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mStruct: inference of population structure in light of both genetic admixing and allele mutations.

Authors
  • Shringarpure, Suyash
  • Xing, Eric P
Type
Published Article
Journal
Genetics
Publication Date
Jun 01, 2009
Volume
182
Issue
2
Pages
575–593
Identifiers
DOI: 10.1534/genetics.108.100222
PMID: 19363128
Source
Medline
License
Unknown

Abstract

Traditional methods for analyzing population structure, such as the Structure program, ignore the influence of the effect of allele mutations between the ancestral and current alleles of genetic markers, which can dramatically influence the accuracy of the structural estimation of current populations. Studying these effects can also reveal additional information about population evolution such as the divergence time and migration history of admixed populations. We propose mStruct, an admixture of population-specific mixtures of inheritance models that addresses the task of structure inference and mutation estimation jointly through a hierarchical Bayesian framework, and a variational algorithm for inference. We validated our method on synthetic data and used it to analyze the Human Genome Diversity Project-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) cell line panel of microsatellites and HGDP single-nucleotide polymorphism (SNP) data. A comparison of the structural maps of world populations estimated by mStruct and Structure is presented, and we also report potentially interesting mutation patterns in world populations estimated by mStruct.

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