Inference of locus-specific ancestry in closely related populations

Autor: Gad Kimmel, Bogdan Pasaniuc, Sriram Sankararaman, Eran Halperin
Rok vydání: 2009
Předmět:
Statistics and Probability
Bioinformatics
Population
European Continental Ancestry Group
Genetic admixture
Inference
Single-nucleotide polymorphism
Locus (genetics)
Biology
Biochemistry
White People
Mathematical Sciences
03 medical and health sciences
0302 clinical medicine
Genetic
Gene Frequency
Information and Computing Sciences
Human Genome Project
Genetic variation
Genetics
Humans
education
Molecular Biology
030304 developmental biology
Genetic association
Recombination
Genetic
African Americans
0303 health sciences
education.field_of_study
Genome
Genome
Human
Computational Biology
Genetic Variation
Biological Sciences
Original Papers
Recombination
Computer Science Applications
Black or African American
Population Genomics
Computational Mathematics
Genetics
Population
Computational Theory and Mathematics
Evolutionary biology
Ismb/Eccb 2009 Conference Proceedings June 27 to July 2
2009
Stockholm
Sweden
030217 neurology & neurosurgery
Imputation (genetics)
Human
Zdroj: Bioinformatics (Oxford, England), vol 25, iss 12
Bioinformatics
ISSN: 1367-4811
1367-4803
DOI: 10.1093/bioinformatics/btp197
Popis: A characterization of the genetic variation of recently admixed populations may reveal historical population events, and is useful for the detection of single nucleotide polymorphisms (SNPs) associated with diseases through association studies and admixture mapping. Inference of locus-specific ancestry is key to our understanding of the genetic variation of such populations. While a number of methods for the inference of locus-specific ancestry are accurate when the ancestral populations are quite distant (e.g. African–Americans), current methods incur a large error rate when inferring the locus-specific ancestry in admixed populations where the ancestral populations are closely related (e.g. Americans of European descent). Results: In this work, we extend previous methods for the inference of locus-specific ancestry by the incorporation of a refined model of recombination events. We present an efficient dynamic programming algorithm to infer the locus-specific ancestries in this model, resulting in a method that attains improved accuracies; the improvement is most significant when the ancestral populations are closely related. An evaluation on a wide range of scenarios, including admixtures of the 52 population groups from the Human Genome Diversity Project demonstrates that locus-specific ancestry can indeed be accurately inferred in these admixtures using our method. Finally, we demonstrate that imputation methods can be improved by the incorporation of locus-specific ancestry, when applied to admixed populations. Availability: The implementation of the WINPOP model is available as part of the LAMP package at http://lamp.icsi.berkeley.edu/lamp Contact: heran@icsi.berkeley.edu
Databáze: OpenAIRE
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