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Question about SNPs data handling in the OMOP CDM

CDM Builders
#1

Hi,

Our research group has been using the CDM for a while now, and with some recent developments, we are going to get access to genotype data of several thousand patients with the aim of using this data for SNPs analyses.
We are interested in implementing this SNPs data to the CDM, and with some searching in these forums, I have come to know about Genomic-CDM. Is there anyone here using it on a regular basis for SNPs data analysis?
We would appreciate it if we can receive some guidance as well as tips and tricks regarding this matter from an experienced user.

Thank you in advance.

#2

@dorukorgun:

What kind of SNP data do you have? Somatic for oncology, or germline for all sorts of diseases?

#3

Hi Christian,

We have germline for all sorts of diseases.

#4

I see. Right now, we have made a collection for cancer. If we wanted to extend that we should figure out how to create a list of meaningful SNPs. Do you have anything like this?

#5

Hey Christian,

I am dearly sorry for the late reply.¨
Is the collection you are talking about implemented to Genomic CDM?¨

We have some ideas for the SNPs we would like to analyse in our projects, mainly related to immune cell or function related genes (interleukin receptors, toll-like receptors … etc.)

Does this answer your question?

Sincerely yours, Doruk

#6

No. It’s implemented through a Measurement vocabulary called OMOP Genomic. It contains variants, either of defined sequences or generally of a gene. There are no categorical concepts like families of genes (interleukin receptors) or pathways. There are also no concepts for gene or domain functions that may be affected.

Show us what you have.

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