SNPs and PharmGKB

Question

[mb2subi]

Hi,

Currently I have a project in the University where I have to infer some SNPs in format GRCh37 to a PharmGKB date base. I saw that is possible to download the datebase, but how can I infer this SNPs to PharmGKB and obtain information of the impact of genetic variation on drug response. It is possible to put all this in a python script and run it on Linux? Thanks in advance!

Answer 1

[Kevin Blighe]

You have to download the translation tables for your genes of interest (from PharmGKB) and then map your variants (per sample) to these translation tables. This will help you to identify to which haplotype your sample belongs for each gene of interest.

After that, you will have to use the available literature in order to gauge how each sample will respond to a given drug.