Genome Wide Association Studies

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or using  
 
or using  
 
[http://www.sph.umich.edu/csg/abecasis/mach MACH] and  
 
[http://www.sph.umich.edu/csg/abecasis/mach MACH] and  
[http://mga.bionet.nsc.ru/%7Eyurii/ABEL/] ProbABEL.
+
[http://mga.bionet.nsc.ru/%7Eyurii/ABEL ProbABEL].
  
 
Our own software for association testing using uncertain genotypes is
 
Our own software for association testing using uncertain genotypes is

Revision as of 15:47, 5 February 2009

Some people in our group work on genome wide association studies (GWAS).

Recommended reading

For an introduction to GWAS, with an emphasis on human studies, you could start with a nice tutorial article [1], and a review of more recent issues [2]. There is also a nice review about approaches for rodent studies [3].

Statistical Methodology

Software

Many statistical methods are implemented in PLINK.

More sophisticated model based genotype imputation and association testing can be performed using IMPUTE and SNPTEST, or using MACH and ProbABEL.

Our own software for association testing using uncertain genotypes is QUICKTEST.

  1. Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet 2006 Oct; 7(10) 781-91. doi:10.1038/nrg1916 pmid:16983374. PubMed HubMed [BaldingTutorial]
  2. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, and Hirschhorn JN. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 2008 May; 9(5) 356-69. doi:10.1038/nrg2344 pmid:18398418. PubMed HubMed [McCarthyReview]
All Medline abstracts: PubMed HubMed