Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas
Fecha
2012-03-08Autor
Galanter, Joshua Mark
Fernández-López, Juan Carlos
Gignoux, Christopher R.
Barnholtz-Sloan, Jill
Fernández-Rozadilla, Ceres
Via, Marc
Hidalgo-Miranda, Alfredo
Contreras, Alejandra V
Uribe Figueroa, Laura
Raska, Paola
Jiménez-Sánchez, Gerardo
Silva Zolezzi, Irma
Torres, María
Ruiz Ponte, Clara
Ruiz, Yarimar
Salas, Antonio
Nguyen, Elizabeth
Eng, Celeste
Borjas, Lisbeth
Zabala, William
Barreto, Guillermo
Rondón González, Fernando
Ibarra, Adriana
Taboada, Patricia
Porras, Liliana
Moreno, Fabián
Bigham, Abigail
Gutiérrez, Gerardo
Brutsaert, Tom
León-Velarde, Fabiola
Moore, Lorna G
Vargas, Enrique
Cruz, Miguel
Escobedo, Jorge
Rodríguez-Santana, José
Rodríguez-Cintrón, William
Chapela, Rocio
Ford, Jean G
Bustamante, Carlos
Seminara, Daniela
Shriver, Mark
Ziv, Elad
Gonzalez Burchard, Esteban
Haile, Robert
Parra, Esteban
Carracedo, Ángel
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Abstract.
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.