Thank you to everyone who attended Using Golden Helix CancerKB to Accelerate NGS Cancer Testing! I had a great time showing off CancerKB and how it can enhance NGS analysis in cancer, I certainly hope you enjoyed it! If you were unable to make the live session, we have added the on-demand recording to our site, or we would be happy to show you in a personalized demo. In this webcast, we discussed:
- How Golden Helix annotations, along with CancerKB, are curated to ensure that the data is of high quality and up to date.
- We explored 6 example report-ready variant interpretations in the CancerKB database for a variety of cancer types.
- How CancerKB can be applied to your cancer workflow to create a clinical report in a matter of minutes.
Everyone asked such great questions during the webcast, and a few of them I was unable to answer during the live session so I would like to take the opportunity now to answer the questions that I could not get to.
How do these interpretations help in hereditary cancer analysis and reporting, HBOC particularly?
Great question! When there is a germline mutation in a gene that is implicated in hereditary cancer, we will capture this information in the interpretations. for HBOC, we have detailed interpretations curated for the BRCA1 and BRCA2 genes for breast, ovarian, prostate, and peritoneal cancers.
Kindly explain the interpretation’s use in AML (specifically BCR-ABL fusions) and FLT3-ITD.
CancerKB has Interpretations for both BCR-ABL1 fusions and FLT3 -ITD and TKD mutations. However, the Interpretations for ABL1-BCR fusions are scoped to Chronic Myelogenous Leukemia and B- Lymphoblastic Leukemia and not necessarily for AML. I think it would be worthwhile to check out these interpretations as they may at least provide some general context, and a good starting point, for the role of ABL1-BCR fusions in hematologic cancers. The FLT3 interpretations are scoped for amplification and missense mutations in Myeloid neoplasms. Myeloid neoplasm is a more general tumor type, as the interpretation contains information about AML, along with FLT3’s role in CMML and APL as well. Other interpretations in CancerKB for AML are for IDH1, IDH2, and NPM1 gene and biomarkers.
Do you detect multiple ITD in FLT3? Do you give allelic burden?
I believe the detection of multiple ITD in FLT3 and the allelic burden would depend on the variant caller or your secondary NGS pipeline. However, independent of the detection method, the allelic burden may be able to be quantified using soft-clipped reads. In the next release of VareSeq, you can explore these soft clipped reads visually in GenomeBrowse.
What is the timeline for expanding CancerKB to more investigational drugs and/or rare cancers?
There are several rare cancers that are linked to prominent biomarkers with drug treatments available and when our curation team encounters these instances we will write up an interpretation. In CancerKB there are some interpretations for tier II level information. As we update CancerKB we hope to continue to bolster these interpretations for investigational drugs. In VarSeq, you can always investigate clinical trials and drug therapies independently of what is curated in CancerKB.
If you have any other questions about the webcast or CancerKB in general, please ask them in the comments section below! If you are interested in learning more about the VarSeq Suite and CancerKB capabilities, please email us at firstname.lastname@example.org.