Maximizing Cancer Care with Golden Helix CancerKB 2.0: Unveiling the Latest in Precision Medicine

         January 26, 2023

Our recent webcast, Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with Golden Helix CancerKB 2.0, was an opportunity to unveil Golden Helix CancerKB v2.0. Our latest VarSeq release was designed to address the changing landscape of cancer genomics, and in this webcast, we discussed the application of our very own Golden Helix CancerKB in the context of cancer precision medicine.

Dr. Rana Smalling introduced the topic by discussing the state of affairs in genomic testing and cancer care. She touched on the observation that genomic testing is being underutilized in precision cancer care even though it is extremely useful for defining a tumor profile and fully assessing cancer risk, prognosis, diagnosis, and therapy selection, and even recommended for certain cancer cases when FDA-approved therapies are available. Studies show this may be due to a lack of expertise in interpreting genomic test results. We then highlighted the ways in which Golden Helix software can help close that gap.

These include:

  • VarSeq is constantly being updated to keep up with the latest tests and technology; case in point, we added support for comprehensive genomic profiling tests such as TSO500, Oncomine Ion Torrent, and others.
  • VarSeq allows users to keep up with the cancer literature and knowledge of therapies and trials. We offer variant evaluation based on up-to-date well-known, and highly reputable cancer annotations and have built out Golden Helix CancerKB as our main database, which expertly facilitates the process of variant interpretation.
  • With Golden Helix CancerKB we lend our expertise to users who seek to confidently adopt NGS testing, as our interpretations are written and reviewed by professional curators who are peers in the cancer genomics field.

Julia Love, our Associate Director of Product Quality, then did a deep dive into all things CancerKB, highlighting the updates since July 2022, describing updates to the CancerKB database, which included new interpretations for genomic signatures, approved disease-level therapies, and drug descriptions. She emphasized that CancerKB is still maintained and updated regularly by adding tier I and tier II therapeutic options as they surface in the cancer space. The all-new Golden Helix CancerKB compliments the VarSeq 2.3.0 via new evaluation settings and scripts and a new Cancer Interpretation database portal.

Julia kicked off the demonstration by showing how the all-new Golden Helix CancerKB compliments VarSeq 2.3.0 via three new features:

  • A new evaluation setting to expand interpretation selection for biomarkers that are added to an evaluation.
  • Using evaluation scripts to automatically add variants to an evaluation, add Ion Torrent genomic signatures, and automatically associate clinical trials with biomarkers in the evaluation.
  • A new Cancer Interpretation database portal, in conjunction with CancerKB, can be used to generate and search your own variant knowledge base.

Finally Dr. Smalling wrapped up the demonstration with a quick tour through interpretation of several variants, highlighting how the new CancerKB 2.0 has made variant interpretation, drug interpretation, and finding clinical trials even easier and more efficient than before. We delved into VSClinical interpretations of PD-L1, a combination biomarker consisting of PD-L1 positive plus wild type EGFR and ALK, MET exon 14 skipping, ERBB2 amplification, CD74-ROS1 Fusion, and a MAP2K1 K57E activating mutation. These examples demonstrated the automated application of CancerKB interpretations once a variant is added to an evaluation, our new VSClinical AMP interface for evaluation of CNVs and fusions, the specificity and comprehensiveness of our interpretations for each interpretation by cancer type, and how well we facilitate finding of Tier 1 and Tier 2 level therapies and point the user to available clinical trials.

We also emphasized the new clinical report formats that incorporate the new biomarker types, such as our combination biomarkers and genomic signatures. As always, we have a variety of reports to suit the needs of our users – our very comprehensive Cancer Drugs and Trials report, which gives all the interpretations in detail with clinical information; our Cancer Biomarkers report, which focuses more on biomarker interpretations and less on clinical findings and our very short Cancer Report which synthesizes all the information that one could find in the longer Cancer Drugs and trials report and displays that information succinctly. Of course, all the reports can be further customized.

To view a replay of the webcast, click here. Please feel free to reach out with any questions, comments, or concerns about Golden Helix CancerKB 2.0.

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