Question: correlating SNP variant with clinical outcome in dbGaP
gravatar for thisisweisemail
3.4 years ago by
thisisweisemail0 wrote:

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.


rna-seq dbgap R • 664 views
ADD COMMENTlink written 3.4 years ago by thisisweisemail0

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

ADD REPLYlink written 3.4 years ago by cpad011214k

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?

ADD REPLYlink written 3.3 years ago by thisisweisemail0
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