Last week, we were in St. Louis to attend the Cancer Genomics Consortium Annual Meeting. It was great to be back in person, listening to all the presentations and discussions about work and advancements being made in the field of cancer genomics.
Here are the key takeaways we took from the meeting:
Interpretation and reporting is one of the key bottlenecks of NGS testing A common issue brought up in a few presentations is the challenge of next-generation sequencing (NGS) data reporting, as well as the interpretation of reports. Kilannin Krysiak from Clinic Interpretations of Variants in Cancer (CIViC) gave a presentation on the need to update interpretation resources because of the complex nature of variant relationships. Not only is the data complex, but clinical guidelines are constantly being updated. Therefore, knowledge bases also need regular updating to ensure proper clinical reporting.
In addition to data reporting, the interpretation of these reports poses their own challenges. This can be attributed to the individual expertise of the person interpreting the data, but also to the fact that not everyone is using the same data source. Valerie Barbie from the Swiss Institute of Bioinformatics provided an overview of a government funded project in Switzerland to build a clinical infrastructure that would allow research to leverage data. The goal is for hospitals to be onboarded and gain access to this central database. They have also developed the Swiss Variant Interpretation Platform (SVIP) for Oncology in an effort to help clinicians. This platform does not just push information out to clinicians, but rather takes input from a panel of experts during a review cycle. In her presentation, Valerie Barbie explains that they recognized the value of the clinicians’ experience, but that their expertise and knowledge was not being documented or captured in any way. The platform enables clinicians to challenge and complement the data for better interpretation.
Is whole genome sequencing (WGS) the future?
It’s difficult to say if WGS will be the future testing modality for cancer care, but several attendees of the meeting believe so. Not only do they believe this to be the case, but they are already performing WGS for solid tumor profiling. When asked, “why not whole exome sequencing first?”, their response was that a whole exome sequencing (WES) test would only give incrementally more information than a 500 gene panel, and they believe a sub-1,000 gene panel would capture the majority of short range coding region level variations that may impact cancer. On the other hand, WGS would provide an important view into structural and large-scale variations that could better inform clinicians about the patient’s cancer that WES cannot. Marcin Imielińsk from New York Genome Center demonstrated how his team’s novel bioinformatics approaches were able to identify 90% of structural variants using short read sequencing technology, so it’s clear that the bag of tools for making sense of WGS data is growing.
Advancements in the last five years is making in-house testing more desirable The topic of in-house vs. send out testing was covered in a presentation by Ravindra Kolhe from Augusta University. NGS testing has advanced significantly in the last five years and as more cancer centers and oncologists get comfortable with data, there is a greater desire to establish precision medicine or precision oncology in-house. The cost of sequencing has also gone down and clinical utility continues to grow, making the case for bringing testing in-house. One point that Ravindra Kolhe made in his presentation is that NGS testing is no longer a cost center and that many institutions are realizing that there is revenue to be made by bringing testing in-house.
Thuy Phung from the University of South Alabama outlined why they made the decision to work with Imagia Canexia Health to bring cancer testing in-house. In addition to being more cost effective, they avoid long wait times associated with sending tests out. Internal testing and processing capabilities at a local health center also simplifies the process and benefits underserved populations by bringing testing to a community that may not otherwise have access to the test, bridging the health equity gap.
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