Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas.

• Main Authors: Joshua Mark Galanter, Juan Carlos Fernandez-Lopez, Christopher R Gignoux, Jill Barnholtz-Sloan, Ceres Fernandez-Rozadilla, Marc Via, Alfredo Hidalgo-Miranda, Alejandra V Contreras, Laura Uribe Figueroa, Paola Raska, Gerardo Jimenez-Sanchez, Irma Silva Zolezzi, Maria Torres, Clara Ruiz Ponte, Yarimar Ruiz, Antonio Salas, Elizabeth Nguyen, Celeste Eng, Lisbeth Borjas, William Zabala, Guillermo Barreto, Fernando Rondón González, Adriana Ibarra, Patricia Taboada, Liliana Porras, Fabián Moreno, Abigail Bigham, Gerardo Gutierrez, Tom Brutsaert, Fabiola León-Velarde, Lorna G Moore, Enrique Vargas, Miguel Cruz, Jorge Escobedo, José Rodriguez-Santana, William Rodriguez-Cintrón, Rocio Chapela, Jean G Ford, Carlos Bustamante, Daniela Seminara, Mark Shriver, Elad Ziv, Esteban Gonzalez Burchard, Robert Haile, Esteban Parra, Angel Carracedo, LACE Consortium
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2012-01-01
• Series: PLoS Genetics
• Online Access: http://europepmc.org/articles/PMC3297575?pdf=render
• ISSN: 1553-7390; 1553-7404

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R² > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.