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Pemberton TJ, Jakobsson M, Conrad DF, Coop G, Wall JD, Pritchard JK et al.. Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Ann Hum Genet 72: 535-546

Institute for Genetic Medicine, University of Southern California, 2250 Alcazar St., Los Angeles, California 90033, USA.
Annals of Human Genetics (Impact Factor: 1.93). 08/2008; 72(Pt 4):535-46. DOI: 10.1111/j.1469-1809.2008.00457.x
Source: PubMed

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.

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    • "associated with the allele frequencies. We note that for five of the Native American populations we report on here, data exist as part of the HGDP-CEPH dataset both for STRPs (Rosenberg et al., 2002; Zhivotovsky et al., 2003) and for SNPs (Li et al., 2008; Pemberton et al., 2008). However, in those cases we have SNP data on additional individuals in those populations and have used the larger dataset. "
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