Development of a panel of genome-wide ancestry informative markers to study admixture throughout the americas
Por:
Galanter J.M., Fernandez-Lopez J.C., Gignoux C.R., Barnholtz-Sloan J., Fernandez-Rozadilla C., Via M., Hidalgo-Miranda A., Contreras A.V., Figueroa L.U., Raska P., Jimenez-Sanchez G., Zolezzi I.S., Torres M., Ponte C.R., Ruiz Y., Salas A., Nguyen E., Eng C., Borjas L., Zabala W., Barreto G., González F.R., Ibarra A., Taboada P., Porras L., Moreno F., Bigham A., Gutierrez G., Brutsaert T., León-Velarde F., Moore L.G., Vargas E., Cruz M., Escobedo J., Rodriguez-Santana J., Rodriguez-Cintrón W., Chapela R., Ford J.G., Bustamante C., Seminara D., Shriver M., Ziv E., Burchard E.G., Haile R., Parra E., Carracedo A.
Publicada:
1 ene 2012
Resumen:
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 (R 2&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.
Filiaciones:
Galanter J.M.:
University of California San Francisco, San Francisco, CA, United States
Fernandez-Lopez J.C.:
Instituto Nacional de Medicina Genómica, Mexico City, Mexico
Gignoux C.R.:
University of California San Francisco, San Francisco, CA, United States
Barnholtz-Sloan J.:
Case Western Reserve University, Cleveland, OH, United States
Fernandez-Rozadilla C.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Via M.:
Universitat de Barcelona, Barcelona, Spain
Hidalgo-Miranda A.:
Instituto Nacional de Medicina Genómica, Mexico City, Mexico
Contreras A.V.:
Instituto Nacional de Medicina Genómica, Mexico City, Mexico
Figueroa L.U.:
Instituto Nacional de Medicina Genómica, Mexico City, Mexico
Raska P.:
Case Western Reserve University, Cleveland, OH, United States
Jimenez-Sanchez G.:
Instituto Nacional de Medicina Genómica, Mexico City, Mexico
Zolezzi I.S.:
Instituto Nacional de Medicina Genómica, Mexico City, Mexico
Torres M.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Ponte C.R.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Ruiz Y.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Salas A.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Nguyen E.:
University of California San Francisco, San Francisco, CA, United States
Eng C.:
University of California San Francisco, San Francisco, CA, United States
Borjas L.:
Universidad del Zulia, Maracaibo, Venezuela
Zabala W.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Universidad del Zulia, Maracaibo, Venezuela
Barreto G.:
Universidad del Valle, Santiago de Cali, Colombia
González F.R.:
Universidad Industrial de Santander, Bucaramanga, Colombia
Ibarra A.:
Universidad de Antioquia, Medellín, Colombia
Taboada P.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Instituto de Investigaciones Forenses, Sucre, Bolivia
Porras L.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
Universidad Tecnológica de Pereira, Pereira, Colombia
Moreno F.:
Unidad de Genética Forense, Servicio Médico-Legal de Chile, Santiago de Chile, Chile
Bigham A.:
University of Michigan, Ann Arbor, MI, United States
Gutierrez G.:
University of Colorado at Boulder, Boulder, CO, United States
Brutsaert T.:
Syracuse University, Syracuse, NY, United States
León-Velarde F.:
Universidad Peruana Cayetano Heredia, Lima, Peru
Moore L.G.:
Wake Forest University, Winston-Salem, NC, United States
Vargas E.:
Universidad Mayor de San Andrés, La Paz, Bolivia
Cruz M.:
Centro Medico Nacional Siglo XXI, Mexican Social Security Institute (IMSS), Mexico City, Mexico
Escobedo J.:
Hospital General Regional 1, IMSS, Mexico City, Mexico
Rodriguez-Santana J.:
Centro de Neumología Pediátrica, San Juan, Puerto Rico
Rodriguez-Cintrón W.:
VA Caribbean Health System, San Juan, Puerto Rico
Chapela R.:
Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
Ford J.G.:
Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
Bustamante C.:
Stanford University, Stanford, CA, United States
Seminara D.:
National Cancer Institute, Bethesda, MD, United States
Shriver M.:
Penn State University, University Park, PA, United States
Ziv E.:
University of California San Francisco, San Francisco, CA, United States
Burchard E.G.:
University of California San Francisco, San Francisco, CA, United States
Haile R.:
University of Southern California, Los Angeles, CA, United States
Parra E.:
University of Toronto at Mississauga, Mississauga, Canada
Carracedo A.:
Fundación Pública Galega de Medicina Xenómica (SERGAS)-CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
All Open Access, Gold
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