Journal article

A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia

Kaustubh Adhikari, Javier Mendoza-Revilla, Anood Sohail, Macarena Fuentes-Guajardo, Jodie Lampert, Juan Camilo Chacon-Duque, Malena Hurtado, Valeria Villegas, Vanessa Granja, Victor Acuna-Alonzo, Claudia Jaramillo, William Arias, Rodrigo Barquera Lozano, Paola Everardo, Jorge Gomez-Valdes, Hugo Villamil-Ramirez, Caio C Silva de Cerqueira, Tabita Hunemeier, Virginia Ramallo, Lavinia Schuler-Faccini Show all

NATURE COMMUNICATIONS | NATURE PUBLISHING GROUP | Published : 2019

Abstract

We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interactions among independently associated alleles. Strongest association with skin pigmentation at 19p13 was observed for an Y182H missense variant (common only in East Asians and Native Americans) in MFSD1..

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University of Melbourne Researchers

Grants

Awarded by Leverhulme Trust


Awarded by BBSRC


Awarded by CONCYTEC-PERU


Awarded by NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING


Funding Acknowledgements

We would like to dedicate this paper to Francisco M. Salzano. We thank the volunteers for their enthusiastic support for this research. We also thank Alvaro Alvarado, Monica Ballesteros Romero, Ricardo Cebrecos, Miguel Angel Contreras Sieck, Francisco de Avila Becerril, Joyce De la Piedra, Maria Teresa Del Solar, Paola Everardo Martinez, William Flores, Martha Granados Riveros, Rosilene Paim, Ricardo Gunski, Sergeant Joao Felisberto Menezes Cavalheiro, Major Eugenio Correa de Souza Junior, Wendy Hart, Ilich Jafet Moreno, Paola Leon-Mimila, Francisco Quispealaya, Diana Rogel Diaz, Ruth Rojas, and Vanessa Sarabia for assistance with volunteer recruitment, sample processing and data entry. We also thank Richard Baker (Centre for Skin Sciences, University of Bradford) for technical assistance with the human skin immunofluorescence, Lewis Griffin (UCL Centre for Computer Science) for assistance in the development of iris color assessment and Emiliano Bellini for the face illustrations in Fig. 3. We also thank Louise Ormond and Aida Andres for helpful discussion on the ABC analysis (UCL Genetics Institute). We are very grateful to the institutions that allowed the use of their facilities for the assessment of volunteers, including: Escuela Nacional de Antropologia e Historia and Universidad Nacional Autonoma de Mexico (Mexico); Universidade Federal do Rio Grande do Sul (Brazil); 13 degrees Companhia de Comunicacoes Mecanizada do Exercito Brasileiro (Brazil); Pontificia Universidad Catolica del Peru, Universidad de Lima and Universidad Nacional Mayor de San Marcos (Peru). Work leading to this publication was funded by grants from: the Leverhulme Trust (F/07134/DF), BBSRC (BB/I021213/1), the Excellence Initiative of Aix-Marseille University-A*MIDEX (a French 'Investissements d'Avenir' programme), Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul (Apoio a Nucleos de Excelencia Program) and Fundacao de Aperfeicoamento de Pessoal de Nivel Superior. J.M.-R. was supported by a doctoral scholarship from CONCYTEC-PERU (224-2014-FONDECYT).