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...
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2013
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oai:doaj.org-article:f67a454426964a82b186f80ce36b0e1e2021-11-18T08:41:02ZA panel of ancestry informative markers for the complex five-way admixed South African coloured population.1932-620310.1371/journal.pone.0082224https://doaj.org/article/f67a454426964a82b186f80ce36b0e1e2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24376522/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Admixture 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 In-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.Michelle DayaLize van der MerweUshma GalalMarlo MöllerMuneeb SalieEmile R ChimusaJoshua M GalanterPaul D van HeldenBrenna M HennChris R GignouxEileen HoalPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 12, p e82224 (2013) |
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Medicine R Science Q |
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Medicine R Science Q Michelle Daya Lize van der Merwe Ushma Galal Marlo Möller Muneeb Salie Emile R Chimusa Joshua M Galanter Paul D van Helden Brenna M Henn Chris R Gignoux Eileen Hoal A panel of ancestry informative markers for the complex five-way admixed South African coloured population. |
| 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 In-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 |
article |
| author |
Michelle Daya Lize van der Merwe Ushma Galal Marlo Möller Muneeb Salie Emile R Chimusa Joshua M Galanter Paul D van Helden Brenna M Henn Chris R Gignoux Eileen Hoal |
| author_facet |
Michelle Daya Lize van der Merwe Ushma Galal Marlo Möller Muneeb Salie Emile R Chimusa Joshua M Galanter Paul D van Helden Brenna M Henn Chris R Gignoux Eileen Hoal |
| author_sort |
Michelle Daya |
| title |
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_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_sort |
panel of ancestry informative markers for the complex five-way admixed south african coloured population. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2013 |
| url |
https://doaj.org/article/f67a454426964a82b186f80ce36b0e1e |
| work_keys_str_mv |
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