Fred Ashbury: How have standards evolved in moving next generation sequencing for diagnosing rare cancers? Is whole genome sequencing being adapted in diagnostic laboratories?
Shashikant Kulkarni: Next generation sequencing (NGS) technology has been used for almost 10 years for oncology applications. NGS has been instrumental in somatic testing to inform targeted therapy treatment decisions based on molecular signatures of the cancer. This technology has also made significant strides in identifying individuals and families who have germline genetic predisposition to several cancers.
Although, whole genome sequencing has not yet been widely implemented in clinical diagnostic space, it is primed to become the method of choice in the next 5 to 10 years. Standards for both somatic and germline testing for rare tumors have been initially defined by professional societies like the Association of Molecular Pathology, American College of Medical Genetics and Genomics, American Society of Clinical Oncology and the College of American Pathology.
Since the initial standards for somatic testing were published three years ago, we have identified several areas in practice guidelines that were not very granular. Professional societies have set up committees to address those nuances and these new guidelines are expected to be published in 2022.
FA: What are the implications for community oncology practitioners to be able to respond to the changing standards for next-generation sequencing?
SK: This rapidly and ever evolving genomics medicine diagnostics space is certainly a challenge for not only community oncologists, but for every healthcare professional today. Community oncology practitioners will have to form professional partnerships with molecular pathologists and genetic counselors to be able to understand and utilize this amazing area of precision genomic medicine we live in. Additionally, it is the responsibility of academic leader molecular pathologists in the diagnostic laboratories to have tools and resources available to help translate this tremendous knowledge we have garnered through decades of research. These tools should transcend molecular tumor boards and should include on-demand webinars, tutorials, help for tele-genetic counseling, and more programs and services that help to elevate understanding and application of the results in all settings, and in particular, the community oncology practice setting where the majority of cancer patients are being seen and where resources have been less available and thereby limit the solutions providers want and need for their patients.
FA: What resources will community oncology practices need to be able to make treatment decisions in response to the changing standards?
SK: Physicians practicing oncology and especially those in community-based settings will need innovative resources for fully utilizing the promise of precision genomics medicine. These resources include, but are not limited to, access to continuous learning tools, molecular pathologists in real time, tele-genetic counseling resources, and artificial intelligence-based platforms that facilitate clinical decision support in real time to answer burning questions immediately that may arise during the patient consult.
FA: What do you think the future of cancer medicine is going to look like in the community because of precision oncology research?
SK: We are entering into an exciting phase of precision oncology where cancer patients will be treated informed by a combinatorial diagnostic approach that will include genomics, transcriptomics, proteomics and epigenomics. With the deluge of data such an approach will produce, there will be a significant need for self-learning artificial intelligence tools that are tethered to an electronic medical record.
These innovative approaches will have to be dynamic in nature and would need to be capable of integrating multi-modal, discrete patient data including physician notes, clinical data (including co-morbidities, allergies, current medications, diagnosis, staging, tumor dimensions, labs, etc.), treatment response data, radiology information, pathology-based tumor data, genomics data and wearables.
Fredrick D. Ashbury, PhD
Chief Scientific Officer, VieCure
Professor (Adj), Department of Oncology University of Calgary
Professor (Adj), DLSPH, University of Toronto
Shashikant Kulkarni, MS,
Baylor College of Medicine
School of Medicine