epidemiological studies. Using 30 Sinhalese men and women, we further established the allele and genotype frequencies of the seven highest priority SNPs identified. These frequencies were compared with those of HapMap populations to understand the genetic identity of the Sinhalese in relation to HapMap populations.
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