Difference between revisions of "Genome Wide Association Studies"

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== Statistical Methodology ==
 
== Statistical Methodology ==
 +
 +
An important and widely used approach to dealing with cryptic population structure <cite>PricePC</cite>, and key references on genotype imputation <cite>ServinImputation</cite><cite>MarchiniImputation</cite>.
  
 
== Software ==
 
== Software ==
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More sophisticated model based genotype imputation and association testing can be performed using  
 
More sophisticated model based genotype imputation and association testing can be performed using  
 
[http://www.stats.ox.ac.uk/%7Emarchini/software/gwas/gwas.html IMPUTE and SNPTEST],
 
[http://www.stats.ox.ac.uk/%7Emarchini/software/gwas/gwas.html IMPUTE and SNPTEST],
or using
+
or  
 
[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], or [http://stephenslab.uchicago.edu/software.html BimBam].
  
 
Our own software for association testing using uncertain genotypes is
 
Our own software for association testing using uncertain genotypes is
 
[http://toby.freeshell.org/software/quicktest.shtml QUICKTEST].
 
[http://toby.freeshell.org/software/quicktest.shtml QUICKTEST].
 +
 +
== References ==
  
 
<biblio>
 
<biblio>
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# McCarthyReview pmid=18398418
 
# McCarthyReview pmid=18398418
 
# FlintReview pmid=15803197
 
# FlintReview pmid=15803197
 +
# PricePC pmid=16862161
 +
# ServinImputation pmid=17676998
 +
# MarchiniImputation pmid=17572673
 
</biblio>
 
</biblio>

Revision as of 16:19, 5 February 2009

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.

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 MACH and ProbABEL, or BimBam.

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

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

</biblio>