ArticleNucleic acids research2023
Rye: genetic ancestry inference at biobank scale.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 citations in OpenAlex.
- Phenome- and laboratory-wide meta-analyses of sickle cell trait reveal multi-system disease associations.American journal of human genetics · 2026Pooled it
- TLS-Tractor: A transfer learning framework for incorporating summary-statistics into local ancestry-aware GWAS in admixed populations.medRxiv : the preprint server for health sciences · 2026Article
- Limited Selection on Neanderthal DNA in 30,780 Recently Admixed Genomes with African-like Ancestry.Molecular biology and evolution · 2026Article
- A transparent and generalizable deep-learning framework for genomic ancestry prediction.American journal of human genetics · 2026Article
- A Genome-First Study of Familial Hypercholesterolemia Comparing African and European Ancestry Individuals.Circulation · 2026Article
- Article
- African ancestry-enriched variants in the GATM gene are associated with elevated serum creatinine levels.Genome medicine · 2026Article
- RNAScope-Ancestry: A Cross-Modality Framework for Inferring Genetic Ancestry from RNA-Seq with Application to MECA.Research square · 2026Article
- KANN: estimation of genetic ancestry profiles by nearest neighbor regression.Nucleic acids research · 2026Article
- GrafAnc: Reliable and reproducible inference of continental and regional population structure.HGG advances · 2026Article
- Admixture mapping identifies complex trait associations with local ancestry in themedRxiv : the preprint server for health sciences · 2025Article
- Pastrami: a fast and efficient algorithm for fine-scale genetic ancestry inference.NAR genomics and bioinformatics · 2025Article
- Characterization of shared and ancestry-specific signals driving complex traits using multi-ancestry fine-mapping.medRxiv : the preprint server for health sciences · 2025Article
- A Reassessment of the Genomic Ancestry of the World's Largest Captive Baboon Colony.American journal of primatology · 2025Article
- Short tandem repeats in populations of the Qinghai-Tibet Plateau and adjacent regions provide insights into high-altitude adaptation.Science advances · 2025Article
- Differential results of genetic risk scoring for multiple sclerosis in European and African American populations.Multiple sclerosis (Houndmills, Basingstoke, England) · 2025Article
- GWAS for Periodontitis Phenotypes Using Multi-Ancestry All of Us Research Platform.medRxiv : the preprint server for health sciences · 2025Article
- Classification of Heterotic Groups and Prediction of Heterosis in Sorghum Based on Whole-Genome Resequencing.International journal of molecular sciences · 2025Article
- SLCO1B1 Functional Variants, Bilirubin, Statin-Induced Myotoxicity, and Recent Sub-Saharan African Ancestry: A Precision Medicine Health Equity Study.Clinical pharmacology and therapeutics · 2025Article
- Genetic ancestry and population structure in the All of Us Research Program cohort.Nature communications · 2025Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Biobank projects are generating genomic data for many thousands of individuals. Computational methods are needed to handle these massive data sets, including genetic ancestry (GA) inference tools. Current methods for GA inference do not scale to biobank-size genomic datasets. We present Rye-a new algorithm for GA inference at biobank scale. We compared the accuracy and runtime performance of Rye to the widely used RFMix, ADMIXTURE and iAdmix programs and applied it to a dataset of 488221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis of genomic variant samples from ancestral reference populations and query individuals. The algorithm's accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares regression. Rye produces highly accurate GA estimates for three-way admixed populations-African, European and Native American-compared to RFMix and ADMIXTURE (${R}^2 = \ 0.998 - 1.00$), and shows 50× runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at both continental and subcontinental levels. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.
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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.