A Comparison of Gene Region Simulation Methods

Audrey E Hendricks, Josée Dupuis, Mayetri Gupta, Mark W Logue and Kathryn L Lunetta

PLOS ONE, 2012, vol. 7, issue 7, 1-12

Abstract: Background: Accurately modeling LD in simulations is essential to correctly evaluate new and existing association methods. At present, there has been minimal research comparing the quality of existing gene region simulation methods to produce LD structures similar to an existing gene region. Here we compare the ability of three approaches to accurately simulate the LD within a gene region: HapSim (2005), Hapgen (2009), and a minor extension to simple haplotype resampling. Methodology/Principal Findings: In order to observe the variation and bias for each method, we compare the simulated pairwise LD measures and minor allele frequencies to the original HapMap data in an extensive simulation study. When possible, we also evaluate the effects of changing parameters. Conclusion: We recommend using Hapgen to simulate replicate haplotypes from a gene region. Hapgen produces moderate sampling variation between the replicates while retaining the overall unique LD structure of the gene region.

Date: 2012
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0040925

DOI: 10.1371/journal.pone.0040925

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