Which studies that can be used for L2G

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1

Hi!

I have a batch of variants that I am using the API to extract in python. The V2G is working great, but I have a question about L2G.

Is there a list of the studies that can be used with L2G? The only one I’m aware of right now is “FINNGEN_R5_E4_DM2” since I found an example script with this study in the Forum.

Also, my variants are identified as potential Alzheimer’s disease targets… does this implicate a certain study_id above as being optimal to use? When using the FINNGEN study all of the L2G results were empty although the V2G worked.

Thank you so much,
Aaron

2

Hi @sosaar, and welcome to the Open Targets Community! :partying_face:

I’m not sure I understand your question.

In the post you are referring to, Andrew used FINNGEN_R5_E4_DM2 as an example of new data in Open Targets Genetics, but you could apply the same code to a different study (not necessarily one from FinnGen), by replacing the study and variant IDs with the ones you are interested in — see an example in the API Playground.

Let me know if this answers your question!

Helena

3

Hi, thank you for your response!

My question is as simple as wondering which studies are available for me to choose from (is there a list somewhere?). I think I may have found my answer by simply typing “Alzheimer’s” into the search bar and jotting down the unique study IDs that pop up.

This leads to a follow-up question. I have 148 SNPs I’d like to examine within the context of Alzheimer’s. Within each study, only some of my SNPs have associated L2G scores. Should I wish to identify V2G/L2G associations for each SNP is this is a viable procedure:

  1. Mine V2G for each variant as V2G provides score at every variant position
  2. Mine L2G for each variant using Alzheimer’s Studies
  3. When available, use L2G over V2G, and when L2G has no hits, default to using the V2G

This procedure would leave me with gene-associations for all my variants, some of which are bolstered by the L2G and some of which have to rely on only V2G.

Thank you so much!
Aaron