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...

Full description

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/
id UDEA2_1790d7887ce0861840209a64a23ce688
oai_identifier_str oai:bibliotecadigital.udea.edu.co:10495/23705
network_acronym_str UDEA2
network_name_str 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 http://bibliotecadigital.udea.edu.co/bitstream/10495/23705/2/license_rdf
http://bibliotecadigital.udea.edu.co/bitstream/10495/23705/1/IbarraAdriana_2012_DevelopmentGenomeAncestry.pdf
http://bibliotecadigital.udea.edu.co/bitstream/10495/23705/3/license.txt
bitstream.checksum.fl_str_mv 1646d1f6b96dbbbc38035efc9239ac9c
935fbaa51d3e0ef38086b3f060758e7e
8a4605be74aa9ea9d79846c1fba20a33
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
_version_ 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.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