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

Zhaohui S. Qin; Shyam Gopalakrishnan; Gonçalo R. Abecasis

doi:10.1093/bioinformatics/bti762

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

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

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

47 Citationer (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.

Originalsprog	Engelsk
Tidsskrift	Bioinformatics
Vol/bind	22
Udgave nummer	2
Sider (fra-til)	220-225
Antal sider	6
ISSN	1367-4803
DOI	https://doi.org/10.1093/bioinformatics/bti762
Status	Udgivet - 2006
Udgivet eksternt	Ja

Bibliografisk note

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.

Adgang til dokumentet

10.1093/bioinformatics/bti762

Biblioteksadgang?

Tjek tilgængelighed hos det Kgl. Bibliotek

Citationsformater

@article{d2b17ad861574a50ad4950021f6b0198,

title = "An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria",

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.",

author = "Qin, {Zhaohui S.} and Shyam Gopalakrishnan and Abecasis, {Gon{\c c}alo R.}",

note = "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.",

year = "2006",

doi = "10.1093/bioinformatics/bti762",

language = "English",

volume = "22",

pages = "220--225",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "2",

}

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

SN - 1367-4803

VL - 22

SP - 220

EP - 225

JO - Bioinformatics

JF - Bioinformatics

IS - 2

ER -