Didn’t catch the webcast live? No worries! We cover ‘VSClinical: A Complete Clinical Workflow Solution’ Q&A’s in this blog post. The webcast, ‘VSClinical: A Complete Clinical Workflow Solution’ demonstrated how solutions provided by Golden Helix can be implemented to cover all requirements of a clinical workspace. Specifically, this webcast focused on a detailed workflow from a bioinformatician, geneticist, and lab director’s perspective.
With the viewpoint of a bioinformatician, we demonstrated how different sample fields and annotations could be used to create a filter logic that could then serve as the basis for a batch script in VSPipeline. VSPipeline can be used for the automation of project creation and maintains and ensures consistency when analyzing new samples. From this perspective, we also covered how users could use the visual interpretation interface integrated into Genome Browse to look at the quality of single nucleotide variants and copy number variants. Once the quality was confirmed the project was saved and then transferred to the geneticist.
Starting with a filtered set of variants, the geneticist showed full capabilities of the ACMG and AMP interface using VSClinical. When demonstrating the AMP guidelines, we covered the utility of the autoscoring criteria and how it could be used to determine if a variant was oncogenic. We also covered the simplicity in creating a biomarker interpretation with relevant drugs and clinical trials on a gene and biomarker level. The project then transitioned into the ACMG interface, where a single nucleotide variant and copy number variant were processed using the updated ACMG guidelines. As a geneticist, multiple comments were made voicing concerns on specific criteria, which would be later evaluated by the lab director. A draft report was created, and the project was saved and then transferred accordingly.
The lab director had full access to the interpretations created by the geneticist. For this portion, we covered how all of the saved interpretations and comments could be visualized or changed as well as how to use other repositories within the VSClinical interface. Once the findings were validated, the draft report was finalized and signed off using a built-in electronic signature. Next, the webcast covered project management capabilities using VSWarehouse. Specifically, the demonstration elaborated on the seamless communication between VarSeq and Warehouse as well as the web browser interface. One focus of the VSWarehouse interface was the ClinVar tracker, which identifies newly added variants into ClinVar or variants that had changed classification. Since the field of genetics is rapidly expanding, this ClinVar tracker implemented in VSWarehouse will undoubtedly be a useful resource for reanalyzing variants of previous samples.
Overall, this was a unique webcast as it demonstrated a complete clinical workflow solution with the consolidated software platform provided by Golden Helix. This demonstration was meant to be all-encompassing but also an overview at a very high level. That said, if you would like to see these processes with your own data, we can schedule a meeting to demonstrate functions that would be suitable for your specific workflows. We hope you enjoy this webcast and if you have questions other than those answered below, please reach out to support@goldenhelix.com.
Questions
Does Warehouse integrate with existing LIMs systems?
A: Integration of Golden Helix solutions with existing LIMs systems is possible. Since all LIMs systems have unique configurations, it would entail modifying parameters of Warehouse to accommodate for the requirements of your lab.
Are all of the features demonstrated in this webcast sold together or separately?
A: We offer a variety of different packages/bundles to meet the needs of your lab. However, you can also select to acquire specific features, which is a discussion that our sales representatives would be happy to have.
Is the VarSeq/Warehouse software stack available in an offline configuration?
A: The answer is yes. Both VarSeq and Warehouse can be available in an offline configuration and this has been implemented with some of our previous customers. Ultimately, VarSeq is a locally downloaded application and all of the contents, such as projects and annotations, are only accessible by users of the software. So the data and information are completely confidential and are not communicated with Golden Helix or other parties.
Can we leverage our cohort data in Warehouse to manage/eliminate false positive variants?
A: Warehouse and VarSeq have excellent communication and we demonstrated near the end of the webcast how variants stored in Warehouse could be used as an annotation source in VarSeq to filter out common variants seen among all cohorts of samples. This can be extremely useful when trying to filter out variants that are common across all of your samples, by using metrics such as allele frequency.
How can you load variants into your Warehouse? 80m seems far more than would be flagged during interpretation.
A: Entire VCF files can be added to the Warehouse interface either directly or through VarSeq. In this demonstration, we focused on a targeted gene panel but as the NGS space moves toward whole-genome data it will be important to have a database that can store all of the sequencing variants. In this case, the 80 million variants were added over time from multiple different projects and samples. Thus, as a user, you have the ability to add as many samples/variants into the Warehouse interface.
What is the difference between Varseq and VSclinical?
A: VarSeq is primarily used for filtering and annotating your variants to identify those that may be clinically relevant, whereas VSClinical allows users to create an interpretation and evaluation according to the ACMG or AMP guidelines that can then be stored and rendered into a clinical report. There is a lot of overlap, but VSClinical provides users with a more in-depth analysis of the clinically relevant variants that were originally filtered in VarSeq.
Do novel variants or VUS identified get updated in ClinVar or similar databases or are they just restricted to Warehouse database?
A: ClinVar is an annotation source that is updated on a monthly basis and these tracks can be updated in your project. That said, when you update ClinVar in your project it annotates only the variants that are present in those samples. If you wanted to see if variant classifications have changed in previous samples, you would need to use the Warehouse feature.
We hope you enjoyed reading this webcast recap for ‘VSClinical: The Complete Clinical Workflow Solution’! If you have any questions about purchasing or demoing one of our products please contact us. Feel free to also check out some of our other blogs that always contain important news and updates for the next-gen sequencing community.