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A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population
Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South A...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869660/ https://www.ncbi.nlm.nih.gov/pubmed/24376522 http://dx.doi.org/10.1371/journal.pone.0082224 |
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author | Daya, Michelle van der Merwe, Lize Galal, Ushma Möller, Marlo Salie, Muneeb Chimusa, Emile R. Galanter, Joshua M. van Helden, Paul D. Henn, Brenna M. Gignoux, Chris R. Hoal, Eileen |
author_facet | Daya, Michelle van der Merwe, Lize Galal, Ushma Möller, Marlo Salie, Muneeb Chimusa, Emile R. Galanter, Joshua M. van Helden, Paul D. Henn, Brenna M. Gignoux, Chris R. Hoal, Eileen |
author_sort | Daya, Michelle |
collection | PubMed |
description | Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's [Image: see text]-statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population. |
format | Online Article Text |
id | pubmed-3869660 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-38696602013-12-27 A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population Daya, Michelle van der Merwe, Lize Galal, Ushma Möller, Marlo Salie, Muneeb Chimusa, Emile R. Galanter, Joshua M. van Helden, Paul D. Henn, Brenna M. Gignoux, Chris R. Hoal, Eileen PLoS One Research Article Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's [Image: see text]-statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population. Public Library of Science 2013-12-20 /pmc/articles/PMC3869660/ /pubmed/24376522 http://dx.doi.org/10.1371/journal.pone.0082224 Text en © 2013 Daya et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Daya, Michelle van der Merwe, Lize Galal, Ushma Möller, Marlo Salie, Muneeb Chimusa, Emile R. Galanter, Joshua M. van Helden, Paul D. Henn, Brenna M. Gignoux, Chris R. Hoal, Eileen A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population |
title | A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population |
title_full | A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population |
title_fullStr | A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population |
title_full_unstemmed | A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population |
title_short | A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population |
title_sort | panel of ancestry informative markers for the complex five-way admixed south african coloured population |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869660/ https://www.ncbi.nlm.nih.gov/pubmed/24376522 http://dx.doi.org/10.1371/journal.pone.0082224 |
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