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Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

Larsson Omberg1*, Jacqueline Salit2, Neil Hackett2, Jennifer Fuller2, Rebecca Matthew3, Lotfi Chouchane3, Juan L Rodriguez-Flores2, Carlos Bustamante4, Ronald G Crystal2 and Jason G Mezey12*

Author Affiliations

1 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA

2 Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10021, USA

3 Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar

4 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA

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BMC Genetics 2012, 13:49  doi:10.1186/1471-2156-13-49

Published: 26 June 2012



Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries.


Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information.


By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

Human migration; Admixture; Arabian Peninsula; Qatar; Support vector machines