Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.

Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in...

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Autores principales:	Rui Pereira, Christopher Phillips, Nádia Pinto, Carla Santos, Sidney Emanuel Batista dos Santos, António Amorim, Ángel Carracedo, Leonor Gusmão
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6e299ec146c346d6812b2afa2855c8d6
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spelling	oai:doaj.org-article:6e299ec146c346d6812b2afa2855c8d62021-11-18T07:30:13ZStraightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.1932-620310.1371/journal.pone.0029684https://doaj.org/article/6e299ec146c346d6812b2afa2855c8d62012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22272242/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies. This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach. HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level. In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.Rui PereiraChristopher PhillipsNádia PintoCarla SantosSidney Emanuel Batista dos SantosAntónio AmorimÁngel CarracedoLeonor GusmãoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e29684 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rui Pereira Christopher Phillips Nádia Pinto Carla Santos Sidney Emanuel Batista dos Santos António Amorim Ángel Carracedo Leonor Gusmão Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
description	Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies. This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach. HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level. In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.
format	article
author	Rui Pereira Christopher Phillips Nádia Pinto Carla Santos Sidney Emanuel Batista dos Santos António Amorim Ángel Carracedo Leonor Gusmão
author_facet	Rui Pereira Christopher Phillips Nádia Pinto Carla Santos Sidney Emanuel Batista dos Santos António Amorim Ángel Carracedo Leonor Gusmão
author_sort	Rui Pereira
title	Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
title_short	Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
title_full	Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
title_fullStr	Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
title_full_unstemmed	Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
title_sort	straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/6e299ec146c346d6812b2afa2855c8d6
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Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.

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