Using population mixtures to optimize the utility of genomic databases

Linkage disequilibrium and association study design in India

T. J. Pemberton, M. Jakobsson, Don Conrad, G. Coop, J. D. Wall, J. K. Pritchard, P. I. Patel, N. A. Rosenberg

Research output: Contribution to journalArticle

30 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)535-546
Number of pages12
JournalAnnals of Human Genetics
Volume72
Issue number4
DOIs
StatePublished - Jul 1 2008
Externally publishedYes

Fingerprint

Linkage Disequilibrium
India
Databases
Haplotypes
Population
Single Nucleotide Polymorphism
HapMap Project
Genotype

Keywords

  • Association mapping
  • Bengali
  • Indian population
  • Portability
  • Single-nucleotide polymorphism
  • Tamil

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Using population mixtures to optimize the utility of genomic databases : Linkage disequilibrium and association study design in India. / Pemberton, T. J.; Jakobsson, M.; Conrad, Don; Coop, G.; Wall, J. D.; Pritchard, J. K.; Patel, P. I.; Rosenberg, N. A.

In: Annals of Human Genetics, Vol. 72, No. 4, 01.07.2008, p. 535-546.

Research output: Contribution to journalArticle

Pemberton, T. J. ; Jakobsson, M. ; Conrad, Don ; Coop, G. ; Wall, J. D. ; Pritchard, J. K. ; Patel, P. I. ; Rosenberg, N. A. / Using population mixtures to optimize the utility of genomic databases : Linkage disequilibrium and association study design in India. In: Annals of Human Genetics. 2008 ; Vol. 72, No. 4. pp. 535-546.
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