On the 10th of June 2022, we will update the VarSome Stable API (stable-api.varsome.com) from version 11.1.6 to version 11.2.12 with data frozen as of the 13th of May 2022. This version has been successfully used in production for over three months, and includes many improvements.
The most recent version, used by VarSome itself, is always available at api.varsome.com.
Functional Changes
The major changes in this version are:
- CNVs: the user can provide phenotypes that will be used to improve the variant classification.
- ACMG classification: improved accuracy & closer adherence to standards.
- AMP Drug rule: major improvements to how Tier I and Tier II drugs are evaluated. As part of this we have ‘normalized’ drug names so that they are as consistent as possible between various databases.
Please refer to the following release notes for more detailed information:
- 11.2 Release note - includes CNV, ACMG & AMP improvements.
- 11.2.5 AMP improvements: further improvement to the Drug rule & AMP tier evaluation.
Database Updates
The following databases have been updated, the JSON schema changes below are should have minimal impact:
|
Databases |
Current |
New Release |
Comment |
|
AACT |
13 Dec 2021 |
17 Apr 2022 |
Additional JSON data keys for 'interventions' and 'last_update_posted_date'. |
|
ACMG, CNV & AMP Classifiers |
11.1.6 |
11.2.8 |
See release notes for detailed list of changes. |
|
Cancer Gene Census |
v94 |
v95 |
|
|
CBioPortal |
17 Sep 2021 |
23 Mar 2022 |
|
|
CGD |
11 Nov 2021 |
15 Mar 2022 |
|
|
ClinGen Gene |
20 Dec 2021 |
23 Feb 2022 |
|
|
Genomics England PanelApp |
10 Dec 2021 |
17 Apr 2022 |
|
|
GHR Genes |
10 Dec 2021 |
15 Mar 2022 |
|
|
GWAS |
10 Dec 2021 |
17 Apr 2022 |
|
|
Jackson Labs CKB |
15 Dec 2021 |
18 Apr 2022 |
|
|
NCBI ClinVar Variants & CNVs |
7 Dec 2021 |
14 Mar 2022 |
|
|
NCBI dbVar |
30 Jun 2021 |
23 Feb 2022 |
|
|
PharmGKB |
11 Nov 2021 |
15 Mar 2022 |
Drug names in the 'normalized_drugs' key are now consistent with other databases. |
|
RefSeq transcripts |
209 |
210 |
|
|
Sanger COSMIC |
v94 |
v95 |
|
|
Sanger DECIPHER |
11 Nov 2021 |
17 Apr 2022 |
|
|
Saphetor Clinically Reported Variants |
4 Feb 2022 |
12 May 2022 |
|
|
UniProt Regions |
7 Dec 2021 |
15 Mar 2022 |
|
|
UniProt Variants |
9 Dec 2021 |
15 Mar 2022 |
|
|
WUSTL CIViC |
10 Dec 2021 |
17 Apr 2022 |
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.
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