A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation

Han, J., Kraft, P., Nan, H., Guo, Q., Chen, C., Qureshi, A., Hankinson, S.E., Hu, F.B., Duffy, D., Zhao, Z.Z., Martin, N. G., Montgomery, G., Hayward, N., Thomas, G., Hoover, R.N., Chanock, S. and Hunter, D.J. (2008) A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Plos Genetics, 4 5: e1000074. doi:10.1371/journal.pgen.1000074

Author Han, J.
Kraft, P.
Nan, H.
Guo, Q.
Chen, C.
Qureshi, A.
Hankinson, S.E.
Hu, F.B.
Duffy, D.
Zhao, Z.Z.
Martin, N. G.
Montgomery, G.
Hayward, N.
Thomas, G.
Hoover, R.N.
Chanock, S.
Hunter, D.J.
Title A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation
Journal name Plos Genetics   Check publisher's open access policy
ISSN 1553-7390
Publication date 2008-05-01
Year available 2008
Sub-type Article (original research)
DOI 10.1371/journal.pgen.1000074
Open Access Status DOI
Volume 4
Issue 5
Start page e1000074
Total pages 11
Place of publication United States
Publisher Public Library of Science
Language eng
Subject C1
970111 Expanding Knowledge in the Medical and Health Sciences
060408 Genomics
Abstract We conducted a multi-stage genome-wide association study of natural hair color in more than 10,000 men and women of European ancestry from the United States and Australia. An initial analysis of 528,173 single nucleotide polymorphisms (SNPs) genotyped on 2,287 women identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. We confirmed these associations in 7,028 individuals from three additional studies. Across these four studies, SLC24A4 rs12896399 and IRF4 rs12203592 showed strong associations with hair color, with p = 6.0×10−62 and p = 7.46×10−127, respectively. The IRF4 SNP was also associated with skin color (p = 6.2×10−14), eye color (p = 6.1×10−13), and skin tanning response to sunlight (p = 3.9×10−89). A multivariable analysis pooling data from the initial GWAS and an additional 1,440 individuals suggested that the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. After adjustment for rs12203592, the association between rs1540771 and hair color was not significant (p = 0.52). One variant in the MATP gene was associated with hair color. A variant in the HERC2 gene upstream of the OCA2 gene showed the strongest and independent association with hair color compared with other SNPs in this region, including three previously reported SNPs. The signals detected in a region around the MC1R gene were explained by MC1R red hair color alleles. Our results suggest that the IRF4 and SLC24A4 loci are associated with human hair color and skin pigmentation.
Keyword Postmenopausal Breast-Cancer
Regulatory Factor Family
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID R03 CA128080
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2009 Higher Education Research Data Collection
School of Medicine Publications
School of Psychology Publications
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 217 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 251 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Wed, 15 Apr 2009, 02:38:44 EST by Amanda Jones on behalf of Medicine - Royal Brisbane and Women's Hospital