Multilocus OCA2 genotypes specify human iris colors |
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Authors: | Tony Frudakis Timothy Terravainen Matthew Thomas |
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Institution: | (1) DNAPrint Genomics, Inc, 1621 W. University Pkwy, Sarasota, FL 34243, USA;(2) Present address: Department of Statistics, Columbia University, 1255 Amsterdam Ave, New York, NY 10027, USA |
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Abstract: | Human iris color is a quantitative, multifactorial phenotype that exhibits quasi-Mendelian inheritance. Recent studies have
shown that OCA2 polymorphism underlies most of the natural variability in human iris pigmentation but to date, only a few
associated polymorphisms in this gene have been described. Herein, we describe an iris color score (C) for quantifying iris melanin content in-silico and undertake a more detailed survey of the OCA2 locus (n = 271 SNPs). In 1,317 subjects, we confirmed six previously described associations and identified another 27 strongly associated
with C that were not explained by continental population stratification (OR 1.5–17.9, P = 0.03 to <0.001). Haplotype analysis with respect to these 33 SNPs revealed six haplotype blocks and 11 hap-tags within
these blocks. To identify genetic features for best-predicting iris color, we selected sets of SNPs by parsing P values among possible combinations and identified four discontinuous and non-overlapping sets across the LD blocks (p-Selected
SNP sets). In a second, partially overlapping sample of 1,072, samples with matching diplotypes comprised of these p-Selected
OCA2 SNPs exhibited a rate of C concordance of 96.3% (n = 82), which was significantly greater than that obtained from randomly selected samples (62.6%, n = 246, P<0.0001). In contrast, the rate of C concordance using diplotypes comprised of the 11 identified hap-tags was only 83.7%, and that obtained using diplotypes comprised
of all 33 SNPs organized as contiguous sets along the locus (defined by the LD block structure) was only 93.3%. These results
confirm that OCA2 is the major human iris color gene and suggest that using an empirical database-driven system, genotypes
from a modest number of SNPs within this gene can be used to accurately predict iris melanin content from DNA.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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