A Monte Carlo test of linkage disequilibrium for single nucleotide polymorphisms

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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 2 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 r 2 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.

Original languageEnglish (US)
Article number124
JournalBMC Research Notes
Volume4
DOIs
StatePublished - Apr 18 2011

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Linkage Disequilibrium
Polymorphism
Single Nucleotide Polymorphism
Nucleotides
Statistics
Haplotypes
Genes
Testing
Genome
Genetic Association Studies
Population

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

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A Monte Carlo test of linkage disequilibrium for single nucleotide polymorphisms. / Xu, Hongyan; George, Varghese.

In: BMC Research Notes, Vol. 4, 124, 18.04.2011.

Research output: Contribution to journalArticle

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