Thursday, August 30, 2007

SLC24A5 and population differentiation

Unfortunately, I don't have full text access to this one. SLC24A5 is a gene that was found to account for about 30% (I believe) of skin color variation between Africans and Europeans. It is also used as an AIM (ancestry informative marker) in admixture studies. Here are links to some other posts I have regarding the gene (here, here, here) and the paper in Science that originally described the locus in zebrafish and made the connection to humans.
In this paper, they find that using this locus in addition to Y-SNPs, it becomes feasible to differentiate some population groups.

The golden gene (SLC24A5) differentiates US sub-populations within the ethnically admixed Y-SNP haplogroups.

Sims LM, Ballantyne J.

Leg Med (Tokyo) 2007 Aug 24; [Epub ahead of print]
Abstract: Y-SNPs are currently being investigated for their potential to predict the ethnogeographic origin of the donor of a crime scene sample. Unfortunately, due to the presence of genetically admixed individuals within ethnic sub-populations within a particular haplogroup (hg), it is sometimes difficult to predict the ethnogeographic ancestry of an individual using only Y-SNPs. In the present work we determine the feasibility of using a combination of the golden pigmentation gene (SLC24A5) SNP and recently described high resolution Y-SNP markers to distinguish some of the different ethnic groups within particular Y-SNP hgs. Four hundred twenty-four individuals (128 African, 206 European, 50 Hispanic/Latin, 20 Pakistan, 20 E.Asian/Indian) were typed for a SNP within the golden gene. The Y-SNP hg was determined for all males and it was found that many of the European derived hg possessed a significant amount of ethnic admixture, with R1b3 having the most. We show the use of the golden gene, in combination with more informative Y-SNPs (U152, U106, and M222) and those that define the major hg, can differentiate between most of the African vs. European and African vs. E. Asian members of these heterogeneous populations.

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