A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals

Taane Clark; Susana Campino; Elisa Anastasi; Sarah Auburn; Yik Teo; Kerrin Small; Kirk Rockett; Dominic Kwiatkowski; Christopher Holmes

doi:10.1093/bioinformatics/btq327

A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals

Taane Clark, Susana Campino, Elisa Anastasi, Sarah Auburn, Yik Teo, Kerrin Small, Kirk Rockett, Dominic Kwiatkowski, Christopher Holmes

Research output: Contribution to journal › Article › peer-review

Abstract

Motivation: Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under selection and/or associated with disease, and may have utility in trans-ethnic mapping studies.

Results: We present a novel pseudo Bayes factor (PBF) approach that assess differences in covariance of genotype frequencies from single nucleotide polymorphism (SNP) data from a genome-wide study. The magnitude of the PBF reflects the strength of evidence for a difference, while accounting for the sample size and number of SNPs, without the requirement for permutation testing to establish statistical significance. Application of the PBF to HapMap and Gambian malaria SNP data reveals regional LD differences, some known to be under selection.

Availability and implementation: The PBF approach has been implemented in the BALD (Bayesian analysis of LD differences) C++ software, and is available from http://homepages.lshtm.ac.uk/tgclark/downloads

Contact: taane.clark@lshtm.ac.uk

Original language	English
Pages (from-to)	1999-2003
Number of pages	5
Journal	Bioinformatics
Volume	26
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/btq327
Publication status	Published - 15 Aug 2010
Externally published	Yes

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10.1093/bioinformatics/btq327

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abstract = "Motivation: Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under selection and/or associated with disease, and may have utility in trans-ethnic mapping studies.Results: We present a novel pseudo Bayes factor (PBF) approach that assess differences in covariance of genotype frequencies from single nucleotide polymorphism (SNP) data from a genome-wide study. The magnitude of the PBF reflects the strength of evidence for a difference, while accounting for the sample size and number of SNPs, without the requirement for permutation testing to establish statistical significance. Application of the PBF to HapMap and Gambian malaria SNP data reveals regional LD differences, some known to be under selection.Availability and implementation: The PBF approach has been implemented in the BALD (Bayesian analysis of LD differences) C++ software, and is available from http://homepages.lshtm.ac.uk/tgclark/downloadsContact: taane.clark@lshtm.ac.uk",

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T1 - A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals

AU - Clark, Taane

AU - Campino, Susana

AU - Anastasi, Elisa

AU - Auburn, Sarah

AU - Teo, Yik

AU - Small, Kerrin

AU - Rockett, Kirk

AU - Kwiatkowski, Dominic

AU - Holmes, Christopher

PY - 2010/8/15

Y1 - 2010/8/15

N2 - Motivation: Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under selection and/or associated with disease, and may have utility in trans-ethnic mapping studies.Results: We present a novel pseudo Bayes factor (PBF) approach that assess differences in covariance of genotype frequencies from single nucleotide polymorphism (SNP) data from a genome-wide study. The magnitude of the PBF reflects the strength of evidence for a difference, while accounting for the sample size and number of SNPs, without the requirement for permutation testing to establish statistical significance. Application of the PBF to HapMap and Gambian malaria SNP data reveals regional LD differences, some known to be under selection.Availability and implementation: The PBF approach has been implemented in the BALD (Bayesian analysis of LD differences) C++ software, and is available from http://homepages.lshtm.ac.uk/tgclark/downloadsContact: taane.clark@lshtm.ac.uk

AB - Motivation: Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under selection and/or associated with disease, and may have utility in trans-ethnic mapping studies.Results: We present a novel pseudo Bayes factor (PBF) approach that assess differences in covariance of genotype frequencies from single nucleotide polymorphism (SNP) data from a genome-wide study. The magnitude of the PBF reflects the strength of evidence for a difference, while accounting for the sample size and number of SNPs, without the requirement for permutation testing to establish statistical significance. Application of the PBF to HapMap and Gambian malaria SNP data reveals regional LD differences, some known to be under selection.Availability and implementation: The PBF approach has been implemented in the BALD (Bayesian analysis of LD differences) C++ software, and is available from http://homepages.lshtm.ac.uk/tgclark/downloadsContact: taane.clark@lshtm.ac.uk

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EP - 2003

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

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A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals

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