Missing colocalisation data in latest Genetics Portal release

Hello Open Targets Community! :wave:

One of our users has reported issues with the colocalisation data in our latest Genetics release (v6). Our team have reviewed the datasets and pipelines and we have identified the issue:

Between 10% - 30% of GWAS colocalisations are showing incorrect values (both GWAS-GWAS colocs, and GWAS-QTL colocs). In these cases, we have most often been reporting a low colocalisation probability where a higher one should be shown. This primarily affects regions where a GWAS or QTL study has multiple signals within 1 Mb of each other.

We are currently preparing for an update and the plan is to release it during w/c 7 February 2022.

If you have any questions or concerns, please comment below or send us an email at helpdesk@opentargets.org.

~ Andrew :slight_smile:


An update on this!

In the latest release (v7), we solved this issue by re-running the >4 million colocalisation tests. Users may therefore notice discrepancies with the colocalisation data from previous releases.

To be clear: colocalisation data from our previous release should not be used.

You can find more information on version 7 of Open Targets Genetics in the release blog: Open Targets Genetics: version 7 is out!