Methods For Investigating Gene-Environment Interactions?

Question

[Faisal]

I am looking for material that give overview statistical methods for gene-environment interaction.

Answer 1

[matted]

Here are some review articles that should get you started (all in Nature Reviews Genetics because why not):

• "Gene–environment interactions in human diseases" (2005)
• "A tutorial on statistical methods for population association studies" (relevant section and citations for GxE effects) (2006)
• "Detecting gene–gene interactions that underlie human diseases" (epistasis detection overlaps with GxE conceptually) (2009)
• "Gene–environment-wide association studies: emerging approaches" (2010)

Answer 2

[Giovanni M Dall'Olio]

Have a look at the work done by Anna Di Rienzo's and Graham Coop's labs, who published many papers on how geographical environmental variables have constrained the genetics of human populations. You should be able to find many interesting articles on their websites.

One work by Di RIenzo and Coop is DBCline, a database that allows to see if the distribution of the allele frequency of a given SNP is correlated with a list of environmental variable. For example, you can see if there are SNPs close to the LCT gene that are correlated for the type of Foraging. Have a look at it.

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screnshot from dbcline:

dbcline allows to check if the allele frequency of a SNP is correlated with a geographical variable, like climate, temperature and diet.