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

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Candille, Sophie I ^a   Absher, Devin M ^b   Beleza, Sandra ^a   Bauchet, Marc ^c   McEvoy, Brian ^d   Garrison, Nanibaa' A ^a,f   Li, Jun Z ^e   Myers, Richard M ^b   Barsh, Gregory S ^b   Tang, Hua ^a   Shriver, Mark D ^c  

^a STANFORD UNIVERSITY   (United States)

^b HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d TRINITY COLLEGE DUBLIN   (Ireland)

^e UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^f STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FILAMIN; LACTASE;

ARTICLE; CONTROLLED STUDY; ETHNICITY; EUROPEAN; EYE COLOR; EYE PIGMENTATION; FEMALE; GENE FREQUENCY; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC DIFFERENCE; GENETIC VARIABILITY; HAIR PIGMENTATION; HAPLOTYPE MAP; HUMAN; IRELAND; ITALY; MALE; PHENOTYPE; PIGMENTATION; POLAND; POPULATION STRUCTURE; PORTUGAL; PRINCIPAL COMPONENT ANALYSIS; QUALITY CONTROL; QUANTITATIVE ANALYSIS; QUANTITATIVE TRAIT LOCUS; REFLECTOMETRY; SELF REPORT; SEX DIFFERENCE; SINGLE NUCLEOTIDE POLYMORPHISM; SKIN PIGMENTATION; CAUCASIAN; EYE; GENETICS; HAIR; METABOLISM;

EUROPEAN CONTINENTAL ANCESTRY GROUP; EYE; FEMALE; GENOME-WIDE ASSOCIATION STUDY; HAIR; HUMANS; MALE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SELF REPORT; SKIN PIGMENTATION;

EID: 84868289448     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048294     Document Type: Article

References (48)

1. Parra EJ (2007) Human pigmentation variation: evolution, genetic basis, and implications for public health. American journal of physical anthropology Suppl 45: 85-105.
2. Jablonski NG, Chaplin G, (2000) The evolution of human skin coloration. Journal of human evolution 39: 57-106.
3. Jablonski NG, Chaplin G, (2010) Colloquium paper: human skin pigmentation as an adaptation to UV radiation. Proc Natl Acad Sci U S A 107Suppl 2: 8962-8968.
4. Norton HL, Kittles RA, Parra E, McKeigue P, Mao X, et al. (2007) Genetic evidence for the convergent evolution of light skin in Europeans and East Asians. Molecular biology and evolution 24: 710-722.
5. Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome research 19: 826-837.
6. Norton HL, Friedlaender JS, Merriwether DA, Koki G, Mgone CS, et al. (2006) Skin and hair pigmentation variation in Island Melanesia. Am J Phys Anthropol 130: 254-268.
7. Sturm RA, Larsson M, (2009) Genetics of human iris colour and patterns. Pigment cell & melanoma research 22: 544-562.
8. Eriksson N, Macpherson JM, Tung JY, Hon LS, Naughton B, et al. (2010) Web-based, participant-driven studies yield novel genetic associations for common traits. PLoS genetics 6: e1000993.
9. Han J, Kraft P, Nan H, Guo Q, Chen C, et al. (2008) A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. PLoS genetics 4: e1000074.
10. Kayser M, Liu F, Janssens AC, Rivadeneira F, Lao O, et al. (2008) Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene. American journal of human genetics 82: 411-423.
11. Liu F, Wollstein A, Hysi PG, Ankra-Badu GA, Spector TD, et al. (2010) Digital quantification of human eye color highlights genetic association of three new loci. PLoS genetics 6: e1000934.
12. Sulem P, Gudbjartsson DF, Stacey SN, Helgason A, Rafnar T, et al. (2008) Two newly identified genetic determinants of pigmentation in Europeans. Nature genetics 40: 835-837.
13. Sulem P, Gudbjartsson DF, Stacey SN, Helgason A, Rafnar T, et al. (2007) Genetic determinants of hair, eye and skin pigmentation in Europeans. Nature genetics 39: 1443-1452.
14. Gerstenblith MR, Shi J, Landi MT, (2010) Genome-wide association studies of pigmentation and skin cancer: a review and meta-analysis. Pigment cell & melanoma research 23: 587-606.
15. Branicki W, Liu F, van Duijn K, Draus-Barini J, Pospiech E, et al. (2011) Model-based prediction of human hair color using DNA variants. Hum Genet 129: 443-454.
16. Walsh S, Wollstein A, Liu F, Chakravarthy U, Rahu M, et al. (2012) DNA-based eye colour prediction across Europe with the IrisPlex system. Forensic Sci Int Genet 6: 330-340.
17. Stokowski RP, Pant PV, Dadd T, Fereday A, Hinds DA, et al. (2007) A genomewide association study of skin pigmentation in a South Asian population. American journal of human genetics 81: 1119-1132.
18. Shriver MD, Parra EJ, (2000) Comparison of narrow-band reflectance spectroscopy and tristimulus colorimetry for measurements of skin and hair color in persons of different biological ancestry. American journal of physical anthropology 112: 17-27.
19. Frudakis T, Terravainen T, Thomas M, (2007) Multilocus OCA2 genotypes specify human iris colors. Human genetics 122: 311-326.
20. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. American journal of human genetics 81: 559-575.
21. Patterson N, Price AL, Reich D, (2006) Population structure and eigenanalysis. PLoS genetics 2: e190.
22. Barrett JC, Fry B, Maller J, Daly MJ, (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
23. Bacanu SA, Devlin B, Roeder K, (2002) Association studies for quantitative traits in structured populations. Genetic epidemiology 22: 78-93.
24. Li Y, Willer C, Sanna S, Abecasis G, (2009) Genotype imputation. Annual review of genomics and human genetics 10: 387-406.
25. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR, (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic epidemiology 34: 816-834.
26. Purcell S, Cherny SS, Sham PC, (2003) Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 19: 149-150.
27. Madrigal L, Kelly W, (2007) Human skin-color sexual dimorphism: a test of the sexual selection hypothesis. American journal of physical anthropology 132: 470-482.
28. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, et al. (2008) Genes mirror geography within Europe. Nature 456: 98-101.
29. Wellcome Trust Case Control Consortium, (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
30. Moskvina V, Smith M, Ivanov D, Blackwood D, Stclair D, et al. (2010) Genetic Differences between Five European Populations. Human heredity 70: 141-149.
31. Campbell CD, Ogburn EL, Lunetta KL, Lyon HN, Freedman ML, et al. (2005) Demonstrating stratification in a European American population. Nature genetics 37: 868-872.
32. Price AL, Butler J, Patterson N, Capelli C, Pascali VL, et al. (2008) Discerning the ancestry of European Americans in genetic association studies. PLoS genetics 4: e236.
33. Eiberg H, Troelsen J, Nielsen M, Mikkelsen A, Mengel-From J, et al. (2008) Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. Human genetics 123: 177-187.
34. Sturm RA, Duffy DL, Zhao ZZ, Leite FP, Stark MS, et al. (2008) A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. American journal of human genetics 82: 424-431.
35. Cook AL, Chen W, Thurber AE, Smit DJ, Smith AG, et al. (2009) Analysis of cultured human melanocytes based on polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P loci. The Journal of investigative dermatology 129: 392-405.
36. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, et al. (2003) Control of confounding of genetic associations in stratified populations. American journal of human genetics 72: 1492-1504.
37. Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, et al. (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310: 1782-1786.
38. Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, et al. (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Human genetics 112: 387-399.
39. Graf J, Hodgson R, van Daal A, (2005) Single nucleotide polymorphisms in the MATP gene are associated with normal human pigmentation variation. Human mutation 25: 278-284.
40. Dessinioti C, Antoniou C, Katsambas A, Stratigos AJ, (2011) Melanocortin 1 receptor variants: functional role and pigmentary associations. Photochemistry and photobiology 87: 978-987.
41. Duffy DL, Box NF, Chen W, Palmer JS, Montgomery GW, et al. (2004) Interactive effects of MC1R and OCA2 on melanoma risk phenotypes. Human molecular genetics 13: 447-461.
42. Duffy DL, Zhao ZZ, Sturm RA, Hayward NK, Martin NG, et al. (2010) Multiple pigmentation gene polymorphisms account for a substantial proportion of risk of cutaneous malignant melanoma. J Invest Dermatol 130: 520-528.
43. Kennedy C, ter Huurne J, Berkhout M, Gruis N, Bastiaens M, et al. (2001) Melanocortin 1 receptor (MC1R) gene variants are associated with an increased risk for cutaneous melanoma which is largely independent of skin type and hair color. J Invest Dermatol 117: 294-300.
44. Latreille J, Ezzedine K, Elfakir A, Ambroisine L, Gardinier S, et al. (2009) MC1R gene polymorphism affects skin color and phenotypic features related to sun sensitivity in a population of French adult women. Photochem Photobiol 85: 1451-1458.
45. Nan H, Kraft P, Hunter DJ, Han J, (2009) Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Int J Cancer 125: 909-917.
46. Takiwaki H, (1998) Measurement of skin color: practical application and theoretical considerations. J Med Invest 44: 121-126.
47. Bonilla C, Boxill LA, Donald SA, Williams T, Sylvester N, et al. (2005) The 8818G allele of the agouti signaling protein (ASIP) gene is ancestral and is associated with darker skin color in African Americans. Hum Genet 116: 402-406.
48. Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, et al. (2008) Analysis and application of European genetic substructure using 300 K SNP information. PLoS genetics 4: e4.