Genome Wide Association Studies

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

Introductory reading

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

Statistical Methodology

An important and widely used approach to dealing with cryptic population structure PricePC, and key references on genotype imputation ServinImputationMarchiniImputation.

A powerful approach to deal with strain structure or relatedness between individuals KangEMMA.

Software

PLINK is an excellent data handling tool, and implements many useful statistical methods. It's the Swiss Army Knife for GWAS.

EIGENSOFT is widely used for population structure analysis and correction.

IMPUTE and SNPTEST, or MACH and ProbABEL, or BimBam, and all be used to perform more sophisticated model based genotype imputation and association testing.

QUICKTEST is our own software for association testing using uncertain genotypes. For quantitative trait analysis, we think it is faster and better than SNPTEST.

References

<biblio>

1. BaldingTutorial pmid=16983374
2. McCarthyReview pmid=18398418
3. FlintReview pmid=15803197
4. PricePC pmid=16862161
5. ServinImputation pmid=17676998
6. MarchiniImputation pmid=17572673
7. KangEMMA pmid=18385116

</biblio>