Gold standard for new L2G scores

Technical Support
1

Hi all,

Thank you for the recent update to the platform including the new L2G scores! I’ve been looking through them and was just wondering, was the gold standard used for the model training the same as in the previous OTG version of L2G scores? Thanks and let me know if I can clarify the question at all!

2

Hi abhukku,

The gold standards used for L2G in the merged platform are similar but expanded compared to the previous OTG portal version. We’ve generated an Effector Gene List, which is comprised of:

  • The medium & high confidence gold standards from OTG 10.2024
  • Gene-drug pairs from CHEMBL which passed clinical trial phases 3 & 4
  • Gene-disease associations with a high evidence score from ClinVar, UniProt, Gene2Phenotype, Genomics England PanelApp and ClinGen.

You can find more detail on how positives/negatives were assigned here:

Let us know if you have any more questions!

1 Like
3

Thanks so much for the helpful reply! Is the Effector Gene List that was utilized publicly available anywhere?

Thanks again for all the help!

4

No problem!

You can access the full gold standard json here: