Entering edit mode
11.0 years ago
anatopf
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0
What would it mean if the SNP frequency is smaller in cases than controls? I hove found this for at least 5 SNPs in a gene of interest Could anyone shed some light? I am confused thanks!
If I understood correctly, it may mean the SNP is protective. You should analyze the p-values using a statistical tool such as PLINK and then see if this makes sense biologically...(of course, you need to validate the results).
thanks, that was my thought too, although I still find it weird that it is not just one SNP, but 5?
(not thread related - with that name you HAVE to be from southamerica. I am Argentinian :-)
May be the five SNPs are in the same haplotype? Have you checked for linkage disequilibrium?
Using PLINK (as Pablo suggested) you may also check association of the haplotype itself with the disease.