ArticlePLoS computational biology2014
Enhanced methods for local ancestry assignment in sequenced admixed individuals.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Sparse vertex discriminant analysis: Variable selection for biomedical classification applications.Computational statistics & data analysis · 2025Article
- Opportunities and challenges of local ancestry in genetic association analyses.American journal of human genetics · 2025Review
- Estimation of genetic admixture proportions via haplotypes.Computational and structural biotechnology journal · 2024Article
- Article
- Unsupervised discovery of ancestry-informative markers and genetic admixture proportions in biobank-scale datasets.American journal of human genetics · 2023Article
- Summix: A method for detecting and adjusting for population structure in genetic summary data.American journal of human genetics · 2021Article
- Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases.International journal of molecular sciences · 2021Review
- Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations.Frontiers in genetics · 2021Article
- Putting RFMix and ADMIXTURE to the test in a complex admixed population.BMC genetics · 2020Article
- Identifying Rare Variant Associations in Admixed Populations.Scientific reports · 2019Article
- Genome-Wide Analysis of SNPs Is Consistent with No Domestic Dog Ancestry in the Endangered Mexican Wolf (Canis lupus baileyi).The Journal of heredity · 2018Article
- Ancestry Testing and the Practice of Genetic Counseling.Journal of genetic counseling · 2017Review
- Association between 8q24 Gene Polymorphisms and the Risk of Prostate Cancer: A Systematic Review and Meta-Analysis.Journal of Cancer · 2017Article
- Recent advances in the study of fine-scale population structure in humans.Current opinion in genetics & development · 2016Review
- Article
- Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.Genetics · 2015Article
- Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations.BMC bioinformatics · 2015Article
- Differential Evolution approach to detect recent admixture.BMC genomics · 2015Article
- Accurate inference of local phased ancestry of modern admixed populations.Scientific reports · 2014Article
- Inferring ancestry from population genomic data and its applications.Frontiers in genetics · 2014Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g., Latino Americans) plays a major role in medical and population genetic inferences, ranging from finding disease-risk loci, to inferring recombination rates, to mapping missing contigs in the human genome. Although many methods for local ancestry inference have been proposed, most are designed for use with genotyping arrays and fail to make use of the full spectrum of data available from sequencing. In addition, current haplotype-based approaches are very computationally demanding, requiring large computational time for moderately large sample sizes. Here we present new methods for local ancestry inference that leverage continent-specific variants (CSVs) to attain increased performance over existing approaches in sequenced admixed genomes. A key feature of our approach is that it incorporates the admixed genomes themselves jointly with public datasets, such as 1000 Genomes, to improve the accuracy of CSV calling. We use simulations to show that our approach attains accuracy similar to widely used computationally intensive haplotype-based approaches with large decreases in runtime. Most importantly, we show that our method recovers comparable local ancestries, as the 1000 Genomes consensus local ancestry calls in the real admixed individuals from the 1000 Genomes Project. We extend our approach to account for low-coverage sequencing and show that accurate local ancestry inference can be attained at low sequencing coverage. Finally, we generalize CSVs to sub-continental population-specific variants (sCSVs) and show that in some cases it is possible to determine the sub-continental ancestry for short chromosomal segments on the basis of sCSVs.
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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.