The input to the platform (/evidence-files/genetics-portal-evidences.json.gz) and the platform view (Open Targets Platform) itself seems to be missing the evidence for TREM2 (“ENSG00000095970”) against Alzheimer’s. This is present in the genetics portal view (Open Targets Genetics).
In fact, only 6 lines of evidence are in the input file (for TREM2) as opposed to 106 in the genetics portal.
Hi Pankaj,
Welcome to the OpenTargets Community! On the OT Genetics Portal gene page you will found all the GWAS loci that could be linked to the gene TREM2.
If you apply a filter on the trait and narrow down the list to loci for Alzheimer disease (trait column drop-down filter), you’ll get only two of them, where the l2g score is 0.012 and 0.016, which are below the 0.05 threshold we apply to generate disease/target evidence for the Platform.
If you are looking for stronger l2g association like from Wojcik GL et al, where the locus was discovered for C-reactive protein measurement and the l2g score is 0.76, you’ll find the association in the relevant evidence page of the Platform.
Please let me know if my comment didn’t fully address your concern. And please don’t hesitate contacting us with further questions.
Best,
Daniel
Thanks, Daniel, that helps. I would have thought that the input file to the platform from the genetics portal would have all the associations. Is there a different file that has data consistent below the 0.05 platform threshold?
Hi Pankaj,
The unfiltered l2g dataset is available from ftp in parquet format: ftp://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/l2g
As this dataset in purely l2g, you might need to join with v2d dataset to get study and association level information: ftp://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/v2d
More details under this thread.
Best,
Daniel