Comparación de cuatro programas utilizados en la determinación de la composición genética ancestral de la población antioqueña
DOI:
https://doi.org/10.22380/2539472X.1031Palabras clave:
mezcla genética, población antioqueña, marcadores informativos de ancestralidadResumen
La población antioqueña posee una estructura genética compleja que refleja su historia de mezclas entre poblaciones europeas, africanas y amerindias. En este estudio se determinó la composición genética de 849 individuos de la población antioqueña, utilizando un panel de 75 marcadores informativos de ancestralidad y 4 programas que implementan métodos bayesianos para inferir la composición de la mezcla ancestral. La contribución europea (60%) fue dos veces mayor que la contribución amerindia (28%), ambas con una distribución amplia, y fue poca la contribución africana (12%). Se estimó el tiempo transcurrido desde el primer evento de mezcla, que fue de 11 generaciones por cada 100 cM, lo cual hace de esta población un recurso útil para implementar estudios de mapeo por mezcla. Se evaluó la utilidad del panel de marcadores, así como la robustez y utilidad de los diferentes programas utilizados.
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Referencias bibliográficas
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Carvajal-Carmona, L. G., Iván D. Soto, Nicolás Pineda, Daniel Ortiz-Barrientos, Constanza Duque, Jorge Ospina-Duque, Mark McCarthy,
Patricia Montoya, Víctor M. Álvarez, Gabriel Bedoya y Andrés Ruiz-Linares. 2000. “Strong Amerind/white Sex Bias and a Possible Sephardic
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Falush, Daniel, Matthew Stephens y Jonathan K. Pritchard. 2003. “Inference of Population Structure Using Multilocus Genotype Data:
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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”.
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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.
Bedoya, Gabriel, Patricia Montoya, Jenny García, Iván Soto, Stephane Bourgeois, Luis Carvajal, Damian Labuda, Víctor Álvarez, Jorge Ospina,
Philip. W. Hedrick y Andrés Ruiz-Linares. 2006. “Admixture Dynamics in Hispanics: A Shift in the Nuclear Genetic Ancestry of a South
American Population Isolate”. Proceedings of the National Academy of Sciences 103 (19): 7234-7239.
Bonilla, Carolina, Esteban J. Parra, Carrie L. Pfaff, Sonia Dios, Julie A. Marshall, Richard F. Hamm an, Robert E. Ferrell, Clive L. Hogg art, Paul
M. McKeigue y Mark D. Shriver. 2004. “Admixture in the Hispanics of the San Luis Valley, Colorado, and Its Implications for Complex
Trait Gene Mapping”. Annals of Human Genetics 68, parte 2: 139-153.
Bryc, Katarzyna, Adam Auton, Matthew R. Nelson, Jorge R. Oksenberg, Stephen L. Hauser, Scott Williams, Alain Froment, Jean M. Bodo,
Charles Wambebe, Sarah A. Tishkoff y Carlos. D. Bustamante. 2010.
“Genome-wide Patterns of Population Structure and Admixture in West Africans and African Americans”. Proceedings of the National
Academy of Sciences 107 (2): 786-791.
Carvajal-Carmona, Luis G., Roel Ophoff, Susan Service, Jaana Hartiala, Julio Molina, Pedro León, Jorge Ospina, Gabriel Bedoya, Nelson Freimer
y Andrés Ruiz-Linares. 2003. “Genetic Demography of Antioquia (Colombia) and the Central Valley of Costa Rica”. Human Genetics
112 (5-6): 534-541.
Carvajal-Carmona, L. G., Iván D. Soto, Nicolás Pineda, Daniel Ortiz-Barrientos, Constanza Duque, Jorge Ospina-Duque, Mark McCarthy,
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.
Gómez-Pérez, Luis, Miguel A. Alfonso-Sánchez, Ana M. Pérez-Miranda, Susana García-Obregón, Juan J. Builes, María L. Bravo, Marian M.
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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Publicado
2012-06-30
Cómo citar
Duque, C. ., Parra, M. V. ., Valencia, A. V. ., Bedoya, . G. ., & Ruiz-Linares, A. . (2012). Comparación de cuatro programas utilizados en la determinación de la composición genética ancestral de la población antioqueña. Revista Colombiana De Antropología, 48(1), 233–257. https://doi.org/10.22380/2539472X.1031
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Cuestiones de método
