HAPGEN2: simulation of multiple disease SNPs - PubMed (original) (raw)
HAPGEN2: simulation of multiple disease SNPs
Zhan Su et al. Bioinformatics. 2011.
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.
Figures
Fig. 1.
LD patterns, in terms of _r_2, in the HapMap reference haplotypes (top) and the simulated haplotypes (bottom).
Fig. 2.
Top plot shows the −log10(_P_-values) under the log-additive test at each SNP in the simulated data. The location of the disease SNPs, _d_1, _d_2, _d_3, are indicated (from left to right) by the vertical lines. Subsequent plots (from the top) show the _P_-values conditioned on the genotypes at _d_1, at _d_1 and _d_2 and at _d_1, _d_2 and _d_3.
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