Open Targets Genetics: version 2 is out
Following our sold-out workshop at ASHG2018, we are excited to announce we have a new release of Open Targets Genetics.
The highlights in this new release are:
- GWAS Catalog curated data now updated to 2019-03-01
- Effect sizes for curated variant-disease associations now harmonised
Improved V2G pipeline
We assign variants to genes using the variant-to-gene (V2G) pipeline, which now includes:
- Distance between variants and canonical TSS within a 500Kb region
- Intronic, UTR variants and NMD variants scored as 0.1 in the V2G assignment
New summary views and tables
In the page for any given genetic variant, e.g. rs4129267 (1_154426264_C_T in GRCh37 coordinates), we have a new summary view, which displays:
- Most severe consequence from the Ensembl Variant Effect Predictor
- Population allele frequencies from gnomAD
- CADD scores, both raw and scaled
The tables throughout the user interface, e.g. table in the Crohn's disease [EA] study page, have now additional columns to include effect size metrics:
- Odds Ratio
- Beta (coefficient)
- 95% Confidence Interval
Effect size metrics are extracted by GWAS Catalog for each defined SNP in the original curated paper and associated with the strongest SNP risk allele
New bulk download options
In addition to an easy-to-use and interactive user interface, you can get all data from Open Targets Genetics data via:
- Google BigQuery, project data set
open-targets-genetics:190303 - Google Cloud Storage (GCS) paywalled public bucket
Note: Although Open Targets makes this data publicly available, anyone who makes queries to bucket open-targets-genetics-releases will be billed to the requester.
More details are available in the Requester Pays feature for Cloud Storage.
We will be shortly copying this data to the Open Targets public FTP as well. Please check again soon.
Questions or comments?
Email and tweet us with your questions or comments. We will be happy to help.
Open Targets Genetics is only six-months old and we have exciting future plans lined up for our upcoming releases.
In the meantime, feel free to dive into our documentation to find more about:
- Technologies we use, e.g. Spark and Scala
- GitHub repositories
- ASHG2018 workshop materials
- Release notes
- FAQs
Save the date
The next release of Open Targets Genetics will be just in time for our workshop at ESHG in Gothenburg, Sweden.
Attending ESHG? Make sure to book your space in the From genetics to new medicines: The Open Targets Genetics Portal workshop on June 15th.
Hope to see you there.