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A SNP Prioritization Method Using Linkage Disequilibrium Network for Disease Association Study

Authors:
Erkhembayar Jadamba
Miyoung Shin

Keywords: SNP marker; disease association study; linkage disequilibrium network; SNP ranking.

Abstract:
The problem of identifying and prioritizing various types of genetic markers including single nucleotide polymorphisms (SNPs), which are involved in human diseases such as cancer, is a one of primary challenge in current disease association studies. In this work, we propose a prioritization method, SNPRank that employs linkage disequilibrium (LD) network to improve the prioritization of candidate SNPs in disease association study. For the construction of LD network structure, we defined mutual links between SNPs based on r2 > 0.6, and prioritized such SNPs that are linked to other highly ranked SNPs. For experiments, we applied our method to identify SNP markers associated with prostate cancers. The results showed that the proposed method can improve upon existing approaches by newly finding disease related SNPs which could not be identified by existing approaches.

Pages: 86 to 88

Copyright: Copyright (c) IARIA, 2012

Publication date: April 29, 2012

Published in: conference

ISSN: 2308-4065

ISBN: 978-1-61208-224-0

Location: Chamonix, France

Dates: from April 29, 2012 to May 4, 2012