Putting RFMix and ADMIXTURE to the test in a complex admixed population
Date
2020
Journal Title
Journal ISSN
Volume Title
Publisher
BMC (part of Springer Nature)
Abstract
Background: Global and local ancestry inference in admixed human populations can be performed using
computational tools implementing distinct algorithms. The development and resulting accuracy of these tools has
been tested largely on populations with relatively straightforward admixture histories but little is known about how
well they perform in more complex admixture scenarios.
Results: Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry
proportions even in a complex 5-way admixed population, in addition to assigning local ancestry with an accuracy
of 89%. The ability of RFMix to determine global and local ancestry to a high degree of accuracy, particularly in
admixed populations provides the opportunity for more accurate association analyses.
Conclusion: This study highlights the utility of the extension of computational tools to become more compatible
to genetically structured populations, as well as the need to expand the sampling of diverse world-wide
populations. This is particularly noteworthy as modern-day societies are becoming increasingly genetically complex
and some genetic tools and commonly used ancestral populations are less appropriate. Based on these caveats and
the results presented here, we suggest that RFMix be used for both global and local ancestry estimation in worldwide
complex admixture scenarios particularly when including these estimates in association studies.
Description
CITATION: Uren, C., Hoal, E. G. & Moller, M. 2020. Putting RFMix and ADMIXTURE to the test in a complex admixed population. BMC Genetics, 21:40, doi:10.1186/s12863-020-00845-3.
The original publication is available at https://bmcinfectdis.biomedcentral.com
Publication of this article was funded by the Stellenbosch University Open Access Fund
The original publication is available at https://bmcinfectdis.biomedcentral.com
Publication of this article was funded by the Stellenbosch University Open Access Fund
Keywords
Population genetics -- Computer programs, RFMix, ADMIXTURE, Racially mixed people -- Genetic aspects, Heridity -- Forcasting, Genealogy -- Computer programs
Citation
Uren, C., Hoal, E. G. & Moller, M. 2020. Putting RFMix and ADMIXTURE to the test in a complex admixed population. BMC Genetics, 21:40, doi:10.1186/s12863-020-00845-3