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Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans.

Publication ,  Journal Article
Zhang, M; Song, F; Liang, L; Nan, H; Zhang, J; Liu, H; Wang, L-E; Wei, Q; Lee, JE; Amos, CI; Kraft, P; Qureshi, AA; Han, J
Published in: Hum Mol Genet
July 15, 2013

Aiming to identify novel genetic loci for pigmentation and skin cancer, we conducted a series of genome-wide association studies on hair color, eye color, number of sunburns, tanning ability and number of non-melanoma skin cancers (NMSCs) among 10 183 European Americans in the discovery stage and 4504 European Americans in the replication stage (for eye color, 3871 males in the discovery stage and 2496 males in the replication stage). We targeted novel chromosome regions besides the known ones for replication. As a result, we identified a new region downstream of the EDNRB gene on 13q22 associated with hair color and the strongest association was the single-nucleotide polymorphism (SNP) rs975739 (P = 2.4 × 10(-14); P = 5.4 × 10(-9) in the discovery set and P = 1.2 × 10(-6) in the replication set). Using blue, intermediate (including green) and brown eye colors as co-dominant outcomes, we identified the SNP rs3002288 in VASH2 on 1q32.3 associated with brown eye (P = 7.0 × 10(-8); P = 5.3 × 10(-5) in the discovery set and P = 0.02 in the replication set). Additionally, we identified a significant interaction between the SNPs rs7173419 and rs12913832 in the OCA2 gene region on brown eye color (P-value for interaction = 3.8 × 10(-3)). As for the number of NMSCs, we identified two independent SNPs on chr6 and one SNP on chromosome 14: rs12203592 in IRF4 (P = 7.2 × 10(-14); P = 1.8 × 10(-8) in the discovery set and P = 6.7 × 10(-7) in the replication set), rs12202284 between IRF4 and EXOC2 (P = 5.0 × 10(-8); P = 6.6 × 10(-7) in the discovery set and P = 3.0 × 10(-3) in the replication set) and rs8015138 upstream of GNG2 (P = 6.6 × 10(-8); P = 5.3 × 10(-7) in the discovery set and P = 0.01 in the replication set).

Duke Scholars

Published In

Hum Mol Genet

DOI

EISSN

1460-2083

Publication Date

July 15, 2013

Volume

22

Issue

14

Start / End Page

2948 / 2959

Location

England

Related Subject Headings

  • White People
  • Skin Pigmentation
  • Skin Neoplasms
  • Quantitative Trait Loci
  • Polymorphism, Single Nucleotide
  • Membrane Transport Proteins
  • Male
  • Interferon Regulatory Factors
  • Humans
  • Genome-Wide Association Study
 

Citation

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ICMJE
MLA
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Zhang, M., Song, F., Liang, L., Nan, H., Zhang, J., Liu, H., … Han, J. (2013). Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans. Hum Mol Genet, 22(14), 2948–2959. https://doi.org/10.1093/hmg/ddt142
Zhang, Mingfeng, Fengju Song, Liming Liang, Hongmei Nan, Jiangwen Zhang, Hongliang Liu, Li-E Wang, et al. “Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans.Hum Mol Genet 22, no. 14 (July 15, 2013): 2948–59. https://doi.org/10.1093/hmg/ddt142.
Zhang M, Song F, Liang L, Nan H, Zhang J, Liu H, et al. Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans. Hum Mol Genet. 2013 Jul 15;22(14):2948–59.
Zhang, Mingfeng, et al. “Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans.Hum Mol Genet, vol. 22, no. 14, July 2013, pp. 2948–59. Pubmed, doi:10.1093/hmg/ddt142.
Zhang M, Song F, Liang L, Nan H, Zhang J, Liu H, Wang L-E, Wei Q, Lee JE, Amos CI, Kraft P, Qureshi AA, Han J. Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans. Hum Mol Genet. 2013 Jul 15;22(14):2948–2959.
Journal cover image

Published In

Hum Mol Genet

DOI

EISSN

1460-2083

Publication Date

July 15, 2013

Volume

22

Issue

14

Start / End Page

2948 / 2959

Location

England

Related Subject Headings

  • White People
  • Skin Pigmentation
  • Skin Neoplasms
  • Quantitative Trait Loci
  • Polymorphism, Single Nucleotide
  • Membrane Transport Proteins
  • Male
  • Interferon Regulatory Factors
  • Humans
  • Genome-Wide Association Study