July 27, 2006

Admixture mapping in African Americans

AJHG has a preprint of an article about admixture mapping in African Americans. It seems that the next-generation SNP tests for admixture estimation, using thousands, as opposed to hundreds of markers are already here. It is probably a matter of time until someone will be able to create tests to determine "national origin", even though in many cases where nations have been formed by recent linguistic/religious/political differences such tests may prove to be impossible.

American Journal of Human Genetics (preprint)

A Genome-Wide SNP panel with High Ancestry Information for African American Admixture

Chao Tian et al.


Admixture mapping requires a genome-wide panel of relatively evenly spaced markers that can distinguish the ancestral origins of chromosomal segments in admixed individuals. Using the results of the International HapMap Project and specific selection criteria the current study has
examined the ability of selected SNPs to extract continental ancestry information in African American subjects and to explore parameters for admixture mapping. Genotyping of two linguistically diverse west African populations (Bini and Kanuri Nigerians who are Niger-Congo
(Bantu) and Nilo-Saharan speakers, respectively), European Americans and African Americans validated a genome-wide set of >4000 SNP ancestry informative markers with mean and median Fst values > 0.59 and mean and median Fisher’s information content >2.5. This set of SNPs extracted a larger amount of ancestry information in African Americans than previous reported SNP panels and provides nearly uniform coverage of the genome. Moreover in the current study, simulations show that this more informative panel improves power for admixture mapping in
African Americans when ethnicity risk ratios are modest. This is particularly important in the application of admixture mapping in complex genetic diseases for which only modest ethnicity risk ratios of relevant susceptibility genes are expected.


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