Why are many studies having a completely empty results page? For example Open Targets Genetics
For studies with small samples sizes, and where none of the hits reached a GWAS-significant level, we report zero associations. This means that the basic information on the study will be in the Genetics portal, but the tables will be empty.
I should note: this information is still important for PheWAS, as we need to know what is associated but also what is not associated when it comes to a variant or target of interest.
I hope that helps!
Hi Helena, thank you very much for your email.
It is clear but still, I have some doubts.
Let’s have a look at CD40 variant rs1883832.
According to Orrù et al, Nat. Genetics 2020 (https://www.nature.com/articles/s41588-020-0684-4)
the variant rs1883832 should be associated to “expression of CD27 on memory-B-cell subsets (effect +0.64 s.d., P = 6.21 × 10−147) and decreases the level of a specific B-cell subset that does not express CD27 (IgD−CD27−; effect −0.39 s.d., P = 7.20 × 10−50)”, but these two strong associations are not present in the phewas plot at https://genetics.opentargets.org/variant/20_46118343_T_C. But the immune traits from that paper can be found (empty) in Opentargets…
Thank you so much for you patience,
I flagged your message to our Genetics team, and you’re right, it seems like the problem here is more complicated. Thank you very much for flagging this! We’re investigating it and we’ll let you know when we have a response.
The reason that the associations are missing for this study is because, while the study was added to the GWAS Catalog in October 2021, the associations themselves were only integrated in February 2022. We ran the release pipeline before the associations were added, so while the study appears in the Genetics portal, the associations do not.
However, those associations should appear on the study page with the next Genetics release. I should note: it usually takes a few months between releases of our data. Therefore, we generally don’t expect that studies updated in the GWAS Catalog will immediately appear in the Genetics portal.
Dear Helena, thank you very much for this feedback.
Are associations already available via the API even if they are not in the web interface? Or will they also be available via the API in the next release?
All the best,
The data that are shown in the web portal are the same as those in the API, so they will only be available in the next release.