Comparison of Four Softwares Used to Determining the Ancestral Genetic Composition of the Antioquian Population
DOI:
https://doi.org/10.22380/2539472X.1031Keywords:
genetic admixture, Antioquian population, ancestry informative markersAbstract
The genetic structure of the population of Antioquia is complex and arises from the historical admixture of European, African and Amerindian populations. The genetic makeup of 849 Antioquian individuals was determined using a set of 75 ancestry informative markers and four computer programs based on Bayesian methods in order to infer the composition of ancestral admixture. A great European component (60%) was twice as high as the Amerindian contribution (28%), both with broad distributions, followed by a smaller African contribution (12%). The average number of generations since the admixture event was 11 generations per 100 cM, which makes this population a useful resource to implement admixture mapping studies. The usefulness of the marker set as well as the power and helpfulness of the computer programs were assessed.
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References
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Journal of Human Genetics 75 (5): 771-789.
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125 (5-6): 565-579.
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Carla Gallo, Giovanni Poletti, Guido Mazzotti, Kim Hill, Ana M.
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Trait Gene Mapping”. Annals of Human Genetics 68, parte 2: 139-153.
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“Genome-wide Patterns of Population Structure and Admixture in West Africans and African Americans”. Proceedings of the National
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112 (5-6): 534-541.
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Patricia Montoya, Víctor M. Álvarez, Gabriel Bedoya y Andrés Ruiz-Linares. 2000. “Strong Amerind/white Sex Bias and a Possible Sephardic
Contribution among the Founders of a Population in Northwest Colombia”. American Journal of Human Genetics 67 (5): 1287-1295.
Falush, Daniel, Matthew Stephens y Jonathan K. Pritchard. 2003. “Inference of Population Structure Using Multilocus Genotype Data:
Linked Loci and Correlated Allele Frequencies”. Genetics 164 (4): 1567-1587.
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de Pancorbo y José A. Pena. 2010. “Genetic Admixture Estimates by Alu Elements in Afro-Colombian and Mestizo Populations from
Antioquia, Colombia”. Annals of Human Biology 37 (4): 488-500. doi: 10.3109/03014460903433810.
Halder, Indrani y Mark D. Shriver. 2003. “Measuring and Using Admixture to Study the Genetics of Complex Diseases”. Human Genomics 1 (1): 52-62.
Hoggart, Clive J., Esteban J. Parra, Mark D. Shriver, Carolina Bonilla, Rick A. Kittles, David G. Clayton y Paul M. McKeigue. 2003. “Control of Confounding of Genetic Associations in Stratified Populations”.
American Journal of Human Genetics 72 (6): 1492-1504. Hoggart, Clive J., Mark D. Shriver, Rick A. Kittles, David G. Clayton y
Paul M. McKeigue. 2004. “Design and Analysis of Admixture Mapping Studies”. American Journal of Human Genetics 74 (5): 965-978.
International HapMap Consortium. 2003. “The International HapMap Project”. Nature 426 (6968): 789-796.
Long, Jeffrey C. 1991. “The Genetic Structure of Admixed Populations”. Genetics 127: 417-428.
Mao, Xianyun, Abigail W. Bigham, Rui Mei, Gerardo Gutiérrez, Ken M. Weiss, Tom D. Brutsaert, Fabiola León-Velarde, Lorna G. Moore, Enrique
Vargas, Paul M. McKeigue, Mark D. Shriver y Esteban J. Parra. 2007. “A Genomewide Admixture Mapping Panel for Hispanic/Latino Populations”. American Journal of Human Genetics 80 (6): 1171-1178.
Martínez-Marignac, Verónica L., Adán Valladares, Emily Cameron, Andrea Chan, Arjuna Perera, Rachel Globus-Goldberg, Niels Wacher, Jesús Kumate, Paul McKeigue, David O’Donnell, Mark D. Shriver, Miguel Cruz y Esteban J. Parra. 2007. “Admixture in Mexico City: Implications for Admixture Mapping of Type 2 Diabetes Genetic Risk Factors”. Human Genetics 120 (6): 807-819.
McKeigue, Paul M. 2005. “Prospects for Admixture Mapping of Complex Traits”. American Journal of Human Genetics 76 (1): 1-7.
Molokhia, Mariam, Clive Hogg art, Alan L. Patrick, Mark Shriver, Esteban Parra, J. Ye, Alan J. Silman y Paul M. McKeigue. 2003. “Relation of Risk of Systemic Lupus Erythematosus to West African Admixture in a Caribbean Population”. Human Genetics 112 (3): 310-318.
Montana, Giovanni y Jonathan K. Pritchard. 2004. “Statistical Tests for Admixture Mapping with Case-control and Cases-only Data”. American
Journal of Human Genetics 75 (5): 771-789.
Parra, Esteban J., Amy Marcini, Joshua Akey, Jeremy Martinson, Mark A. Batzer, Richard Cooper, Terrence Forrester, David B. Allison, Ranjan
Deka, Robert E. Ferrell y Mark D. Shriver. 1998. “Estimating African American Admixture Proportions By Use of Population-specific
Alleles”. American Journal of Human Genetics 63 (6): 1839-1851.
Patterson, Nick, Neil Hattangadi, Barton Lane, Kirk E. Lohmueller, David A. Hafler, Jorge R. Oksenberg, Stephen L. Hauser, Michael W. Smith, Stephen J. O’Brien, David Altshuler, Mark J. Daly y David Reich. 2004. “Methods for High-Density Admixture Mapping of Disease Genes”. American Journal of Human Genetics 74 (5): 979-1000.
Price, Alkes L., Nick Patterson, Fuli Yu, David R. Cox, Alicj a Waliszewska, Gavin J. McDonald, Arti Tandon, Chistine Schirmer, Julie Neubauer,
Gabriel Bedoya, Constanza Duque, Alberto Villegas, María Catira Bortolini, Francisco M. Salzano, Carla Gallo, Guido Mazzotti, Marcela
Tello-Ruiz, Laura Riba, Carlos A. Aguilar-Salinas, Samuel Canizales-Quinteros, Marta Menjivar, William Klitz, Brian Henderson, Christopher A. Haiman, Cheryl Winkler, Teresa Tusie-Luna, Andrés Ruiz-Linares y David Reich. 2007. “A Genomewide Admixture Map for Latino Populations”. American Journal of Human Genetics 80 (6): 1024-1036.
Pritchard, Jonathan K. y Noah A. Rosenberg. 1999. “Use of Unlinked Genetic Markers to Detect Population Stratification in Association
Studies”. American Journal of Human Genetics 65 (1): 220-228.
Pritchard, Jonathan K., Matthew Stephens y Peter Donnelly. 2000. “Inference of Population Structure Using Multilocus Genotype Data”. Genetics 155 (2): 945-959.
Reich, David y Nick Patterson. 2005. “Will Admixture Mapping Work to Find Disease Genes?”. Philosophical Transactions of the Royal
Society: Biological Sciences 360 (1460): 1605-1607.
Sánchez Albornoz, Nicolás. 1977. La poblacion de America Latina: desde los tiempos precolombinos. Madrid: Alianza.
Seldin, Michael F. 2007. “Admixture Mapping as a Tool in Gene Discovery”. Current Opinion in Genetics and Development 17 (3):177-181.
Seldin, Michael F., Bogdan Pasaniuc y Alkes L. Price. 2011. “New Approaches to Disease Mapping in Admixed Populations”. Nature Reviews Genetics 12 (8): 523-528.
Service, Susan, Joseph DeYoung, María Karayiorgou, J. Louw Roos, Herman Pretorious, Gabriel Bedoya, Jorge Ospina, Andrés Ruiz-Linares, Antonio Macedo, Joana A. Palha, Peter Heutink, Yurii Aulchenko, Ben Oostra, Cornelia van Duijn, Marjo Riitta Jarvelin, Tepp o Varilo, Lynette Pedd le, Proton Rahman, Giovanna Piras, María Monne, Sarah Murray, Luana Galver, Leena Peltonen, Chiara Sabatti, Andrew Collins y Nelson Freimer. 2006. “Magnitude and Distribution of Linkage Disequilibrium in Population Isolates and Implications for Genome-wide Association Studies”. Nature Genetics 38 (5): 556-560.
Shriver, Mark D., Esteban J. Parra, Sonia Dios, Carolina Bonilla, Heather Norton, Celina Jovel, Carrie Pfaff, Cecily Jones, Aisha Massac, Neil Cameron, Archie Baron, Tabitha Jackson, George Argyropoulos, Li Jin, Clive J. Hoggart, Paul M. McKeigue y Rick A. Kittles. 2003. “Skin Pigmentation, Biogeographical Ancestry and Admixture Mapping”. Human Genetics 112 (4): 387-399.
Smith, Michael W. y Stephen J. O’Brien. 2005. “Mapping by Admixture Linkage Disequilibrium: Advances, Limitations and Guidelines”. Nature Reviews Genetics 6 (8): 623-632.
Smith, Michael W., Nick Patterson, James A. Lautenberger, Ann L. Truelove, Gavin J. McDonald, Alicj a Waliszewska, Bailey D. Kessing, Michael J. Malasky, Charles Scafe, Ernest Le, Philip L. De Jager, André A. Mignault, Zeng Yi, Guy De The, Myron Essex, Jean L. Sankale, Jason H. Moore, Kwabena Poku, John P. Phair, James J. Goedert, David Vlahov, Scott M. Williams, Sarah A. Tishkoff, Cheryl A. Winkler, Francisco M. de la Vega, Trevor Woodage, John J. Sninsky, David A. Hafler, David
Altshuler, Dennis. A. Gilbert, Stephen J. O’Brien y David Reich. 2004. “AHigh-density Admixture Map for Disease Gene Discovery in African Americans”. American Journal of Human Genetics 74 (5): 1001-1013.
Tang, Kai, Dong J. Fu, Dominique Julien, Andreas Braun, Charles R. Cantor y Hubert Koster. 1999. “Chip-based Genotyping by Mass
Spectrometry”. Proceedings of the National Academy of Sciences 96 (18): 10016-10020.
Tian, Chao, David A. Hinds, Russell Shigeta, Rick Kittles, Dennis G. Ballinger y Michael F. Seldin. 2006. “A Genomewide Single-nucleotidepolymorphism
Panel with High Ancestry Information for African American Admixture Mapping”. American Journal of Human Genetics
79 (4): 640-649. doi: S0002-9297(07)63074-2 [pii].
Vergara, Candelaria, Luis Caraballo, Dilia Mercado, Silvia Jiménez, Winston Rojas, Nicholas Rafaels, Tracey Hand, Mónica Camp bell, Yuhjung
J. Tsai, Li Gao, Constanza Duque, Sergio López, Gabriel Bedoya, Andrés Ruiz-Linares y Kathleen C. Barnes. 2009. “African Ancestry
is Associated with Risk of Asthma and High Total Serum IgE in a Population from the Caribbean Coast of Colombia”. Human Genetics
125 (5-6): 565-579.
Wang, Sijia, Nicolas Ray, Winston Rojas, María V. Parra, Gabriel Bedoya,
Carla Gallo, Giovanni Poletti, Guido Mazzotti, Kim Hill, Ana M.
Hurtado, Beatriz Camrena, Humberto Nicolini, William Klitz, Ramiro Barrantes, Julio A. Molina, Nelson B. Freimer, María Catira Bortolini, Francisco M. Salzano, María L. Petzl-Erler, Luiza T. Tsuneto, José E. Dipierri, Emma L. Alfaro, Graciela Bailliet, Néstor O. Bianchi, Elena Llop, Francisco Rothhamm er, Laurent Excoffier y Andrés Ruiz-Linares. 2008. “Geographic Patterns of Genome Admixture in Latin American Mestizos”. PLoS Genetics 4 (3): e1000037.
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Published
2012-06-30
How to Cite
Duque, C. ., Parra, M. V. ., Valencia, A. V. ., Bedoya, . G. ., & Ruiz-Linares, A. . (2012). Comparison of Four Softwares Used to Determining the Ancestral Genetic Composition of the Antioquian Population. Revista Colombiana De Antropología, 48(1), 233–257. https://doi.org/10.22380/2539472X.1031
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Cuestiones de método
