Title: A novel statistical algorithm for enhancing the utility of HapMap data to design genomic association studies in non-HapMap populations

Authors: Neeta Sarkar-Roy; Debabrata Mondal; Paramita Bhattacharya; Partha Majumder

Addresses: TCG-ISI Centre for Population Genomics, Institute of Molecular Medicine, Kolkata, India. ' TCG-ISI Centre for Population Genomics, Institute of Molecular Medicine, Kolkata, India. ' TCG-ISI Centre for Population Genomics, Institute of Molecular Medicine, Kolkata, India. ' TCG-ISI Centre for Population Genomics, Institute of Molecular Medicine, Kolkata, India

Abstract: The HapMap database should be effectively used in designing disease association studies in non-HapMap populations. The efficiency of portability of tagSNPs from HapMap to non-HapMap populations is widely variable. A new algorithm is proposed for selecting SNPs from HapMap for use in non-HapMap populations by simultaneously considering and combining data on allele frequencies and linkage-disequilibrium values in the four HapMap populations. Empirical comparison and validation of the algorithm are provided by using Tagger, available HapMap data and data from an Indian population. The proposed method is shown to be efficient and effective. A software implementing this algorithm is freely available.

Keywords: linkage disequilibrium; MAF; minor allele frequency; heterozygosity; haplotype; tagSNPs; portability; genomic associations; disease association; bioinformatics; India; genetic associations; single nucleotide polymorphisms.

DOI: 10.1504/IJDMB.2011.045418

International Journal of Data Mining and Bioinformatics, 2011 Vol.5 No.6, pp.706 - 716

Received: 30 May 2009
Accepted: 28 Dec 2009
Published online: 24 Jan 2015 *

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