Sunday, February 28, 2010

Predicting hair, eye, and skin color from a small set of SNPs

They examined the association between 75 SNPs in 24 genes and skin, eye and hair color among 789 people of various ethnic backgrounds. Since this is for forensic purposes, they were looking for a small set of SNP markers (i.e. 3) that could reliably predict these pigmentation phenotypes, independent of ethnic origin. Their sample consisted mostly of individuals of European descent, but a decent number of several other ethnic groups.

Hair color:

SLC45A2, SLC24A5 and MC1R - R squared: 76.3% (one SNP per gene listed)
Skin color:
SLC24A5, SLC45A2, ASIP - R squared: 45.7% ... interaction term of ASIP and SLC45A2 increased r-squared to 49.6% (one SNP per gene listed)
Eye color:
HERC2, SLC24A5, SLC25A2 - R squared: 76.4%... (HERC2 appears to be doing the vast majority of the explaining)

The obvious remaining question from all this is how high does the proportion of variance explained go if you use information from all markers together. Anyway, it appears that, as they mention, five SNPs in five genes account for much of the variation.
Given that most subjects were Eur, it would have been nice to see the extent to which they were driving the results, by for example, doing the same analysis only on them. In other words how different would the results be if most subjects were African or Native American etc...?
I did not know that HERC2 is adjacent (5' side) to OCA2, and contains a promoter region for OCA2.

Predicting Phenotype from Genotype: Normal Pigmentation
Valenzuela RK, Henderson MS, Walsh MH, Garrison NA, Kelch JT, Cohen-Barak O, Erickson DT, John Meaney F, Bruce Walsh J, Cheng KC, Ito S, Wakamatsu K, Frudakis T, Thomas M, Brilliant MH.
J Forensic Sci. 2010 Feb 11. [Epub ahead of print]

Abstract:Genetic information in forensic studies is largely limited to CODIS data and the ability to match samples and assign them to an individual. However, there are circumstances, in which a given DNA sample does not match anyone in the CODIS database, and no other information about the donor is available. In this study, we determined 75 SNPs in 24 genes (previously implicated in human or animal pigmentation studies) for the analysis of single- and multi-locus associations with hair, skin, and eye color in 789 individuals of various ethnic backgrounds. Using multiple linear regression modeling, five SNPs in five genes were found to account for large proportions of pigmentation variation in hair, skin, and eyes in our across-population analyses. Thus, these models may be of predictive value to determine an individual's pigmentation type from a forensic sample, independent of ethnic origin.


Charles Iliya Krempeaux said...

I wonder what this test will say about people, like me, who have had their eyes, hair, and complexion change as they got older.

Yann Klimentidis said...

that's getting complicated. I assume there's a window in mid-life (say 15 to 35) when these things do not change. I'm not sure what the age range was in this sample.

Charles Iliya Krempeaux said...

I think you'd have to push the lower bound of that window up to 20 for me.

(Not sure about 35 upper bound though. Haven't reached it yet.)

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