Hdl Handle:
http://hdl.handle.net/10675.2/739
Title:
A Monte Carlo test of linkage disequilibrium for single nucleotide polymorphisms
Authors:
Xu, Hongyan; George, Varghese
Abstract:
Background: Genetic association studies, especially genome-wide studies, make use of linkage disequilibrium(LD) information between single nucleotide polymorphisms (SNPs). LD is also used for studying genome structure and has been valuable for evolutionary studies. The strength of LD is commonly measured by r2, a statistic closely related to the Pearson's x2 statistic. However, the computation and testing of linkage disequilibrium using r2 requires known haplotype counts of the SNP pair, which can be a problem for most population-based studies where the haplotype phase is unknown. Most statistical genetic packages use likelihood-based methods to infer haplotypes. However, the variability of haplotype estimation needs to be accounted for in the test for linkage disequilibrium.; Findings: We develop a Monte Carlo based test for LD based on the null distribution of the r2 statistic. Our test is based on r2 and can be reported together with r2. Simulation studies show that it offers slightly better power than existing methods.; Conclusions: Our approach provides an alternative test for LD and has been implemented as a R program for ease of use. It also provides a general framework to account for other haplotype inference methods in LD testing.
Citation:
BMC Res Notes. 2011 Apr 14; 4:124
Issue Date:
14-Apr-2011
URI:
http://hdl.handle.net/10675.2/739
DOI:
10.1186/1756-0500-4-124
PubMed ID:
21492446
PubMed Central ID:
PMC3096569
Type:
Article
ISSN:
1756-0500
Appears in Collections:
Department of Biochemistry and Molecular Biology: Faculty Research and Presentations

Full metadata record

DC FieldValue Language
dc.contributor.authorXu, Hongyanen_US
dc.contributor.authorGeorge, Vargheseen_US
dc.date.accessioned2012-10-26T20:27:53Zen
dc.date.available2012-10-26T20:27:53Zen
dc.date.issued2011-04-14en_US
dc.identifier.citationBMC Res Notes. 2011 Apr 14; 4:124en_US
dc.identifier.issn1756-0500en_US
dc.identifier.pmid21492446en_US
dc.identifier.doi10.1186/1756-0500-4-124en_US
dc.identifier.urihttp://hdl.handle.net/10675.2/739en
dc.description.abstractBackground: Genetic association studies, especially genome-wide studies, make use of linkage disequilibrium(LD) information between single nucleotide polymorphisms (SNPs). LD is also used for studying genome structure and has been valuable for evolutionary studies. The strength of LD is commonly measured by r2, a statistic closely related to the Pearson's x2 statistic. However, the computation and testing of linkage disequilibrium using r2 requires known haplotype counts of the SNP pair, which can be a problem for most population-based studies where the haplotype phase is unknown. Most statistical genetic packages use likelihood-based methods to infer haplotypes. However, the variability of haplotype estimation needs to be accounted for in the test for linkage disequilibrium.en_US
dc.description.abstractFindings: We develop a Monte Carlo based test for LD based on the null distribution of the r2 statistic. Our test is based on r2 and can be reported together with r2. Simulation studies show that it offers slightly better power than existing methods.en_US
dc.description.abstractConclusions: Our approach provides an alternative test for LD and has been implemented as a R program for ease of use. It also provides a general framework to account for other haplotype inference methods in LD testing.en_US
dc.rightsCopyright ©2011 Xu et al; licensee BioMed Central Ltd.en_US
dc.subjectShort Reporten_US
dc.titleA Monte Carlo test of linkage disequilibrium for single nucleotide polymorphismsen_US
dc.typeArticleen_US
dc.identifier.pmcidPMC3096569en_US
dc.contributor.corporatenameDepartment of Biostatistics and Epidemiologyen

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