Question and Answers: Cancer Gene Panels Webcast

         March 17, 2015

Last week we conducted a webcast on “Cancer Gene Panels”; you can find the recording here. We had some excellent questions which we answered during the webcast and a few more that we didn’t get to in the allotted time. Please find answers to those questions here:

1. Are Cancer Gene Panels just another stepping stone on the way to whole exome/genome analysis?

Cancer gene panels answer a very targeted question. Is this tumor mutated in a gene that has a known association to cancer AND do we have a treatment option for this particular mutation? If so, the clinician can continue the work of finalizing the diagnosis and putting a treatment plan together. If not, then we are dealing with a case that requires a more research oriented focus. Along the same lines, the usage of a panel approach minimizes the issue of incidental findings.

On a technical level, coverage is also a consideration – at least for now. For cancer gene panels we want to have coverage of 1000x or better to accurately detect mutations in just a fraction of biopsied cells. The standard coverage for whole exomes is currently about 100-200x.

VarSeq is designed to handle gene panels of any complexity. That being saidit can also be used to conduct a whole exome or genome analysis. VarSeq is able to cover a wide array of the analytic requirements in testing labs.

2. What annotation sources can be chosen in VarSeq?
VarSeq offers a very flexible environment for selecting annotation sources to apply to your data. You may select from a broad set of popular public annotation sources maintained by our team of experts, or you may configure VarSeq to read from your own annotation data. VarSeq supports the creation of a custom variant database that captures findings made in your own lab.

3. Given a tumor – normal sample, can VarSeq filter out germline variants?

Yes, this is a very common approach. VarSeq can compare and contrast between tumor and normal data. It is able to very effectively remove any germline variants observed in the normal sample, from the list of tumor variants.

4. Can you elaborate on the business model for VarSeq?

Based on our customer feedback, we have adopted a simple software license model for VarSeq. It’s a reasonable annual fee. If you would like to learn more about license bundles and our introductory period, please reach out to one of our territory managers by requesting pricing here.

Many of our competitors charge a per-sample fee, sometimes even on top of a base-line annual fee. This makes the true acquisition costs very difficult to assess and to budget for. It creates a potentially grey area, because very often samples have to be rerun and reanalyzed for quality control reasons. In the end, it penalizes labs that are successfully ramping up their testing work. We’d like to stay out of our clients business and don’t require any ongoing reporting back to us. Ultimately, we are interested in forming long-term, mutually beneficial relationships in this industry as we have been here for the last 16 years.

5. How many customers does Golden Helix have?

Golden Helix has been in business since 1998. We are doing business with hundreds of organizations around the globe. Our software platforms are used by thousands across the globe and we have been referenced in over 880 publications to date. Here are some of the latest VarSeq announcements:

Prevention Genetics

NorthShore Next Generation Sequencing lab

Fluxion BioSciences

Leave a Reply

Your email address will not be published. Required fields are marked *