TY - JOUR
T1 - An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
AU - Qin, Zhaohui S.
AU - Gopalakrishnan, Shyam
AU - Abecasis, Gonçalo R.
N1 - Funding Information:
We are grateful to Drs Mike Boehnke, Randy Pruim and the three anonymous reviewers for critical comments on an early version of this manuscript. This work is partially supported by NIH RO1-HG002651-01 to G.A.
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
U2 - 10.1093/bioinformatics/bti762
DO - 10.1093/bioinformatics/bti762
M3 - Journal article
C2 - 16269414
AN - SCOPUS:32144431911
VL - 22
SP - 220
EP - 225
JO - Bioinformatics (Online)
JF - Bioinformatics (Online)
SN - 1367-4811
IS - 2
ER -