An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria

Zhaohui S. Qin*, Shyam Gopalakrishnan, Gonçalo R. Abecasis

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

46 Citations (Scopus)

Abstract

Motivation: Selecting SNP markers for genome-wide association studies is an important and challenging task. The goal is to minimize the number of markers selected for genotyping in a particular platform and therefore reduce genotyping cost while simultaneously maximizing the information content provided by selected markers. Results: We devised an improved a lgorithm for tagSNP selection using the pairwise r2 criterion. We first break down large marker sets into disjoint pieces, where more exhaustive searches can replace the greedy algorithm for tagSNP selection. These exhaustive searches lead to smaller tagSNP sets being generated. In addition, our method evaluates multiple solutions that are equivalent according to the linkage disequilibrium criteria to accommodate additional constraints. Its performance was assessed using HapMap data.

Original languageEnglish
JournalBioinformatics
Volume22
Issue number2
Pages (from-to)220-225
Number of pages6
ISSN1367-4803
DOIs
Publication statusPublished - 2006
Externally publishedYes

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