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HAPGEN2: simulation of multiple disease SNPs.

ABSTRACT:

Motivation

Performing experiments with simulated data is an inexpensive approach to evaluating competing experimental designs and analysis methods in genome-wide association studies. Simulation based on resampling known haplotypes is fast and efficient and can produce samples with patterns of linkage disequilibrium (LD), which mimic those in real data. However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application.

Results

We introduce a new simulation algorithm based on a successful resampling method, HAPGEN, that can simulate multiple nearby disease SNPs on the same chromosome. The new method, HAPGEN2, retains many advantages of resampling methods and expands the range of disease models that current simulators offer.

Availability

HAPGEN2 is freely available from http://www.stats.ox.ac.uk/~marchini/software/gwas/gwas.html.

Contact

zhan@well.ox.ac.uk

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Su Z

PROVIDER: S-EPMC3150040 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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HAPGEN2: simulation of multiple disease SNPs.

Su Zhan Z Marchini Jonathan J Donnelly Peter P

Bioinformatics (Oxford, England) 20110608 16

<h4>Motivation</h4>Performing experiments with simulated data is an inexpensive approach to evaluating competing experimental designs and analysis methods in genome-wide association studies. Simulation based on resampling known haplotypes is fast and efficient and can produce samples with patterns of linkage disequilibrium (LD), which mimic those in real data. However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application.<h4 ...[more]

PMID: 21653516

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