Webcast Recap: VSWarehouse: Tracking Changing Variant Evidence and Classifications

         March 11, 2021

Thank you to those who attended the recent webcast, “VSWarehouse: Tracking Changing Variant Evidence and Classifications”. For those who could not attend but wish to watch, here is a link to the recording.

The webcast covered some general highlights of VSWarehouse value but also presented some specific capabilities covering the ClinVar classification tracker. Golden Helix provides complete solutions to handle all secondary and tertiary analysis stages for your next-gen sequencing data. However, there is a critical need for a solution that not only stores all your genomic content but allows users the ability to query through the data efficiently. VSWarehouse handles this massive data issue with ease in a number of ways.

VSWarehouse provides a range of functionality including:

  • Standardized clinical workflows utilized in VarSeq
  • Filtering out common variants or artifacts from cohort data
  • Standardized catalog of variant ACMG and AMP classifications Standardized clinical reports
  • Easy queries among millions of variants
  • User access management
  • ClinVar classification tracker (the focus of webcast)

Classification tracking in VSWarehouse is a simple solution to a massive problem. Over time, new evidence comes out that can influence variant classification and many research projects undergo huge efforts and re-evaluating classifications for millions of samples. VSWarehouse has the ability to list new classifications for variants seen across all projects, catalogs, and reports stored in the genomic repository. In the demonstration, we covered not only the means of viewing the classification changes in VSWarehouse but also how to carry out the re-evaluation process in VarSeq to update the validated databases plus final classifications.

As with all of our webcasts, the final step was to answer viewer questions. Here are the responses:

Question: Deployment capability of Warehouse: Is this in the cloud or on-premises?

Answer: Both .. we have a lot of customers that like to install this software on their own servers behind the firewall. This option is in particular attractive for organizations that have strong HIPAA concerns. Increasingly popular is also to run the whole technology stack in a private cloud set up leveraging AWS or Microsoft Azure.

Question: Can I automate importing data into VSWarehouse from my secondary analysis pipeline?

Answer: Yes, Warehouse makes it easy to add samples to projects directly from VCF files created by your secondary analysis. It should work with any variant caller choice you have in place, or with Sentieon. It’s as simple as moving or linking new samples into the proper queue folder and it will be picked up on the next scheduled import (by default nightly).

Question: Is there a way you can make it easy for multiple clinical labs to share the same instance of VSWarehouse, each with their own compliance depts? Or possibly do monthly or quarterly syncs between their VSWarehouse instances.

Answer: Absolutely. Multiple labs can easily setup designated access in a single Warehouse server. For example, Group A may submit a project that allows for certain viewable content for group B though group B cannot alter the project content.

Question: Does the final report show the updates that were made?

Answer: Yes, once you open the link to Warehouse, update the report results from the VarSeq software, the new results will be posted in the latest report from the Warehouse viewer.

Question: What is the hardware requirement for an in-house server to VSWarehouse?

Answer: Handling larger data may require higher performance hardware but default requirements are 12 GB RAM minimum, 8 core CPU minimum, 1 – 5 TB Fast Random Access Local Storage. Here too is a link to requirements on our company site

Question: Is it possible to amend a ClinVar entry (classification) if you think their classification was a little tentative or perhaps too bold – and then use that classification to classify your variant?

Answer: Unfortunately, you won’t be able to modify a ClinVar submission from VarSeq or Warehouse but instead have to go through the formal submission process. However, the ClinVar classification is only one layer of evidence for the final ACMG classification in VarSeq. Other database impacting criteria include frequency population catalogs, functional predictions, literature review, phenotypic information, and gene impact just to name a few.

Question: I must have missed it, does the software only use ClinVar for variant classification or can you add your own data?

Answer: No, the ACMG classification in VarSeq is based on a number of databases used to assess guideline criteria. See the example list in the previous answer above. Each of the databases utilized undergoes the same automated curation process but the version release time frame may vary. Fortunately, VarSeq also has a conversion tool to include any custom annotations you would like to incorporate into your standardized workflow.

The general purpose of any webcast is to showcase the capabilities of our software. If you would like to have a more in-depth introduction to all GoldenHelix solutions please contact us at info@goldenhelix.com. Thank you again to all of those who attended and we look forward to having you join us for our future demonstrations.

Feel free to also check out some of our other blogs that contain important, useful news and updates for the next-gen sequencing community.

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