correlating SNP variant with clinical outcome in dbGaP

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6.9 years ago

thisisweisemail • 0

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 • 1.2k views

ADD COMMENT • link 6.9 years ago by thisisweisemail • 0

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

ADD REPLY • link 6.9 years ago by cpad0112 21k

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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 REPLY • link 6.8 years ago by thisisweisemail • 0

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