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Saturday, 11/24/2007 6:49:03 PM

Saturday, November 24, 2007 6:49:03 PM

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In collaboration with the Shriver lab, which published the Bauchet et al., 2007 paper, DNAPrint® mined the chip marker used to create the Bauchet et al., 2007 paper, looking for the SNPs that provided most of the European Ancestry Information.


Measuring European Population Stratification with Microarray Genotype Data
Author(s) Marc Bauchet, Brian McEvoy, Laurel N. Pearson, Ellen E. Quillen, Tamara Sarkisian, Kristine Hovhannesyan, Ranjan Deka, Daniel G. Bradley, and Mark D. Shriver
Identifiers The American Journal of Human Genetics, volume 80 (2007), pages 948–956
DOI: 10.1086/513477
PubMed ID: 17436249

Availability This site: PS | HTML | PDF (596.3k)
Copyright © 2007, The American Society of Human Genetics.
Abstract A proper understanding of population genetic stratificationdifferences in individual ancestry within a populationis crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of 10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Étude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.


SLC24A5 (solute carrier family 24, member 5) is a gene that is thought to be one of many genes that control skin pigmentation in humans, and therefore implicated in defining race.

Research done by a large team at Penn State University and a number of other institutions discovered that the gene has two primary alleles that differ in only one nucleotide, changing the 111th amino acid from alanine to threonine. [1][2][3]

The threonine allele was present in 98.7 to 100% among several European samples, while the alanine form was found in 93 to 100% of samples of Africans, East Asians and Indigenous Americans. The variation is a SNP polymorphism rs1426654, which had been previously shown to be second among 3011 tabulated SNPs ranked as ancestry-informative markers. They also showed that SLC24A5 explains between 25 and 38% of the European-African difference in skin melanin index.

The discovery of this gene may have interesting social consequences because of its bearing on the genetics of racial differences. It has obvious application to forensic science as well.

The SLC24A5 gene is located on the long (q) arm of chromosome 15 on position 21.1, from base pair 46,200,461 to base pair 46,221,881.

It is currently estimated that the threonine allele originated among Europeans 6,000 to 12,000 years ago.[4]

^ Lamason RL, Mohideen MA, Mest JR, et al (2005). "SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans". Science 310 (5755): 1782-6. doi:10.1126/science.1116238. PMID 16357253.
^ BBC article
^ Penn State University article
^ Gibbons A (2007). "American Association of Physical Anthropologists meeting. European skin turned pale only recently, gene suggests". Science 316 (5823): 364. doi:10.1126/science.316.5823.364a. PMID 17446367.


October 21, 2007
Eye Color and Your Genes
Although it was once thought to be a classic Mendelian trait, eye color is now well known to be subject to polygenic (i.e., multiple genes are involved) inheritance. Our current catalog of genetic variation affecting eye color is incomplete.

However, in a paper published online today in Nature Genetics (abstract here, subscription required for full paper), Dr. Kari Stefansson and colleagues at deCode Genetics report the results of a genome-wide association study focusing on eye color (in addition to hair color and freckling) as a phenotypic trait. This study adds considerably to our knowledge of the genetics of human eye color, in addition to hair color and freckling.

The authors initially studied about 3,000 Icelanders and then performed replication studies in another ~2700 Icelanders and about 1200 Dutch individuals. With respect to eye color, they found the previously reported association with OCA2 gene variants - not big news but providing confidence in the methods. However, the authors also found association of a new gene - SLC24A4 - with both eye and hair color. Additionally, two coding variants in the TYR gene were found to be associated with eye color and freckles.

Interestingly, the SLC24A4 gene is similar to SLC24A5; a SLC24A5 coding single nucleotide polymorphism has previously been shown to be associated with skin color in African-Americans and African-Caribbean populations.

The authors then went on to derive a model in which they attempted to predict eye color based on genotypes. They showed that variants in OCA2 dominate the distinction between brown and blue eyes and that the newly reported variants can contribute significantly to the more subtle distinction between blue and green eyes.

It will be interesting to see what deCode may have in mind with respect to commercialization of this new information.