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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

Authors:

G.Gayani Harendra ,

PhD Student, Human Genetics Unit, Faculty of Medicine, University of Colombo, LK
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Rohan W. Jayasekara,

Chair and Senior Professor of Anatomy; Director and Medical Geneticist, Human Genetics Unit, Faculty of Medicine, University of Colombo, LK
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Vajira H.W. Dissanayake

Professor, Department of Anatomy; Medical Geneticist, Human Genetics Unit, Faculty of Medicine, University of Colombo, LK
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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.

DOI: http://dx.doi.org/10.4038/sljbmi.v2i1.2926

Sri Lanka Journal of Bio-Medical Informatics 2011;2:21-37

 

How to Cite: Harendra, G.G., Jayasekara, R.W. & Dissanayake, V.H.W., (2011). 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. Sri Lanka Journal of Bio-Medical Informatics. 2(1), pp.21–37. DOI: http://doi.org/10.4038/sljbmi.v2i1.2926
Published on 07 Nov 2011.
Peer Reviewed

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