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  A different view on fine-scale population structure in Western African populations

Chaichoompu, K., Abegaz, F., Cavadas, B., Fernandes, V., Mueller-Myhsok, B., Pereira, L., et al. (2020). A different view on fine-scale population structure in Western African populations. Human Genetics, 139(1), 45-59. doi:10.1007/s00439-019-02069-7.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-FBB4-5 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-FBB5-4
Genre: Journal Article

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Chaichoompu, Kridsadakorn, Author
Abegaz, Fentaw, Author
Cavadas, Bruno, Author
Fernandes, Veronica, Author
Mueller-Myhsok, Bertram1, 2, Author              
Pereira, Luisa, Author
Van Steen, Kristel, Author
Affiliations:
1RG Müller-Myhsok, Dept. Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Max Planck Society, ou_2040288              
2RG Statistical Genetics, Dept. Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Max Planck Society, ou_2040288              

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 Abstract: Due to its long genetic evolutionary history, Africans exhibit more genetic variation than any other population in the world. Their genetic diversity further lends itself to subdivisions of Africans into groups of individuals with a genetic similarity of varying degrees of granularity. It remains challenging to detect fine-scale structure in a computationally efficient and meaningful way. In this paper, we present a proof-of-concept of a novel fine-scale population structure detection tool with Western African samples. These samples consist of 1396 individuals from 25 ethnic groups (two groups are African American descendants). The strategy is based on a recently developed tool called IPCAPS. IPCAPS, or Iterative Pruning to CApture Population Structure, is a genetic divisive clustering strategy that enhances iterative pruning PCA, is robust to outliers and does not require a priori computation of haplotypes. Our strategy identified in total 12 groups and 6 groups were revealed as fine-scale structure detected in the samples from Cameroon, Gambia, Mali, Southwest USA, and Barbados. Our finding helped to explain evolutionary processes in the analyzed West African samples and raise awareness for fine-scale structure resolution when conducting genome-wide association and interaction studies.

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Language(s): eng - English
 Dates: 2019-10-192020
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
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Title: Human Genetics
Source Genre: Journal
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Publ. Info: Berlin : Springer-Verlag
Pages: - Volume / Issue: 139 (1) Sequence Number: - Start / End Page: 45 - 59 Identifier: ISSN: 0340-6717
CoNE: https://pure.mpg.de/cone/journals/resource/954925519623