Data source scores ot_genetics_portal vs L2G in final association score

General
1

Hi,

I am wondering about ot_genetics_portal and l2g score. Some genes that have L2G score of >0.65 has been given a score of 0.5 for ot_genetics_portal. I am wondering why is that. The gene has no other genetic evidences such as gene_burden, genomics_england etc etc. Does that bring down the l2g score ?

2

Hi @gatla, and welcome to the Open Targets Community! :tada:

The L2G scores for genes are the evidence scores for the OT Genetics datasource. We apply a harmonic sum to the evidence scores, divided by the theoretical maximum, to calculate the data source score.


As a simple example, let’s take a look at the OT Genetics evidence for PCSK9 in familial hypercholesterolemia:

Screenshot 2024-05-08 at 12.00.28
Screenshot 2024-05-08 at 12.00.282618×1074 311 KB


  • There is one L2G score: 0.76377
  • If we divide this by the theoretical maximum, we have: 0.76377/1.644 = 0.46458…
  • This is the OT Genetics score that you can see by hovering over the cell (0.46)



You can find more information about the scoring calculations in our documentation.


Let me know if you have further questions!