Predicting Phenotype from Genotype: Normal Pigmentation (Valenzuela et al. 2010)

Yann Klimentidis points me to this new paper on predicting human pigmentation phenotype from genotype. The paper is interesting in view of the recent finding that lactose intolerance phenotype is not very well captured by the known genetic variation.

The current paper looks at how well normal pigmentation (skin, hair, and eye color) is predicted from known genotypes. The sample consists of individuals from the University of Arizona.

From the paper:

The three most frequent SNPs found in the range from the highest R² model to the first inflection of the graph were used to construct an MLR model for each trait. These models accounted for significant variation in each of the four measured traits: scalp-hair total melanin (76.3%), natural log of the ratio of eumelanin-to-pheomelanin (43.2%), skin reflectance (45.7%), and eye color (74.8%) (Table 3).

Obviously two caveats should be raised:

(i) that the associations are dependent on the sample. It is not clear how the percentage of variation explained would be altered in a population of different ethnic origins -not represented in the UoA.

(ii) that the associations may be mediated by other genetic factors, not yet discovered.

With respect to (ii), pigmentation appears to be a "success story" of genome-wide association studies, as a relatively small number of SNPs accounts for such a high level of variation (about 3/4 for the best traits). However, the missing 1/4 should also make us cautious when we attempt to infer the pigmentation of a sample, in either a forensic or an archaeological context.

Journal of Forensic Science doi:10.1111/j.1556-4029.2009.01317.x

Predicting Phenotype from Genotype: Normal Pigmentation

Robert K. Valenzuela et al.

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.

Link