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. 2017 Jul;136(7):847-863.
doi: 10.1007/s00439-017-1808-5. Epub 2017 May 12.

Global skin colour prediction from DNA

Affiliations

Global skin colour prediction from DNA

Susan Walsh et al. Hum Genet. 2017 Jul.

Erratum in

  • Erratum to: Global skin colour prediction from DNA.
    Walsh S, Chaitanya L, Breslin K, Muralidharan C, Bronikowska A, Pospiech E, Koller J, Kovatsi L, Wollstein A, Branicki W, Liu F, Kayser M. Walsh S, et al. Hum Genet. 2017 Jul;136(7):865-866. doi: 10.1007/s00439-017-1817-4. Hum Genet. 2017. PMID: 28578451 Free PMC article. No abstract available.

Abstract

Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.

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Conflict of interest statement

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Figures

Fig. 1
Fig. 1
Illustration of the accumulative contribution of each of the selected 36 SNP predictors towards AUC prediction accuracy of 5 skin colour categories based on the full set of 1423 individual. SNP predictors were added to the prediction model one by one in the sequential order from highest to lowest prediction rank. Each colour-coded line represents one of the 5 DNA-predicted skin colour categories. Skin colour phenotyping was via skin types derived from the Fitzpatrick scale
Fig. 2
Fig. 2
Illustration of the prediction performance of the set of 36 SNPs for the 5-category (a) and the 3-category (b) skin colour prediction model using ROC curves with AUC estimates (including the cross-validated measures) using the full training set of 1423 individuals from 29 populations. Skin colour phenotyping was via skin types derived from the Fitzpatrick scale
Fig. 3
Fig. 3
Proof-of-principle illustration of the power of the developed model for predicting skin colour on a global scale, regardless of bio-geographic ancestry. Probability outputs from the 5-category skin colour prediction model based on genotypes of the 36 SNP set are shown together with a skin image of the respective DNA donor. Fourteen individuals were chosen from the ‘model comparison set’ based on their parental country of birth, both in and outside the US, representing globally distributed individuals. The order of the images is 1–14 with the following parental birth countries recorded 1-US, 2-US, 3-US, 4-US, 5-Syria, 6-Columbia, 7-China, 8-Vietnam, 9-El Salvador, 10-India, 11-Mexico, 12-Nigeria, 13-Vietnam, 14-Nigeria

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