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PMID: 18513279 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India.

Annals of human genetics ·Vol. 72 ·No. Pt 4 ·2008-07-00 ·Pages 535-46

Pemberton TJ, Jakobsson M, Conrad DF, Coop G, Wall JD, Pritchard JK, Patel PI, Rosenberg NA

Abstract

When performing association studies in populations that have not been the focus of large-scale investigations of haplotype variation, it is often helpful to rely on genomic databases in other populations for study design and analysis - such as in the selection of tag SNPs and in the imputation of missing genotypes. One way of improving the use of these databases is to rely on a mixture of database samples that is similar to the population of interest, rather than using the single most similar database sample. We demonstrate the effectiveness of the mixture approach in the application of African, European, and East Asian HapMap samples for tag SNP selection in populations from India, a genetically intermediate region underrepresented in genomic studies of haplotype variation.

MeSH Terms
Databases, Genetic/standards Genetics, Population Genome, Human Haplotypes Humans India Linkage Disequilibrium Polymorphism, Single Nucleotide Population Groups/genetics Research Design
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Pemberton T J
Institute for Genetic Medicine, University of Southern California, 2250 Alcazar St., Los Angeles, California 90033, USA.
Jakobsson M
Conrad D F
Coop G
Wall J D
Pritchard J K
Patel P I
Rosenberg N A
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Article Info
Journal
Annals of human genetics
Abbr.
Ann Hum Genet
ISSN
0003-4800
DOI
10.1111/j.1469-1809.2008.00457.x
Published
2008-07-00
Epub
2007-00-30
Pages
535-46
Language
English
Region
England
NLM ID
0416661
PMCID
PMC2495051
Subset
IM
Grants
NCRR NIH HHS · RR10600-01 · United States
NIGMS NIH HHS · R01 GM081441 · United States
NCI NIH HHS · C06 CA062528 · United States
NCRR NIH HHS · RR14514-01 · United States
NIGMS NIH HHS · R01 GM081441-02 · United States
NIGMS NIH HHS · GM081441 · United States
NCRR NIH HHS · C06 RR014514 · United States
NCI NIH HHS · CA62528-01 · United States
External Links
PubMed source DOI: 10.1111/j.1469-1809.2008.00457.x PMC Full Text View journal details
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