Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations

Sophie I. Candille, Devin M. Absher, Sandra Beleza, Marc Bauchet, Brian McEvoy, Nanibaa' A. Garrison, Jun Z. Li, Richard M. Myers, Gregory S. Barsh, Hua Tang, Mark Shriver

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world.

Original languageEnglish (US)
Article numbere48294
JournalPloS one
Volume7
Issue number10
DOIs
StatePublished - Oct 31 2012

Fingerprint

Skin Pigmentation
Genome-Wide Association Study
Pigmentation
skin (animal)
pigmentation
Hair
hairs
Skin
Genes
eyes
Hair Color
Eye Color
Phenotype
Population
phenotype
Color
Portugal
color
Poland
Ireland

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Candille, Sophie I. ; Absher, Devin M. ; Beleza, Sandra ; Bauchet, Marc ; McEvoy, Brian ; Garrison, Nanibaa' A. ; Li, Jun Z. ; Myers, Richard M. ; Barsh, Gregory S. ; Tang, Hua ; Shriver, Mark. / Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations. In: PloS one. 2012 ; Vol. 7, No. 10.
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abstract = "Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35{\%} of the variation in skin pigmentation, 31{\%} of the variation in hair pigmentation, and 40{\%} of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world.",
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Candille, SI, Absher, DM, Beleza, S, Bauchet, M, McEvoy, B, Garrison, NA, Li, JZ, Myers, RM, Barsh, GS, Tang, H & Shriver, M 2012, 'Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations', PloS one, vol. 7, no. 10, e48294. https://doi.org/10.1371/journal.pone.0048294

Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations. / Candille, Sophie I.; Absher, Devin M.; Beleza, Sandra; Bauchet, Marc; McEvoy, Brian; Garrison, Nanibaa' A.; Li, Jun Z.; Myers, Richard M.; Barsh, Gregory S.; Tang, Hua; Shriver, Mark.

In: PloS one, Vol. 7, No. 10, e48294, 31.10.2012.

Research output: Contribution to journalArticle

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AU - Candille, Sophie I.

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AU - McEvoy, Brian

AU - Garrison, Nanibaa' A.

AU - Li, Jun Z.

AU - Myers, Richard M.

AU - Barsh, Gregory S.

AU - Tang, Hua

AU - Shriver, Mark

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