Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas
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 a...
- Autores:
-
Galanter, Joshua Mark
Fernández López, Juan Carlos
Gignoux, Christopher
Barnholtz Sloan, Jill
Fernández Rozadilla, Ceres
Via, Marc
Hidalgo Miranda, Alfredo
Contreras, Alejandra
Uribe Figueroa, Laura
Raska, Paola
Jiménez Sánchez, Gerardo
Silva Zolezzi, Irma
Torres, Maria
Ruíz Ponte, Clara
Ruíz, Yarimar
Salas, Antonio
Nguyen, Elizabeth
Eng, Celeste
Borjas, Lisbeth
Zabala, William
Barreto, Guillermo
Rondón González, Fernando
Ibarra Rodríguez, Adriana Alexandra
Taboada, Patricia
Porras, Liliana
Moreno, Fabián
Bigham, Abigail
Gutierrez, Gerardo
Brutsaert, Tom
León Velarde, Fabiola
Moore, Lorna
Vargas, Enrique
Cruz, Miguel
Escobedo, Jorge
Rodríguez Santana, José
Rodríguez Cintrón, William
Chapela, Rocio
Ford, Jean
Bustamante, Carlos
Seminara, Daniela
Shriver, Mark
Ziv, Elad
González Burchard, Esteban
Haile, Robert
Parra, Esteban
Carracedo, Ángel
- Tipo de recurso:
- Article of investigation
- Fecha de publicación:
- 2012
- Institución:
- Universidad de Antioquia
- Repositorio:
- Repositorio UdeA
- Idioma:
- eng
- OAI Identifier:
- oai:bibliotecadigital.udea.edu.co:10495/23705
- Acceso en línea:
- http://hdl.handle.net/10495/23705
- Palabra clave:
- Genética de Población
Genetics, Population
América Latina
Latin America
Herencia
Heredity
Genética Humana
Human Genetics
- Rights
- openAccess
- License
- http://creativecommons.org/licenses/by/2.5/co/
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oai:bibliotecadigital.udea.edu.co:10495/23705 |
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UDEA2 |
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Repositorio UdeA |
repository_id_str |
|
dc.title.spa.fl_str_mv |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
title |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas |
spellingShingle |
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas Genética de Población Genetics, Population América Latina Latin America Herencia Heredity Genética Humana Human Genetics |
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 |
dc.creator.fl_str_mv |
Galanter, Joshua Mark Fernández López, Juan Carlos Gignoux, Christopher Barnholtz Sloan, Jill Fernández Rozadilla, Ceres Via, Marc Hidalgo Miranda, Alfredo Contreras, Alejandra Uribe Figueroa, Laura Raska, Paola Jiménez Sánchez, Gerardo Silva Zolezzi, Irma Torres, Maria Ruíz Ponte, Clara Ruíz, Yarimar Salas, Antonio Nguyen, Elizabeth Eng, Celeste Borjas, Lisbeth Zabala, William Barreto, Guillermo Rondón González, Fernando Ibarra Rodríguez, Adriana Alexandra Taboada, Patricia Porras, Liliana Moreno, Fabián Bigham, Abigail Gutierrez, Gerardo Brutsaert, Tom León Velarde, Fabiola Moore, Lorna Vargas, Enrique Cruz, Miguel Escobedo, Jorge Rodríguez Santana, José Rodríguez Cintrón, William Chapela, Rocio Ford, Jean Bustamante, Carlos Seminara, Daniela Shriver, Mark Ziv, Elad González Burchard, Esteban Haile, Robert Parra, Esteban Carracedo, Ángel |
dc.contributor.author.none.fl_str_mv |
Galanter, Joshua Mark Fernández López, Juan Carlos Gignoux, Christopher Barnholtz Sloan, Jill Fernández Rozadilla, Ceres Via, Marc Hidalgo Miranda, Alfredo Contreras, Alejandra Uribe Figueroa, Laura Raska, Paola Jiménez Sánchez, Gerardo Silva Zolezzi, Irma Torres, Maria Ruíz Ponte, Clara Ruíz, Yarimar Salas, Antonio Nguyen, Elizabeth Eng, Celeste Borjas, Lisbeth Zabala, William Barreto, Guillermo Rondón González, Fernando Ibarra Rodríguez, Adriana Alexandra Taboada, Patricia Porras, Liliana Moreno, Fabián Bigham, Abigail Gutierrez, Gerardo Brutsaert, Tom León Velarde, Fabiola Moore, Lorna Vargas, Enrique Cruz, Miguel Escobedo, Jorge Rodríguez Santana, José Rodríguez Cintrón, William Chapela, Rocio Ford, Jean Bustamante, Carlos Seminara, Daniela Shriver, Mark Ziv, Elad González Burchard, Esteban Haile, Robert Parra, Esteban Carracedo, Ángel |
dc.subject.decs.none.fl_str_mv |
Genética de Población Genetics, Population América Latina Latin America Herencia Heredity Genética Humana Human Genetics |
topic |
Genética de Población Genetics, Population América Latina Latin America Herencia Heredity Genética Humana Human Genetics |
description |
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. |
publishDate |
2012 |
dc.date.issued.none.fl_str_mv |
2012 |
dc.date.accessioned.none.fl_str_mv |
2021-11-02T19:10:02Z |
dc.date.available.none.fl_str_mv |
2021-11-02T19:10:02Z |
dc.type.spa.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.coarversion.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
dc.type.hasversion.spa.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.coar.spa.fl_str_mv |
http://purl.org/coar/resource_type/c_2df8fbb1 |
dc.type.redcol.spa.fl_str_mv |
https://purl.org/redcol/resource_type/ART |
dc.type.local.spa.fl_str_mv |
Artículo de investigación |
format |
http://purl.org/coar/resource_type/c_2df8fbb1 |
status_str |
publishedVersion |
dc.identifier.citation.spa.fl_str_mv |
Galanter JM, Fernandez-Lopez JC, Gignoux CR, Barnholtz-Sloan J, Fernandez-Rozadilla C, et al. (2012) Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas. PLoS Genet 8(3): e1002554. doi:10.1371/journal.pgen.1002554 |
dc.identifier.issn.none.fl_str_mv |
1553-7390 |
dc.identifier.uri.none.fl_str_mv |
http://hdl.handle.net/10495/23705 |
dc.identifier.doi.none.fl_str_mv |
10.1371/journal.pgen.1002554 |
dc.identifier.eissn.none.fl_str_mv |
1553-7404 |
identifier_str_mv |
Galanter JM, Fernandez-Lopez JC, Gignoux CR, Barnholtz-Sloan J, Fernandez-Rozadilla C, et al. (2012) Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas. PLoS Genet 8(3): e1002554. doi:10.1371/journal.pgen.1002554 1553-7390 10.1371/journal.pgen.1002554 1553-7404 |
url |
http://hdl.handle.net/10495/23705 |
dc.language.iso.spa.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartofjournalabbrev.spa.fl_str_mv |
PLoS Genet. |
dc.rights.spa.fl_str_mv |
info:eu-repo/semantics/openAccess |
dc.rights.uri.*.fl_str_mv |
http://creativecommons.org/licenses/by/2.5/co/ |
dc.rights.accessrights.spa.fl_str_mv |
http://purl.org/coar/access_right/c_abf2 |
dc.rights.creativecommons.spa.fl_str_mv |
https://creativecommons.org/licenses/by/4.0/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
http://creativecommons.org/licenses/by/2.5/co/ http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
dc.format.extent.spa.fl_str_mv |
16 |
dc.format.mimetype.spa.fl_str_mv |
application/pdf |
dc.publisher.spa.fl_str_mv |
Public Library of Science |
dc.publisher.group.spa.fl_str_mv |
Identificación Genética - IdentiGEN |
dc.publisher.place.spa.fl_str_mv |
San Francisco, Estados Unidos |
institution |
Universidad de Antioquia |
bitstream.url.fl_str_mv |
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bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 MD5 |
repository.name.fl_str_mv |
Repositorio Institucional Universidad de Antioquia |
repository.mail.fl_str_mv |
andres.perez@udea.edu.co |
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1812173097529245696 |
spelling |
Galanter, Joshua MarkFernández López, Juan CarlosGignoux, ChristopherBarnholtz Sloan, JillFernández Rozadilla, CeresVia, MarcHidalgo Miranda, AlfredoContreras, AlejandraUribe Figueroa, LauraRaska, PaolaJiménez Sánchez, GerardoSilva Zolezzi, IrmaTorres, MariaRuíz Ponte, ClaraRuíz, YarimarSalas, AntonioNguyen, ElizabethEng, CelesteBorjas, LisbethZabala, WilliamBarreto, GuillermoRondón González, FernandoIbarra Rodríguez, Adriana AlexandraTaboada, PatriciaPorras, LilianaMoreno, FabiánBigham, AbigailGutierrez, GerardoBrutsaert, TomLeón Velarde, FabiolaMoore, LornaVargas, EnriqueCruz, MiguelEscobedo, JorgeRodríguez Santana, JoséRodríguez Cintrón, WilliamChapela, RocioFord, JeanBustamante, CarlosSeminara, DanielaShriver, MarkZiv, EladGonzález Burchard, EstebanHaile, RobertParra, EstebanCarracedo, Ángel2021-11-02T19:10:02Z2021-11-02T19:10:02Z2012Galanter JM, Fernandez-Lopez JC, Gignoux CR, Barnholtz-Sloan J, Fernandez-Rozadilla C, et al. (2012) Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas. PLoS Genet 8(3): e1002554. doi:10.1371/journal.pgen.10025541553-7390http://hdl.handle.net/10495/2370510.1371/journal.pgen.10025541553-7404ABSTRACT: 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.COL003542916application/pdfengPublic Library of ScienceIdentificación Genética - IdentiGENSan Francisco, Estados Unidosinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_2df8fbb1https://purl.org/redcol/resource_type/ARTArtículo de investigaciónhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/2.5/co/http://purl.org/coar/access_right/c_abf2https://creativecommons.org/licenses/by/4.0/Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the AmericasGenética de PoblaciónGenetics, PopulationAmérica LatinaLatin AmericaHerenciaHeredityGenética HumanaHuman GeneticsPLoS Genet.PLoS Genetics11683CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8927http://bibliotecadigital.udea.edu.co/bitstream/10495/23705/2/license_rdf1646d1f6b96dbbbc38035efc9239ac9cMD52ORIGINALIbarraAdriana_2012_DevelopmentGenomeAncestry.pdfIbarraAdriana_2012_DevelopmentGenomeAncestry.pdfArtículo de investigaciónapplication/pdf1110304http://bibliotecadigital.udea.edu.co/bitstream/10495/23705/1/IbarraAdriana_2012_DevelopmentGenomeAncestry.pdf935fbaa51d3e0ef38086b3f060758e7eMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748http://bibliotecadigital.udea.edu.co/bitstream/10495/23705/3/license.txt8a4605be74aa9ea9d79846c1fba20a33MD5310495/23705oai:bibliotecadigital.udea.edu.co:10495/237052021-11-02 14:10:02.63Repositorio Institucional Universidad de Antioquiaandres.perez@udea.edu.coTk9URTogUExBQ0UgWU9VUiBPV04gTElDRU5TRSBIRVJFClRoaXMgc2FtcGxlIGxpY2Vuc2UgaXMgcHJvdmlkZWQgZm9yIGluZm9ybWF0aW9uYWwgcHVycG9zZXMgb25seS4KCk5PTi1FWENMVVNJVkUgRElTVFJJQlVUSU9OIExJQ0VOU0UKCkJ5IHNpZ25pbmcgYW5kIHN1Ym1pdHRpbmcgdGhpcyBsaWNlbnNlLCB5b3UgKHRoZSBhdXRob3Iocykgb3IgY29weXJpZ2h0Cm93bmVyKSBncmFudHMgdG8gRFNwYWNlIFVuaXZlcnNpdHkgKERTVSkgdGhlIG5vbi1leGNsdXNpdmUgcmlnaHQgdG8gcmVwcm9kdWNlLAp0cmFuc2xhdGUgKGFzIGRlZmluZWQgYmVsb3cpLCBhbmQvb3IgZGlzdHJpYnV0ZSB5b3VyIHN1Ym1pc3Npb24gKGluY2x1ZGluZwp0aGUgYWJzdHJhY3QpIHdvcmxkd2lkZSBpbiBwcmludCBhbmQgZWxlY3Ryb25pYyBmb3JtYXQgYW5kIGluIGFueSBtZWRpdW0sCmluY2x1ZGluZyBidXQgbm90IGxpbWl0ZWQgdG8gYXVkaW8gb3IgdmlkZW8uCgpZb3UgYWdyZWUgdGhhdCBEU1UgbWF5LCB3aXRob3V0IGNoYW5naW5nIHRoZSBjb250ZW50LCB0cmFuc2xhdGUgdGhlCnN1Ym1pc3Npb24gdG8gYW55IG1lZGl1bSBvciBmb3JtYXQgZm9yIHRoZSBwdXJwb3NlIG9mIHByZXNlcnZhdGlvbi4KCllvdSBhbHNvIGFncmVlIHRoYXQgRFNVIG1heSBrZWVwIG1vcmUgdGhhbiBvbmUgY29weSBvZiB0aGlzIHN1Ym1pc3Npb24gZm9yCnB1cnBvc2VzIG9mIHNlY3VyaXR5LCBiYWNrLXVwIGFuZCBwcmVzZXJ2YXRpb24uCgpZb3UgcmVwcmVzZW50IHRoYXQgdGhlIHN1Ym1pc3Npb24gaXMgeW91ciBvcmlnaW5hbCB3b3JrLCBhbmQgdGhhdCB5b3UgaGF2ZQp0aGUgcmlnaHQgdG8gZ3JhbnQgdGhlIHJpZ2h0cyBjb250YWluZWQgaW4gdGhpcyBsaWNlbnNlLiBZb3UgYWxzbyByZXByZXNlbnQKdGhhdCB5b3VyIHN1Ym1pc3Npb24gZG9lcyBub3QsIHRvIHRoZSBiZXN0IG9mIHlvdXIga25vd2xlZGdlLCBpbmZyaW5nZSB1cG9uCmFueW9uZSdzIGNvcHlyaWdodC4KCklmIHRoZSBzdWJtaXNzaW9uIGNvbnRhaW5zIG1hdGVyaWFsIGZvciB3aGljaCB5b3UgZG8gbm90IGhvbGQgY29weXJpZ2h0LAp5b3UgcmVwcmVzZW50IHRoYXQgeW91IGhhdmUgb2J0YWluZWQgdGhlIHVucmVzdHJpY3RlZCBwZXJtaXNzaW9uIG9mIHRoZQpjb3B5cmlnaHQgb3duZXIgdG8gZ3JhbnQgRFNVIHRoZSByaWdodHMgcmVxdWlyZWQgYnkgdGhpcyBsaWNlbnNlLCBhbmQgdGhhdApzdWNoIHRoaXJkLXBhcnR5IG93bmVkIG1hdGVyaWFsIGlzIGNsZWFybHkgaWRlbnRpZmllZCBhbmQgYWNrbm93bGVkZ2VkCndpdGhpbiB0aGUgdGV4dCBvciBjb250ZW50IG9mIHRoZSBzdWJtaXNzaW9uLgoKSUYgVEhFIFNVQk1JU1NJT04gSVMgQkFTRUQgVVBPTiBXT1JLIFRIQVQgSEFTIEJFRU4gU1BPTlNPUkVEIE9SIFNVUFBPUlRFRApCWSBBTiBBR0VOQ1kgT1IgT1JHQU5JWkFUSU9OIE9USEVSIFRIQU4gRFNVLCBZT1UgUkVQUkVTRU5UIFRIQVQgWU9VIEhBVkUKRlVMRklMTEVEIEFOWSBSSUdIVCBPRiBSRVZJRVcgT1IgT1RIRVIgT0JMSUdBVElPTlMgUkVRVUlSRUQgQlkgU1VDSApDT05UUkFDVCBPUiBBR1JFRU1FTlQuCgpEU1Ugd2lsbCBjbGVhcmx5IGlkZW50aWZ5IHlvdXIgbmFtZShzKSBhcyB0aGUgYXV0aG9yKHMpIG9yIG93bmVyKHMpIG9mIHRoZQpzdWJtaXNzaW9uLCBhbmQgd2lsbCBub3QgbWFrZSBhbnkgYWx0ZXJhdGlvbiwgb3RoZXIgdGhhbiBhcyBhbGxvd2VkIGJ5IHRoaXMKbGljZW5zZSwgdG8geW91ciBzdWJtaXNzaW9uLgo= |