Human eye color explained by a three-SNP haplotype

A very exciting new preprint in AJHG describes how a haplotype defined by three SNPs, i.e., single-letter changes in the genetic code, describes most variation in human eye color. I am sure that this paper will make the news once its edited version appears, but this is very exciting development for many different reasons.

• First, it shows that a very striking observable difference among humans can be explained by minute differences in the genetic code. This should be a reminder to those who engage in grocery-style genetics. Quantity matters not.
• Second, eye color is an important phenotypical character that people actually care about. Genetics becomes exciting when it's about stuff that people are interested in (intelligence, eye color, the chance of getting cancer before 40, etc.).
• Third, we are finally getting to the point where genetics can be used to infer characteristics of organisms that are not preserved in bones. This will doubtlessly lead to applications in ancient DNA research (see also here).

American Journal of Human Genetics (preprint)

A three-SNP haplotype in the first intron of OCA2 explains most human eye color variation

David L. Duffy, Grant W. Montgomery, Wei Chen, Zhen Zhen Zhao, Lien Le, Michael R. James, Nicholas K. Hayward, Nicholas G. Martin, Richard A. Sturm

Abstract

We have previously shown that a QTL linked to the OCA2 region of 15q accounts for 74% of variation in human eye color. We conducted additional genotyping to clarify the role of the OCA2 locus in the inheritance of eye color and other pigmentary traits associated with skin cancer risk in white populations. Fifty eight synonymous and non-synonymous exonic SNPs and tagging SNPs were typed in a collection of 3839 adolescent twins, their sibs, and parents. The highest association for blue:non-blue eye color was found with three OCA2 SNPs; rs7495174 T/C, rs6497268 G/T and rs11855019 T/C (P-values of 1.02x10-61, 1.57x10-96, and 4.45x10-54 respectively) in intron 1. These three SNPs are in one major haplotype block with TGT representing 78.4% of alleles. The TGT/TGT diplotype found in 62.2% of samples was the major genotype seen to modify eye color, with a frequency of 0.905 in blue or green compared with only 0.095 in brown eye color. This genotype was also at highest frequency in subjects with light brown hair and was more frequent in fair and medium skin types, consistent with the TGT haplotype acting as a recessive modifier of lighter pigmentary phenotypes. Homozygotes for rs11855019 C/C were predominantly without freckles and had decreased mole counts. The minor population impact of the nonsynonymous coding region polymorphisms Arg305Trp and Arg419Gln associated with non-blue eyes, and the tight linkage of the major TGT haplotype within the first intron of OCA2 with blue eye color and lighter hair and skin tones, suggest that differences within the 5’ proximal regulatory control region of OCA2 gene alter expression or mRNA transcript levels and may be responsible for these associations.

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