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].
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 +
== References ==
  
 
<biblio>
 
<biblio>
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# McCarthyReview pmid=18398418
 
# McCarthyReview pmid=18398418
 
# FlintReview pmid=15803197
 
# FlintReview pmid=15803197
 +
# PricePC pmid=16862161
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# ServinImputation pmid=17676998
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# MarchiniImputation pmid=17572673
 
</biblio>
 
</biblio>

Revision as of 15:19, 5 February 2009

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

Contents

Introductory 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

An important and widely used approach to dealing with cryptic population structure [4], and key references on genotype imputation [5][6].

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

Error fetching PMID 16983374:
Error fetching PMID 18398418:
Error fetching PMID 15803197:
Error fetching PMID 16862161:
Error fetching PMID 17676998:
Error fetching PMID 17572673:
  1. Error fetching PMID 16983374: [BaldingTutorial]
  2. Error fetching PMID 18398418: [McCarthyReview]
  3. Error fetching PMID 15803197: [FlintReview]
  4. Error fetching PMID 16862161: [PricePC]
  5. Error fetching PMID 17676998: [ServinImputation]
  6. Error fetching PMID 17572673: [MarchiniImputation]
All Medline abstracts: PubMed HubMed