ArticleJournal of computational biology : a journal of computational molecular cell biology2013
Ancestry inference in complex admixtures via variable-length Markov chain linkage models.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.Human molecular genetics · 2014Pooled it
- Systematic Review on Local Ancestor Inference From a Mathematical and Algorithmic Perspective.Frontiers in genetics · 2021Review
- A comprehensive survey of models for dissecting local ancestry deconvolution in human genome.Briefings in bioinformatics · 2019Article
- ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium.BMC genetics · 2015Article
- Parente2: a fast and accurate method for detecting identity by descent.Genome research · 2015Article
- Inferring ancestry from population genomic data and its applications.Frontiers in genetics · 2014Review
- Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation.Bioinformatics (Oxford, England) · 2013Article
- Fast and accurate inference of local ancestry in Latino populations.Bioinformatics (Oxford, England) · 2012Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Inferring the ancestral origin of chromosomal segments in admixed individuals is key for genetic applications, ranging from analyzing population demographics and history, to mapping disease genes. Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes. In this paper we introduce ALLOY, an efficient method that incorporates generalized, but highly expressive, linkage disequilibrium models. ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations via an inhomogeneous variable-length Markov chain. We test ALLOY in a broad range of scenarios ranging from recent to ancient admixtures with up to four ancestral populations. We show that ALLOY outperforms the previous state of the art, and is robust to uncertainties in model parameters.
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Registered trials
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