期刊论文详细信息
PeerJ
Comparing local ancestry inference models in populations of two- and three-way admixture
article
Ryan Schubert1  Angela Andaleon2  Heather E. Wheeler2 
[1] Department of Mathematics and Statistics, Loyola University Chicago;Department of Biology, Loyola University Chicago;Program in Bioinformatics, Loyola University Chicago;Department of Public Health Sciences, Loyola University Chicago
关键词: Local ancestry;    Human genetics;    Admixture;    Benchmarking;    Population genetics;   
DOI  :  10.7717/peerj.10090
学科分类:社会科学、人文和艺术(综合)
来源: Inra
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【 摘 要 】

Local ancestry estimation infers the regional ancestral origin of chromosomal segments in admixed populations using reference populations and a variety of statistical models. Integrating local ancestry into complex trait genetics has the potential to increase detection of genetic associations and improve genetic prediction models in understudied admixed populations, including African Americans and Hispanics. Five methods for local ancestry estimation that have been used in human complex trait genetics are LAMP-LD (2012), RFMix (2013), ELAI (2014), Loter (2018), and MOSAIC (2019). As users rather than developers, we sought to perform direct comparisons of accuracy, runtime, memory usage, and usability of these software tools to determine which is best for incorporation into association study pipelines. We find that in the majority of cases RFMix has the highest median accuracy with the ranking of the remaining software dependent on the ancestral architecture of the population tested. Additionally, we estimate the O(n) of both memory and runtime for each software and find that for both time and memory most software increase linearly with respect to sample size. The only exception is RFMix, which increases quadratically with respect to runtime and linearly with respect to memory. Effective local ancestry estimation tools are necessary to increase diversity and prevent population disparities in human genetics studies. RFMix performs the best across methods, however, depending on application, other methods perform just as well with the benefit of shorter runtimes. Scripts used to format data, run software, and estimate accuracy can be found at https://github.com/WheelerLab/LAI_benchmarking.

【 授权许可】

CC BY   

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