How to choose SNPs for a case control study?

Question

[bio.informatics.016]

Hello everyone,

Before conducting a case control study about the genetic bases of certain disease based on candidate gene(s), it is a very important step to know which SNPs are more suitable for that disease in a given population. I found that we have to choose SNPs with certain characteristics such as: their position, functionality, association with other diseases and whether they are tagging SNPs or not. Unfortunately, until now I do not know how and from where we can determine these SNPs. Therefore, I am looking for the correct steps to follow in such approach in order to get better results.

Thanks a lot.

Answer 1

[Ibrahim Tanyalcin]

Dear,

I do not know which disorder you are interested however you can check clinvar (http://www.ncbi.nlm.nih.gov/clinvar/), dbsnp (http://www.ncbi.nlm.nih.gov/SNP/ this one also integrates Clinvar), ensembl variation database (http://www.ensembl.org/biomart/martview/) or cosmic database (http://cancer.sanger.ac.uk/cosmic). If you want to check more in depth the relationship with a given SNV and a research conducted, go for OMIM.

Regards,

[bio.informatics.016]

Dear Ibrahim,

First of all, I'd like to thank you for your useful answer as it directed me toward more specific research. The problem is that I'm a beginner in bioinformatics; therefore I cann't find the required information easily from these databases. I'm kindly looking for an assistance in this field...

Warm regards.

Answer 2

[mastal511]

If you are looking at candidate genes, then presumably you have the results of a previous study or studies which implicated certain genes, and you now want to have a more detailed look at those genes or regions of the chromosomes.

[bio.informatics.016]

Thank you for your kind response, but actually what happens now is that I'm using those results from previously published articles. What I need is to know how to determine the most correct SNPs for my research, to avoid getting less informative results like what happened to my colleague in his research,since he built the study on such published data. For example, I've read an article that used the threshold of being >45% difference in the genotypic frequencies in African vs Non-African ancestries as a criteria for SNP inclusion in the study. So, what is the factor that determines this threshold?!! From where to get such information about SNPs?!!