Reporting on Cancer Biomarkers may seem like a daunting task, both in determining the scope of what a biomarker can encompass and which information to include. Biomarkers can come in the form of small variants (SNPs and INDELs), copy number variants, and structural variants. Biomarkers can also be sourced from external cancer kits in the form of a Genomic Signature, such as a tumor mutation burden (TMB) or Micro-Satellite Instability (MSI) score. The interpretation of cancer biomarkers can be a complex and time-consuming task. The good news: VarSeq and VSClinical work to make Biomarker curation and interpretation easy! This is done by both providing pre-written interpretations from our very own CancerKB team and by allowing a user to create their own biomarker summaries. Our knowledge base contains useful information on cancer biomarkers, including the role of genes in cancer, drug sensitivity, and resistance information, diagnostic summaries, and prognostic information. These biomarker interpretations can be scoped to a specific cancer type or applied to a broader category of cancer types.
Golden Helix Cancer Knowledge Base (CancerKB) is our in-house database, curated by cancer professionals, to give our users quick access to written cancer interpretations (Figure 1). With over 550 written biomarker summaries, CancerKB is a great start for analyzing some of the most common mutations found across prevalent cancer types.
As mentioned before, biomarkers encompass the breadth of small variants to structural variants and Genomic Signatures, with many layers in between. By leveraging the CancerKB pre-rendered interpretations, you can easily add these to your final report. For more information about CancerKB, check out this blog, which highlights some of our major database updates.
Notably, our users are not limited in scope to the pre-rendered biomarker summaries presented with CancerKB. As seen in Figure 1, there is an Edit Interpretation button, indicating that all of these interpretations are fully customizable. Not only can you adjust the scope for cancer type and impact, but the Biomarker Interpretations can be edited and saved for internal use. Once edited, you may even share your additions and changes anonymously with the Golden Helix Curation team (Figure 2) for potential inclusion in a future release of CancerKB, therefore assisting other cancer professionals around the world. You may also choose not to share your custom interpretations.
Beyond that, you can make custom biomarker summaries from scratch! One tab our typical VSClinical user has not explored is the Cancer Interpretations Tab (Figure 3). This opens up an entirely different workspace dedicated to your own custom interpretations. You will be able to pick your associated Cancer Type, search previously made interpretations, create new drug sensitivity curations, write new gene interpretations, and more! Like editing a pre-made interpretation, these can also be submitted to our CancerKB team for review.
The ability to create new interpretations is important to cover the scope of cancer types and drug treatments. Moreover, we anticipate that the ability to build custom annotations will become even more important in the coming years. For example, growing fields such as DNA methylation analysis, as of the writing of this blog, do not have any official ACMG or AMP guidelines and no targeted therapies related to methylation biomarkers. That being said, this is a rapidly emerging field of research and development. Our users will be able to make custom interpretations for newly defined biomarkers and their subsequent treatments, making their analysis the most flexible and cutting-edge.
If you have any questions about how Biomarker Interpretations can make your somatic analysis that much smoother, please email [email protected] and one of our qualified area directors will schedule a demo call.