ArticlePeerJ2020
Comparing local ancestry inference models in populations of two- and three-way admixture.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals.Nature genetics · 2023Pooled it
- Admixture-informed polygenic risk reporting using the ePRS framework.Nature communications · 2026Article
- Old vs. new local ancestry inference in HCHS/SOL: a comparative study.Human molecular genetics · 2025Article
- Phase-free local ancestry inference mitigates the impact of switch errors on phase-based methods.G3 (Bethesda, Md.) · 2025Article
- Genome-wide association analyses reveal susceptibility variants linked to Parkinson's disease in the South African population using inferred global and local ancestry.medRxiv : the preprint server for health sciences · 2025Article
- Potential Adaptive Introgression From Dogs in Iberian Grey Wolves (Canis lupus).Molecular ecology · 2025Article
- Opportunities and challenges of local ancestry in genetic association analyses.American journal of human genetics · 2025Review
- Old vs. New Local Ancestry Inference in HCHS/SOL: A Comparative Study.bioRxiv : the preprint server for biology · 2025Article
- Characterizing features affecting local ancestry inference performance in admixed populations.American journal of human genetics · 2025Article
- The expected polygenic risk score (ePRS) framework: an equitable metric for quantifying polygenetic risk via modeling of ancestral makeup.medRxiv : the preprint server for health sciences · 2024Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Characterizing features affecting local ancestry inference performance in admixed populations.bioRxiv : the preprint server for biology · 2024Article
- Article
- Article
- Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee.Genome biology and evolution · 2023Article
- AICRF: ancestry inference of admixed population with deep conditional random field.Journal of genetics · 2023Article
- GWAS in the southern African context.PloS one · 2022Article
- The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock.Animals : an open access journal from MDPI · 2021Review
- Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases.International journal of molecular sciences · 2021Review
- Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power.Nature genetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.