title: HAPGEN2: simulation of multiple disease SNPs.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  HAPGEN2 is freely available from http://www.stats.ox.ac.uk/~marchini/software/gwas/gwas.html.
  
  
  BACKGROUND
  zhan@well.ox.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK. zhan@well.ox.ac.uk
authors.forename: Zhan
authors.initials: Z
authors.lastname: Su
authors.forename: Jonathan
authors.initials: J
authors.lastname: Marchini
authors.forename: Peter
authors.initials: P
authors.lastname: Donnelly
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004194:Disease / Q000235:genetics*; D055106:Genome-Wide Association Study; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012984:Software