Monday, October 29, 2007

Genomewide association of skin color in South Asians

I liked this paper quite a lot. It looked at natural variation in skin color among people from South Asia. (see abstract below)
What they did is looked at 1.6 million SNPs in the individuals in the top 20% of skin darkness versus individuals in the bottom 20% in skin darkness.
Razib has an extensive post on this paper. I'm going to follow the FAQ format that John Hawks sometimes uses (only two questions here, though):

Why this is new and exciting?

According to the authors this is the first genome wide association study on skin pigmentation They focus on subjects who come from a somewhat localized population or set of populations (India, Pakistan, Bangladesh, Sri Lanka), but that have a wide range of skin darkness. One potential caveat is that the subjects live in the UK, thereby minimizing degree of skin darkness, especially given that the researchers use points of measurement that are not all that sun-hidden (forearm and just above the elbow).

So what does it say about the genetics of skin color?

They find the usual suspects (TYR, SLC24A5, and SLC45A2). This can be surprising or unsurprising depending on how you look at it. First it highlights that the effect of SLC24A5 (associated with light skin color in Europeans but not Asians) extends all the way to South Asia. This could be interpreted in several ways. The fact that they find only three genes with strong associations is intriguing, and the fact that SLC24A5 accounts for 30% of skin color variation confirms earlier studies and may highlight once again that skin color may not be controlled by all that many loci... Although, the authors mention that this is likely an underestimate because of reduced power due to the Bonferroni correction.
Lastly, they also state that the "contributions of these polymorphisms to skin pigmentation were found to be independent and additive across genes,"

A Genomewide Association Study of Skin Pigmentation in a South Asian Population

Renee P. Stokowski, P. V. Krishna Pant, Tony Dadd, Amelia Fereday, David A. Hinds, Carl Jarman, Wendy Filsell, Rebecca S. Ginger, Martin R. Green, Frans J. van der Ouderaa, and David R. Cox

The American Journal of Human Genetics, volume 81 (2007), page 000
We have conducted a multistage genomewide association study, using 1,620,742 single-nucleotide polymorphisms to systematically investigate the genetic factors influencing intrinsic skin pigmentation in a population of South Asian descent. Polymorphisms in three genes SLC24A5, TYR, and SLC45A2 yielded highly significant replicated associations with skin-reflectance measurements, an indirect measure of melanin content in the skin. The associations detected in these three genes, in an additive manner, collectively account for a large fraction of the natural variation of skin pigmentation in a South Asian population. Our study is the first to interrogate polymorphisms across the genome, to find genetic determinants of the natural variation of skin pigmentation within a human population.

No comments:

Locations of visitors to this page