Question About Gwas And Shared Controls.

Question

[bloodyangel.minus2]

I'm doing a GWAS using shared controls for 2 diseases, and I need to check if there is any statistical relation between the controls. I'm doing the 1-d.f. Mantel-extension test for differences in allele frequencies of SNPs between subjects, and I'm not really sure abut the results of the test. Which p-value is a "good" one on this kind of test for ensuring that there is no relation between the controls? Thanks in advance.

[lanjinglingxiaoni]

May I know how to do Mantel-extension test for differences in allele frequencies of SNPs?

I have read some materials but I am still very confused about how to prepare the data and which variable correspond to which one?

I am too desperate to ask here.........

Thanks

[Istvan Albert]

please don't post questions in the answer section, if you have a different question post it as such.

Answer 1

[Joachim]

I think you are looking for this publications:

• Zaykin and Kozbur, "P-value based analysis for shared controls design in genome-wide association studies", Genet Epidemiol. 2010 Nov;34(7):725-38., http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190645/

First paragraph from their discussion:

In this manuscript, we describe methods for combining and adjusting P-values in the context of the shared controls design. We suggest that P-value based analysis provides powerful means of inference for association studies that reuse control individuals.

Hope that helps.

[bloodyangel.minus2]

I had read that publication, however it doesn't have a reference value for checking the relation between controls. Thanks, though.