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PMID: 18482828 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

HapMap tagSNP transferability in multiple populations: general guidelines.

Genomics ·Vol. 92 ·No. 1 ·2008-07-00 ·Pages 41-51

Xing J, Witherspoon DJ, Watkins WS, Zhang Y, Tolpinrud W, Jorde LB

Abstract

Linkage disequilibrium (LD) has received much attention recently because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian sample and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r(2) >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations.

MeSH Terms
Animals Chromosome Mapping Gene Frequency Genetic Diseases, Inborn/genetics Genome, Human Human Genome Project Humans Linkage Disequilibrium Polymorphism, Single Nucleotide Racial Groups/genetics
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Xing Jinchuan
Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
Witherspoon David J
Watkins W Scott
Zhang Yuhua
Tolpinrud Whitney
Jorde Lynn B
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Article Info
Journal
Genomics
Abbr.
Genomics
ISSN
1089-8646
DOI
10.1016/j.ygeno.2008.03.011
Published
2008-07-00
Epub
2008-00-14
Pages
41-51
Language
English
Region
United States
NLM ID
8800135
PMCID
PMC2471876
Subset
IM
Grants
NIGMS NIH HHS · R01 GM059290-07 · United States
NHLBI NIH HHS · HL-070048 · United States
NIGMS NIH HHS · R01 GM059290 · United States
NIGMS NIH HHS · GM-59290 · United States
NHLBI NIH HHS · R01 HL070048 · United States
External Links
PubMed source DOI: 10.1016/j.ygeno.2008.03.011 PMC Full Text View journal details
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