VarSome API Update - v 9.1.8

Summary

On Friday 2nd April 2021 (morning, CET), the Stable VarSome API will be updated from version 8.4.16 to 9.1.8. This release only affects users of the Stable API service, and does not affect VarSome.com, VarSome Premium or VarSome Clinical users. We strongly recommend you review these changes and test your code against the Staging API, where the changes for this release are already deployed for immediate review. Learn more about VarSome API Environments and release schedules.

List of changes in the API version 9.1.8

Below you may find all the changes since the last release (8.4.16 in Nov 2020), that could affect your usage of the VarSome API. There are no major API changes, but some changes to how data is presented:

• The UniProt database has been updated & the capitalisation of disease names in UniProt has changed.
• The ClinVar database has been updated and diseases now include Mondo identifiers for some entries.
• In-Silico predictions no longer uses Cosmic.FATTHM unless the variant is annotated in “somatic” mode.
• dbNSFP:
  • Results are formatted per transcript, ie: “deogen2_pred” changes from [“D”] to [null, null, “D”, null]
  • New fields for: ensembl_proteinid and ensembl_transcriptid

• New databases:
  • Cancer HotSpots (“cancer_hotspots”)
  • cBioPortal (“cbio_portal”)
  • Cancer Gene Census from Sanger (“cancer_gene_census”)
  • FDA Table of Pharmacogenomic Biomarkers in Drug Labeling (“fda_pharmacogenomic_biomarkers”)
• The data format has changed in existing cancer database to summarise the data instead of listing 1000s of entries:
  • ICGC Somatic
  • NIH GDC
  • IARC TP53 Somatic
  • IARC TP53 Germline

Please contact us if you need further details on this data representation change, it is very similar to how the data is displayed in VarSome:

Somatic Databases

We have added a number of new databases related to cancer. These databases can be large and we strongly recommend that users refrain from using “add-all-data=1” as this will incur significant additional costs and instead explicitly list any additional databases required above the ones used by ACMG (which are automatically added if add-ACMG-annotation==1).

Example

In this example we annotate with the minimum databases required by ACMG, but add BRAVO & Kaviar data too:

• https://api.varsome.com/lookup/chr11-117222650-A-?add-ACMG-annotation=1&add-source-databases=bravo,isb_kaviar3

(these examples require an authorised API token to work).

AMP annotation

ANP classification is currently only available in the Live API with the flag “add-AMP-annotation=1” ( this also enables ACMG). Inline with our release protocol, AMP classification will not be available for users of the Stable API for another 3 months. Learn more about VarSome's Implementation of AMP Guidelines.

Example

Here we request the new AMP cancer annotation for TP53:R273H, which pulls in data from cBioPortal, Cancer HotSpots amongst others:

• https://api.varsome.com/lookup/TP53:R273H?add-AMP-annotation=1

Note that the full ACMG annotation has been included too along with all the databases required for both AMP & ACMG classification.

Database Version changes

The previous Stable API contained data as of 20th November 2020.

This new version will contain a snapshot of the Live database as of the 12th Feb 2021.

Further Information and Support

An overview of the VarSome API is available here with more detailed information here.

Please contact us at the usual address support@varsome.com should you require any additional information or run into any major issues. As ever we look forward to your feedback and suggestions to improve our platform.