Identification of a novel locus associated with skin colour in African-admixed populations

Natalia Hernandez-Pacheco, Carlos Flores, Santos Alonso, Celeste Eng, Angel C.Y. Mak, Scott Hunstman, Donglei Hu, Marquitta J. White, Sam S. Oh, Kelley Meade, Harold J. Farber, Pedro C. Avila, Denise Serebrisky, Shannon M. Thyne, Emerita Brigino-Buenaventura, William Rodriguez-Cintron, Saunak Sen, Rajesh Kumar, Michael Lenoir, Jose R. Rodriguez-SantanaEsteban G. Burchard, Maria Pino-Yanes*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10-5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10-14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10-10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10-9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.

Original languageEnglish (US)
Article number44548
JournalScientific reports
Volume7
DOIs
StatePublished - Mar 16 2017

ASJC Scopus subject areas

  • General

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