Any Recommendation On Program That Could Simulate Gwa Case/Control Data ?

Question

[Tg]

Hi, I wonder is program for simulate a gwa case/control data with LD pattern intact ( I want to use LD pattern from CEU hapmap). I want to simulate genotype for illumina/affymetrix chip.

From what I googling, I found gwasimulator (http://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator) and plink. Are these two ok for a jobs ? Or there's any better alternative ?

thanks

[jvijai]

Would permutation testing of the hapmap data work for your purpose. If the reason for simulation is to generate empirical p-values, then PLINK may work. http://pngu.mgh.harvard.edu/~purcell/plink/perm.shtml

Answer 1

[Genotepes]

Hi

GenomeSimla si doing OK. HapGen is not too bas neither and may require slightly less involvment and time to understand the parameters.

Disclaimer : didn't work on any of these program but used them both.

Answer 2

[Stephen]

Take a look at genomeSIMLA, also from Vanderbilt. Disclaimer: I worked on this project for a time when I was at Vanderbilt. It uses a forward-time approach with Hardy-Weinberg principles to generate LD. You can embed a disease model to simulate case-control outcomes, or simulate quantitative traits, including gene-gene interaction. The developer working on genomeSIMLA, Eric, is pretty prompt about answering questions or troubleshooting. Give it a try.

http://chgr.mc.vanderbilt.edu/genomeSIMLA/

Answer 3

[Larry_Parnell]

We do not do such here. We'd prefer to use real data. In that regard, I suggest you look at the GWAS data available from the Wellcome Trust Consortium.

I know some people who use PLINK but have never heard of them using it for the purpose you propose.

Added in edit 20 Sep 2011: There is a timely paper from the Butte group at Stanford using the available Wellcome Trust data to show that when one examines GWAS data by sex, there are important findings with respect to sex differences and disease risk. Take a look at the paper for details on analyzing data (genotypes) generated by another group.

[jvijai]

Would doing a permutation testing of the Hapmap data work for you? PLINK can do that.

[Tg]

Well, I just skim on it, didn't really go into detail on plink.

I do have some GWAS data (not wtccc one though) but I'm looking for some way to validate my analysis beside testing with real data.

Answer 4

[0Asa]

Note that there are also these:

• GENOME
• GCTA
• HAPGEN
• FREGEN

Haven't used any of them yet but planning to.

Also, I just asked a similar question right here.