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correlating SNP variant with clinical outcome in dbGaP

Hi, I have identified a SNP variant in a certain protein that has a RS number. I want to, using data in dbGaP or other databases to identify whether or not this SNP variant is correlated with poorer survival or disease outcome.

For example, I have the variant RS12345, and I would like to see if it is correlated with worse inflammatory bowel disease, or whether is it protective against IBD. How do I approach this problem?

Please assume that I have access to sequencing level data from dbGaP and that I have a high performance computing cluster.

Thanks!

rna-seq r dbgap
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written by thisisweisemail • thisisweisemail

Do you have patient demography data? If you have, you can do survival curve analysis between case and controls.

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written by cpad0112 cpad0112

Hello, sorry for the late reply. No, I haven't requested any data as of today. I am hoping to do exploratory analysis with public data first before diving into a request for controlled-access data.

Any suggestions?

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written by thisisweisemail • thisisweisemail

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