Aggeliki Karabassi
CTO
On 8th September 2023 we will be releasing the Q3 API changes for the VarSome API (stable-api.varsome.com).
The Stable API will update version 11.7.2 to version 11.8.0 with data frozen as of the 4th August 2023. This version has been successfully used in production for over a month.
The most recent version, used by VarSome itself, is always available at api.varsome.com.
Functional Changes
The major changes introduced in version 11.8 affecting API users are listed below:
- Germline classification:
- Premium users have access to curated publications by the VarSome curation team, which are also taken into account with enhanced importance in the clinical evidence rules
- Following updated ClinGen recommendations, our classifier is now excluding the frequencies from the Ashkenazi Jewish and Finnish populations in the BA1 rule.
Please see the 11.8 release note for more detailed information.
Database Updates
The following databases have been updated:
|
Source |
Data Type | Current (Stable, Q2 '23) | Next Release (Stable, Q3 '23) | Comment |
| AACT Clinical Trials | gene | 21-Feb-23 | 13-Jun-23 | |
| ACMG classifier | variant | 11.7.2 | 11.8.0 | |
| AMP classifier | variant | 11.7.2 | 11.8.0 | |
| cBioPortal | variant | 21-Jun-22 | 06-Jun-23 | |
| CGD | gene | 20-Oct-22 | 05-May-23 | |
| ClinVar | variant | 03-Apr-23 | 31-Jul-23 | |
| ClinVar | region / CNV | 03-Apr-23 | 31-Jul-23 | |
| CPIC | gene | 21-Jan-23 | 06-Jun-23 | |
| DGI | gene | 21-Feb-23 | 12-Jul-23 | |
| Genomics England PanelAPP | gene | 22-Feb-23 | 11-Jul-23 | |
| GHR | gene | 21-Feb-23 | 13-Jun-23 | |
| gnomAD | variant | 3.1.2 | 3.1.2 | |
| GWAS | variant | 21-Feb-23 | 11-Jul-23 | |
| Jackson Laboratory CKB | gene | 22-Feb-23 | 20-Jul-23 | |
| Jackson Laboratory CKB | variant | 22-Feb-23 | 20-Jul-23 | |
| LUMC LOVD | variant | 04-Apr-23 | 31-Jul-23 | |
| MitoMap | variant | 12-Aug-22 | 11-Jul-23 | |
| NIH ClinGen | variant | 21-Feb-23 | 20-Jun-23 | |
| OMIM | gene | 11-Apr-23 | 17-Jul-23 | |
| OMIM | variant | 11-Apr-23 | 17-Jul-23 | |
| PharmGKB | gene | 05-Mar-23 | 12-Jul-23 | |
| PharmGKB | variant | 05-Mar-22 | 12-Jul-23 | |
| Sanger Cosmic | variant | v97 | v98 | API customers with a valid Cosmic license |
| Sanger DECIPHER | region / CNV | 21-Feb-23 | 10-Jul-23 | |
| Saphetor Known Pathogenic | gene | 02-May-23 | 01-Aug-23 | All clinical classifications from all sources. |
| Saphetor Known Pathogenic | variant | 02-May-23 | 01-Aug-23 | All clinical classifications from all sources. |
| Pubmed | variant | 03-May-23 | 02-Aug-23 | |
| UniProt Variants | variant | 20-Jan-23 | 05-May-23 |
JSON Schema Changes
Reminder: all the data structures returned by the VarSome API are documented here.
Variant Annotation Schema Changes
Body modifications
In GET /lookup/{spec_query}/{ref_genome} parameters, the parameters to add or exclude databases have been updated:
Response modifications
The response changes in this section concern both GET /lookup/{spec_query}/{ref_genome} and POST /lookup/batch/{ref_genome} requests.
The gnomad_exomes attribute in the responses has been modified to include additional information:
"nonpar": {
"type": "integer",
"required": false,
"read_only": false,
"label": "Variant (on sex chromosome) falls outside a pseudoautosomal region"
}
The lumc_lovd attribute in the responses has been modified to include additional information:
"lovd_link": {"type": "string",
”required": false,
"read_only": false,
"label": "LOVD link"
}
Gene Annotation Schema Changes
Body modifications
In [POST]/lookup/genes/batch/{ref_genome} the genes array is now limited to 10.
Response modifications
The response changes in this section concern both GET /gene/{gene_symbol}/{ref_genome} and POST /genes/batch/{ref_genome} requests.
The responses has been modified to include additional information:
"lovd_gene": {
"type": "object",
"title": "LUMC LOVD",
"properties": {
"version": {
"type": "string",
"required": true,
"read_only": false,
"label": "LOVD Version"
},
"lovd_link": {
"type": "string",
"required": false,
"read_only": false,
"label": "LOVD link"
},
"number_of_individuals": {
"type": "integer",
"required": false,
"read_only": false,
"label": "Number of individuals"
},
"number_of_variants": {
"type": "integer",
"required": false,
"read_only": false,
"label": "Number of variants"
},
"phenotypes": {
"type": "array",
"title": "Phenotypes",
"items": {
"type": "object",
"properties": {
"accession": {
"type": "string",
"required": false,
"read_only": false,
"label": "Accession"
},
"source": {
"type": "string",
"required": false,
"read_only": false,
"label": "Source"
},
"term": {
"type": "string",
"required": false,
"read_only": false,
"label": "Term"
},
"inheritance_pattern": {
"type": "object",
"title": "Inheritance Pattern",
"properties": {
"accession": {
"type": "string",
"required": false,
"read_only": false,
"label": "Accession"
},
"source": {
"type": "string",
"required": false,
"read_only": false,
"label": "Source"
},
"term": {
"type": "list",
"required": false,
"read_only": false,
"label": "Term",
"items": {
"type": "string"
}
}
}
}
}
}
}
}
},
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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