Hello biostars,
There are many options for downloading GWAS studies. For instance, the NHGRI GWAS catalog enables access to many of the studies at the level of association summary statistics via its ftp site. Alternatively, a search for "download GWAS data" in Google returns many hits, such as the IEU OpenGWAS project or the Atlas of genome wide association studies; there are even doit scripts available on github.
I am writing to ask if any one may have experience with the different options available, which one(s) you ultimately selected, and why you chose what you chose. For clarity, I am hoping to learn from your experience as well as learn about any caveats, e.g. "this one is good for this, but bad for this; this one is the largest; or even, across the board XYZ resource is the best."
Thank you,
1 answer
Hopefully you have your answer by now, but in case not: The NHGRI-EBI GWAS Catalog is by far the biggest resource of human GWAS summary statistics. Several of the other resources you might find, such as the IEU Open GWAS Catalog, the Knowledge Portal Network (https://kp4cd.org/), and GWAS Central, actually ingest data from the GWAS Catalog.
They do each have some additional studies that might not be available in the GWAS Catalog, though. For example, OpenGWAS have ingested several additional datasets in bulk, such as the Neale lab UKBiobank data. Knowledge Portals and GWAS Central take direct submissions from authors, some of which might not be available on the GWAS Catalog, although the GWAS Catalog is considered the main submission repository for GWAS. I would recommend starting with the GWAS Catalog and then checking the other resources if you don't find what you need.
The GWAS Catalog and OpenGWAS have minimum requirements for data ingest; both harmonise summary statistics and make them available in their own standard format. In the Knowledge Portals and GWAS Central you may find data in a mixture of formats.
Each resource has it's own "flavour". The GWAS Catalog is focused on submission, annotation and ensuring data is findable, accessible, interoperable and reusable. Data is ontology-annotated and searchable. The downloadable summary statistics are integrated with searchable "top associations" (extracted from publications, even when full genomewide summary statistics are not available), so you have a complete Catalog of GWAS results available to you. It has an API, but doesn't really offer any analytical tools. OpenGWAS is integrated with an analytical platform including widely used tools like MRBase, PRSice and coloc. The Knowledge Portals are also tools-based and are focused around specific research areas (e.g. cardiovascular disease), so it can be easy to find datasets of interest if that's your field. GWAS Central includes some nice tools for comparing and visualising datasets.
in summary, if you simply want GWAS data to download, the GWAS Catalog is the place to start. The other resources are valuable to find additional datasets or if you're planning to use their tools.
You also mentioned the GWAS Atlas - this resource was spun up to support a specific research project and hasn't been updated since 2019. The other resources mentioned above are actively maintained and updated regularly.
You might also be interested in Open Targets https://platform.opentargets.org/ - another platform that ingests data from the GWAS Catalog and other places, and performs fine mapping and integration with other data types, for drug target identification.
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