Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry

Rawofi, Lida and Edwards, Melissa and Krithika, S. and Le, Phuong and Cha, David and Yang, Zhaohui and Ma, Yanyun and Wang, Jiucun and Su, Bing and Jin, Li and Norton, Heather L. and Parra, Esteban J. (2017) Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. PeerJ, 5. e3951. ISSN 2167-8359

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Official URL: https://doi.org/10.7717/peerj.3951

Abstract

Background: Currently, there is limited knowledge about the genetics underlying pigmentary traits in East Asian populations. Here, we report the results of the first genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. Methods: We obtained quantitative skin pigmentation measures (M-index) in the inner upper arm of the participants using a portable reflectometer (N = 305). Quantitative measures of iris color (expressed as L*, a* and b* CIELab coordinates) were extracted from high-resolution iris pictures (N = 342). We also measured the color differences between the pupillary and ciliary regions of the iris (e.g., iris heterochromia). DNA samples were genotyped with Illumina’s Infinium Multi-Ethnic Global Array (MEGA) and imputed using the 1000 Genomes Phase 3 samples as reference haplotypes. Results: For skin pigmentation, we did not observe any genome-wide significant signal. We followed-up in three independent Chinese samples the lead SNPs of five regions showing multiple common markers (minor allele frequency ≥ 5%) with good imputation scores and suggestive evidence of association (p-values < 10−5). One of these markers, rs2373391, which is located in an intron of the ZNF804B gene on chromosome 7, was replicated in one of the Chinese samples (p = 0.003). For iris color, we observed genome-wide signals in the OCA2 region on chromosome 15. This signal is driven by the non-synonymous rs1800414 variant, which explains 11.9%, 10.4% and 6% of the variation observed in the b*, a* and L* coordinates in our sample, respectively. However, the OCA2 region was not associated with iris heterochromia. Discussion: Additional genome-wide association studies in East Asian samples will be necessary to further disentangle the genetic architecture of pigmentary traits in East Asian populations.

Item Type: Journal Article
Keywords: Skin pigmentation, Genome-wide association study, Iris color, East Asia
Faculty: ARCHIVED Faculty of Science & Technology (until September 2018)
Depositing User: Lisa Blanshard
Date Deposited: 30 Jul 2020 12:38
Last Modified: 09 Sep 2021 18:58
URI: https://arro.anglia.ac.uk/id/eprint/705727

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