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

  • Author(s): Hernandez-Pacheco, Natalia;
  • Flores, Carlos;
  • Alonso, Santos;
  • Eng, Celeste;
  • Mak, Angel CY;
  • Hunstman, Scott;
  • Hu, Donglei;
  • White, Marquitta J;
  • Oh, Sam S;
  • Meade, Kelley;
  • Farber, Harold J;
  • Avila, Pedro C;
  • Serebrisky, Denise;
  • Thyne, Shannon M;
  • Brigino-Buenaventura, Emerita;
  • Rodriguez-Cintron, William;
  • Sen, Saunak;
  • Kumar, Rajesh;
  • Lenoir, Michael;
  • Rodriguez-Santana, Jose R;
  • Burchard, Esteban G;
  • Pino-Yanes, Maria
  • et al.

Published Web Location

https://doi.org/10.1038/srep44548
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.

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