Stratification analysis

[micky]

Hello every one

I need a specialistic help on stratification analysis.

I'm doing a case/contro study on a multifactrorial genetics disease. 90 SNPs are analysed in the 2 populations (affected vs unaffected). The 90 SNPs have been choosen already in the literature for being reported to be associated with the disease. Populations are from Europe on the same country. Now the question is: is possible to run a stratification test with these SNPs? My concern is that the SNP are not covering all the autosomes and they are already selected to be associated somehow (even if they are not significant in my populations)

What is your opinion ? In closely related populations how many SNPs should be runned?

Cheers

Micky