NGS Reporting, Whole Genome Sequencing, and In-House Testing

Interpretation and Reporting: Two Key NGS Testing Bottlenecks

Next-generation sequencing (NGS) has two main challenges: variant detection and reporting variant clinical interpretation. At the Cancer Genomics Consortium (CGC) conference in 2022, Kilannin Krysiak from Clinic Interpretations of Variants in Cancer (CIViC) gave a presentation on the need to update interpretation resources due to 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 variant reporting, interpreting these reports poses its own challenges. This is not only attributed to the person interpreting the data’s individual expertise but also to the fact that not everyone is using the same data source. This makes it difficult to compare findings across clinical reports. 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 researchers to leverage constantly growing data. The goal is for hospitals to use this central database to produce consistent variant reporting. They’ve 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 CGC presentation, Valerie Barbie explained that while they value a clinician's experience, their expertise and knowledge were not being documented or captured in any way. The platform enables clinicians to challenge and complement the data for better interpretation.

Whole Genome Sequencing (WGS) — Where Does it Stand?

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 did they believe this to be the case, but they were already performing WGS for solid tumor profiling. When asked, “Why not whole exome sequencing first?” they responded that a whole exome sequencing (WES) test would only give incrementally more information than a 500 gene panel. Further, they believed 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, picking up where WES fell short. Marcin Imielińsk from the 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, a sign that WGS interpretation tools are growing.

Advancements Make 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 advancements grew significantly over the last five years, especially as more cancer centers and oncologists get comfortable with data. That’s leading to a greater desire to establish precision medicine, or precision oncology, in-house. While sequencing cost is dropping, clinical utility continues to grow, thus 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 major cost and that many institutions are realizing that there is revenue to be made by bringing testing in-house. 

Dr. Thuy Phung, previously with the University of South Alabama, outlined why they decided to work with Avitia’s technology (previously with Imagia Canexia Health) to bring cancer testing in-house. In addition to being more cost-effective, they avoided long wait times associated with sending tests out. Internal testing and processing capabilities at a local health center also simplified the process and benefited underserved populations. By bringing testing into a community that may not otherwise have access to the test, it bridges the health equity gap and ultimately improves patient outcomes.

To learn more about our solution and how we can help your organization bring liquid biopsy testing in-house, contact us at hello@avitiatesting.com 

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