GIANT Consortium 2025 BMI GWAS Integration in Open Targets Genetics

General
1

Hi Open Targets team,

I wanted to check whether GWAS summary statistics from the GIANT consortium (e.g., BMI and related anthropometric traits) are currently incorporated into the Open Targets Genetics platform.

Specifically:

  • Are GIANT studies included as part of the GWAS evidence base?

  • If so, are they used in downstream analyses such as fine-mapping and L2G scoring?

  • More broadly, how does Open Targets handle large meta-analyses like GIANT relative to UK Biobank–derived datasets in terms of signal prioritization or deduplication?

We are assessing whether incorporating GIANT data into our internal pipelines would provide incremental value beyond what is already represented in Open Targets, so any clarification on coverage and integration would be very helpful.

Best regards,
Shicheng

2

Dear @Shicheng_Guo

All of our GWAS summary statistics studies are available in study dataset, please search for GIANT in the cohorts field, requested pubmedId, publicationTitle or GWAS Catalog identifier in studyId field to find relevant studies.

In short, we do not include other gwas data apart from Finngen r12 and GWAS Catalog, all meta analysis are ingested from GWAS Catalog, so if the meta analysis was ingested there before the platform release, it should be accessible on the platform.

Given the meta analysis comes from multiple ancestries, we use PICS fine-mapping to resolve. Currently we do not implement any deduplication strategy, although we are looking for implementing the replication flag for credible sets in upcoming releases which should give an insight on the signal duplication.

BW,
Szymon