ArticleBioinformatics (Oxford, England)2012
Fast and accurate inference of local ancestry in Latino populations.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 171 papers, 6 of them syntheses that pooled it.
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Who cites it
171 citing papers in PubMed, 6 syntheses or guidelines pooled it, 264 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Population genetic considerations for using biobanks as international resources in the pandemic era and beyond.BMC genomics · 2021Pooled it
- An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos.The Journal of allergy and clinical immunology · 2019Pooled it
- Genome-wide association studies suggest that APOL1-environment interactions more likely trigger kidney disease in African Americans with nondiabetic nephropathy than strong APOL1-second gene interactions.Kidney international · 2018Pooled it
- Admixture mapping of uterine fibroid size and number in African American women.Fertility and sterility · 2017Pooled it
- Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.Human molecular genetics · 2014Pooled it
- Ancestry and genetic associations with bronchopulmonary dysplasia in preterm infants.American journal of physiology. Lung cellular and molecular physiology · 2018Trial
- GPC: An expressive and tractable deep generative model for genetic variation data.PLoS genetics · 2026Article
- Local ancestry inference with poorly-matched reference panels.PLoS genetics · 2026Article
- Allele frequency patterns of 78,122,254 SNPs illuminate diverse possible evolutionary trajectories of human populations.Scientific reports · 2026Article
- Admixture-informed polygenic risk reporting using the ePRS framework.Nature communications · 2026Article
- Strategies in Global Ancestry and Local Ancestry Inference.Current protocols · 2026Article
- Genomic landscape of hereditary cancer syndromes in the largest cohort in Colombia: a retrospective study.Lancet regional health. Americas · 2026Article
- From individuals to ancestries: Towards attributing trait variation to haplotypes.PLoS genetics · 2025Article
- Phase-free local ancestry inference mitigates the impact of switch errors on phase-based methods.G3 (Bethesda, Md.) · 2025Article
- Recomb-Mix: fast and accurate local ancestry inference.Bioinformatics (Oxford, England) · 2025Article
- AncestryGeni: a novel genetic ancestry classification pipeline for small and noisy sequence data.Bioinformatics (Oxford, England) · 2025Article
- SURFBAT: a surrogate family based association test building on large imputation reference panels.G3 (Bethesda, Md.) · 2025Article
- Opportunities and challenges of local ancestry in genetic association analyses.American journal of human genetics · 2025Review
- Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses.Nature communications · 2025Article
111 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
Abstract
motivationIt is becoming increasingly evident that the analysis of genotype data from recently admixed populations is providing important insights into medical genetics and population history. Such analyses have been used to identify novel disease loci, to understand recombination rate variation and to detect recent selection events. The utility of such studies crucially depends on accurate and unbiased estimation of the ancestry at every genomic locus in recently admixed populations. Although various methods have been proposed and shown to be extremely accurate in two-way admixtures (e.g. African Americans), only a few approaches have been proposed and thoroughly benchmarked on multi-way admixtures (e.g. Latino populations of the Americas).
resultsTo address these challenges we introduce here methods for local ancestry inference which leverage the structure of linkage disequilibrium in the ancestral population (LAMP-LD), and incorporate the constraint of Mendelian segregation when inferring local ancestry in nuclear family trios (LAMP-HAP). Our algorithms uniquely combine hidden Markov models (HMMs) of haplotype diversity within a novel window-based framework to achieve superior accuracy as compared with published methods. Further, unlike previous methods, the structure of our HMM does not depend on the number of reference haplotypes but on a fixed constant, and it is thereby capable of utilizing large datasets while remaining highly efficient and robust to over-fitting. Through simulations and analysis of real data from 489 nuclear trio families from the mainland US, Puerto Rico and Mexico, we demonstrate that our methods achieve superior accuracy compared with published methods for local ancestry inference in Latinos.
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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.