For the sake of consistency with the individual variant calling, we are introducing Sentieon’s DNAscope as the tool of preference for the joint calling of germline, and TNhaplotyper2 in the case of somatic variants. No variants above the noise threshold should be affected.
In addition to the recently added OMIM® data source card we have integrated OMIM® data into the clinical platform in the following way:
For further information please read the OMIM® integration help document.
It is now possible, for germline samples, to obtain the full, current data that VarSome Premium users would see for all card data sources, rather than just seeing the data stored at the time of the Sample Run.
To avoid confusion The table heading will make it very clear when you are using the 'Current' annotation.
Following the introduction of data being displayed in a 'card view' we have received feedback requesting an even more “Compact” version. This can be selected by selecting 'Compact View' in the settings option:
It is now possible to launch a CNV analysis using the VarSome Clinical API. Details on how to use this new feature can be found in the VarSome Clinical API documentation.
Although we highlight the quality score of the CNV call in the QC report we also now display a number of warnings on the variant table.
An additional column has been added to the CNV variant table that shows the CNV cytoband information:
We now show a warning message that alerts you to the fact that when you are viewing an SNP there is also an associated CNV or deleted gene. We display 3 new messages:
In order to avoid confusion with the naming of the frequency filter we have renamed the “Allele frequency filter” to “Population frequency”
We have implemented most of the ClinGen standards & guidelines for mitochondrial variants:
We will continue refining this implementation in our next release.
We also made some minor improvements for missense variants:
We are very proud that this release sees the launch of our new GenomeBrowser.
The new browser is quicker to load and easier to navigate. It also introduces key new features:
Over the next few months we will be making further improvements.
If you have any suggestions or experience please let us know. You can provide feedback using the option on the top right corner of the browser.
If you would like to go back to the legacy browser you can click the link on the top left hand corner
For further details on the features and best way to use the new browser please refer to the Region Browser User Guide.
MitoTip and APOGEE pathogenicity scores have been add to the in-silico prediction scores:
Clinical Pharmacogenetics Implementation Consortium (CPIC)
CPIC is a data source designed to help clinicians better understand how to optimize drug therapy. Recently they have added several new fields which we now display in VarSome Premium:
Not already a VarSome Premium, VarSome API or VarSome Clinical user? Get in touch and ask for a free trial.
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 support@varsome.com
- The VarSome Team