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Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset
Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203783/ https://www.ncbi.nlm.nih.gov/pubmed/27797945 http://dx.doi.org/10.1093/gbe/evw244 |
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author | Sengupta, Dhriti Choudhury, Ananyo Basu, Analabha Ramsay, Michèle |
author_facet | Sengupta, Dhriti Choudhury, Ananyo Basu, Analabha Ramsay, Michèle |
author_sort | Sengupta, Dhriti |
collection | PubMed |
description | Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto–Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India. |
format | Online Article Text |
id | pubmed-5203783 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-52037832017-01-06 Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset Sengupta, Dhriti Choudhury, Ananyo Basu, Analabha Ramsay, Michèle Genome Biol Evol Research Article Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto–Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India. Oxford University Press 2016-11-09 /pmc/articles/PMC5203783/ /pubmed/27797945 http://dx.doi.org/10.1093/gbe/evw244 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Research Article Sengupta, Dhriti Choudhury, Ananyo Basu, Analabha Ramsay, Michèle Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset |
title | Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset |
title_full | Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset |
title_fullStr | Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset |
title_full_unstemmed | Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset |
title_short | Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset |
title_sort | population stratification and underrepresentation of indian subcontinent genetic diversity in the 1000 genomes project dataset |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203783/ https://www.ncbi.nlm.nih.gov/pubmed/27797945 http://dx.doi.org/10.1093/gbe/evw244 |
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