Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas
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 in...
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| Format: | Online |
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Public Library of Science
2012
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297575/ |
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pubmed-32975752012-03-12 Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas Galanter, Joshua Mark Fernandez-Lopez, Juan Carlos Gignoux, Christopher R. Barnholtz-Sloan, Jill Fernandez-Rozadilla, Ceres Via, Marc Hidalgo-Miranda, Alfredo Contreras, Alejandra V. Figueroa, Laura Uribe Raska, Paola Jimenez-Sanchez, Gerardo Silva Zolezzi, Irma Torres, Maria Ponte, Clara Ruiz 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 Gutierrez, Gerardo Brutsaert, Tom León-Velarde, Fabiola Moore, Lorna G. Vargas, Enrique Cruz, Miguel Escobedo, Jorge Rodriguez-Santana, José Rodriguez-Cintrón, William Chapela, Rocio Ford, Jean G. Bustamante, Carlos Seminara, Daniela Shriver, Mark Ziv, Elad Gonzalez Burchard, Esteban Haile, Robert Parra, Esteban Carracedo, Angel Research Article 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. Public Library of Science 2012-03-08 /pmc/articles/PMC3297575/ /pubmed/22412386 http://dx.doi.org/10.1371/journal.pgen.1002554 Text en This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Galanter, Joshua Mark Fernandez-Lopez, Juan Carlos Gignoux, Christopher R. Barnholtz-Sloan, Jill Fernandez-Rozadilla, Ceres Via, Marc Hidalgo-Miranda, Alfredo Contreras, Alejandra V. Figueroa, Laura Uribe Raska, Paola Jimenez-Sanchez, Gerardo Silva Zolezzi, Irma Torres, Maria Ponte, Clara Ruiz 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 Gutierrez, Gerardo Brutsaert, Tom León-Velarde, Fabiola Moore, Lorna G. Vargas, Enrique Cruz, Miguel Escobedo, Jorge Rodriguez-Santana, José Rodriguez-Cintrón, William Chapela, Rocio Ford, Jean G. Bustamante, Carlos Seminara, Daniela Shriver, Mark Ziv, Elad Gonzalez Burchard, Esteban Haile, Robert Parra, Esteban Carracedo, Angel |
| spellingShingle |
Galanter, Joshua Mark Fernandez-Lopez, Juan Carlos Gignoux, Christopher R. Barnholtz-Sloan, Jill Fernandez-Rozadilla, Ceres Via, Marc Hidalgo-Miranda, Alfredo Contreras, Alejandra V. Figueroa, Laura Uribe Raska, Paola Jimenez-Sanchez, Gerardo Silva Zolezzi, Irma Torres, Maria Ponte, Clara Ruiz 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 Gutierrez, Gerardo Brutsaert, Tom León-Velarde, Fabiola Moore, Lorna G. Vargas, Enrique Cruz, Miguel Escobedo, Jorge Rodriguez-Santana, José Rodriguez-Cintrón, William Chapela, Rocio Ford, Jean G. Bustamante, Carlos Seminara, Daniela Shriver, Mark Ziv, Elad Gonzalez Burchard, Esteban Haile, Robert Parra, Esteban Carracedo, Angel Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
| author_facet |
Galanter, Joshua Mark Fernandez-Lopez, Juan Carlos Gignoux, Christopher R. Barnholtz-Sloan, Jill Fernandez-Rozadilla, Ceres Via, Marc Hidalgo-Miranda, Alfredo Contreras, Alejandra V. Figueroa, Laura Uribe Raska, Paola Jimenez-Sanchez, Gerardo Silva Zolezzi, Irma Torres, Maria Ponte, Clara Ruiz 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 Gutierrez, Gerardo Brutsaert, Tom León-Velarde, Fabiola Moore, Lorna G. Vargas, Enrique Cruz, Miguel Escobedo, Jorge Rodriguez-Santana, José Rodriguez-Cintrón, William Chapela, Rocio Ford, Jean G. Bustamante, Carlos Seminara, Daniela Shriver, Mark Ziv, Elad Gonzalez Burchard, Esteban Haile, Robert Parra, Esteban Carracedo, Angel |
| author_sort |
Galanter, Joshua Mark |
| title |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
| title_short |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
| title_full |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
| title_fullStr |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
| title_full_unstemmed |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
| title_sort |
development of a panel of genome-wide ancestry informative markers to study admixture throughout the americas |
| description |
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. |
| publisher |
Public Library of Science |
| publishDate |
2012 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297575/ |
| _version_ |
1611511645142515712 |