13 February 2023 20:35
Hi Open Targets Community,
I downloaded the evidence data from ftp ( 22.11/output/etl/json/evidence/sourceId=ot_genetics_portal) to find variants associated with diseases of our interest. However, studies shown in the website and those in the downloaded data seem inconsistent.
For instance, the website shows the association of this study and COL1A1
However, in the downloaded data, the variant 17_49868692_C_T linked to ‘Liver enzyme levels (alkaline phosphatase)’ is only relevant to the nearest gene TAC4.
Could anyone help explain the difference? Any questions or recommendations are also welcome.
15 February 2023 15:18
My hypothesis now is the
prefiltration procedures (L2G=0.05), as this is also the min score in the local database. Any other comments are also welcome.
16 February 2023 18:43
@tzukuo! Welcome to the Open Targets Community
From my understanding, this is correct. As you saw in the documentation, the Open Targets Platform only includes associations where the L2G score is above a certain threshold.
Let us know if you have any further questions!
17 February 2023 07:45
Thank you for your kind feedback,
22 February 2023 14:47
@tzukuo! Someone else had the same question, and you might find this response helpful:
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 l…