Our December release sees the introduction of some exciting new features that we hope you will enjoy along with some general improvements.
- Publications: we have now fully incorporated & tagged all publications from PubMed that are related to genomics. We now also identify organs & tissues mentioned in publications.
- Publications Timeline: a new interactive visualization tool that enables you to graph the terms identified in publications over time, with the ability to drill-down into the data.
- ACMG classification: improved accuracy
- CIVIC updates. Include mapping to HG38, new variant assertion table, variant group information and gene description.
- CNVs: Some small improvements
As always, we hope these changes reflect our company mission statement “To enable anyone to find, share, use the most comprehensive human genome data - and to collaborate to improve health and lives around the world.” and we continue to value your feedback so that we can continue to improve in all areas of development.
We have now incorporated into VarSome the entire database of PubMed publications relevant to genes and variants. This equates to over 4 million articles related to genomics.
Additionally VarSome AI has linked over 150,000 publications to variants and genes that were not previously linked by any other source.
We have added organs and tissue names to our list of tags:
Publication Timeline Viewer
This new interactive viewer allows you to quickly see the number of publications by year, broken down by gene, disease, variants etc. with the ability to then further drill-down and identify specific publications related to the topic you are researching.
The TimeLine viewer is accessible from the top of the Publications component:
A new graph is displayed showing the number of publications over time and which key terms they contain:
It is then possible to drill-down into sub-categories of terms, for example to see what diseases are associated with a particular gene:
Clicking on any of the “bubbles” will then display the list of associated publications, for example the list of publications related to cancer:
Full documentation is on how to use this feature is available here: Publications Timeline - User Instructions
ACMG - Germline classifier
Building on the improvements introduced in the 10.3 release of VarSome, we have continued to seek ways to better classify variants in the absence of clinical evidence:
- Refined thresholds used when considering PhyloP100Way conservation.
- Frequency rules BS1, BS2 & PM2 have been extended to trigger for non-coding variants (for which no gene statistics are available), using very conservative thresholds. Used in conjunction with conservation, this improves the classification of non-coding variants.
- Rule PM1: we have refined the types of UniProt domains considered, in particular removing “disulfide bond”.
- Rule PM4: refined the handling of stop-loss variants, leveraging conservation to significantly improve accuracy - this is similar to UK guidelines that advocate using PVS1 for stop-loss variants.
- Rules PP3 & BP4: refined the thresholds used when there are multiple conflicting pathogenic & benign in-silico predictions.
Drug Database - Civic Updates
Previously we only showed CIVIC data for variants on the hg19 reference genome. If variant data is available we also now map to the hg38 reference genome.
For Civic variants
If variant data is available on CIVIC we display a new Assertion Details table. This table provides an overall summary of the clinical evidence for a variant and shows clinical significance which is supported by evidence that appears in CIVIC or that CIVIC has drawn from another source.
We display Variant Groups if available.
We have added a variant evidence score to the Variant Summary section
For Civic Variants and Genes
In the CIVIC Clinical Evidence table we have added a new General Information column that shows the last review date and clinical trial identifiers (if data is available in CIVIC).
We have added phenotypes within the Disease column.
Drug interaction type is included in the drug and evidence state column.
On the gene page only we have added the Civic Description
CNV: improvements to the Structural Variants browser
It now possible to filter by CNV type in the Structural Variants browser:
Illumina amplicon kits: the rule for selecting relevant reads was modified to retain only reads starting immediately after the primer. This affects Illumina amplicon regions with overlapping artefacts of unknown provenance.
For CNVs the QC report now provides a subanalysis and we have removed empty sections from the multisample CVN analysis.
It is now possible to upload files with both CNVs and small variants in the same file. If a file contains at least one CNV, then it is treated as a CNV file and non-CNV variants will be ignored. It is still necessary to upload the small variants separately.
Further Information and Support
As ever we hope you find these changes and improvements helpful, we’d love to hear any suggestions you may have, support is available as usual from firstname.lastname@example.org
- The VarSome Team