A novel statistical algorithm for enhancing the utility of HapMap data to design genomic association studies in non-HapMap populations. (1st January 2011)

• Record Type: Journal Article
• Authors: Sarkar-Roy, Neeta; Mondal, Debabrata; Bhattacharya, Paramita; Majumder, Partha
• Is Part Of: International journal of data mining and bioinformatics. Volume 5:Number 6(2011)
• Page Start: 706
• Page End: 716
• Publication Date: 2011-01-01
• Subjects: linkage disequilibrium -- MAF -- minor allele frequency -- heterozygosity -- haplotype -- tagSNP -- portability; Data mining -- Periodicals; Bioinformatics -- Periodicals; 006.312
• DOI: 10.1504/IJDMB.2011.045418
• Languages: English
• ISSNs: 1748-5673

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.