Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models

@article{Bercovici2012AncestryII,
  title={Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models},
  author={Sivan Bercovici and Jesse M. Rodriguez and Megan Elmore and Serafim Batzoglou},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  year={2012},
  volume={20 3},
  pages={
          199-211
        }
}
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… 

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References

SHOWING 1-10 OF 28 REFERENCES

Inferring Ancestries Efficiently in Admixed Populations with Linkage Disequilibrium

TLDR
This article presents a novel framework for the inference of ancestry at each chromosomal location that is polynomial in the number of markers and concludes that, with sufficient ancestral haplotypes, this framework can provide higher accuracy in inferring ancestral origin.

Reconstructing genetic ancestry blocks in admixed individuals.

TLDR
The Markov-hidden Markov model (MHMM) makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel, and one application of the method is to perform admixture mapping without genotyping special ancestry-informative-marker panels.

Effect of genetic divergence in identifying ancestral origin using HAPAA.

TLDR
A novel approach for ancestry inference, HAPAA (HMM-based analysis of polymorphisms in admixed ancestries), is described that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy.

Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

TLDR
HAPMIX will be of particular utility for mapping disease genes in recently admixed populations, as its accurate estimates of local ancestry permit admixture and case-control association signals to be combined, enabling more powerful tests of association than with either signal alone.

Methods for high-density admixture mapping of disease genes.

Admixture mapping (also known as "mapping by admixture linkage disequilibrium," or MALD) has been proposed as an efficient approach to localizing disease-causing variants that differ in frequency

Inference of locus-specific ancestry in closely related populations

TLDR
Previous methods for the inference of locus-specific ancestry are extended by the incorporation of a refined model of recombination events, resulting in a method that attains improved accuracies; the improvement is most significant when the ancestral populations are closely related.

Recombination rates in admixed individuals identified by ancestry-based inference

TLDR
The results suggest that outside of structurally variable regions, admixture does not substantially disrupt the factors controlling recombination rates in humans.

Estimating local ancestry in admixed populations.

The genetic structure of admixed populations.

TLDR
A chi-square test used to detect heterogeneity of admixture estimates from different alleles, or loci, can now be corrected for both sources of random errors, and its value for the detection of natural selection from heterogeneous admixtures estimates is improved.

Informativeness of genetic markers for inference of ancestry.

TLDR
In a worldwide human microsatellite data set, a general measure, the informativeness for assignment (I(n), is introduced, applicable to any number of potential source populations, for determining the amount of information that multiallelic markers provide about individual ancestry.