Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants

Precision Medicine uses genetic information from individual patients. This may include the following areas:

• Diagnosis
• Treatment
• Prevention

Specifically, in the cancer space, data derived from Next-Gen Sequencing (NGS) is used to diagnose and prognose diseases, select a targeted therapy and potentially evaluate the suitability of a patient to be part of a clinical trial. The entire NGS-based cancer diagnostic space received a push in 2018 when Medicaid issued standard reimbursement codes for NGS-based tests. NGS allows us to look at any number of genes that are potentially involved in the oncogenesis of a patient’s tumor. The usage of an NGS platform is more efficient at a lower cost point than other methods such as Sanger-Sequencing and provides a much better resolution compared to microarrays. Hence, its adoption is spreading fast on a global basis.

In order to put this in perspective, I will elaborate on how this field is expanding at the macro level. The global NGS market is valued at USD 5.70 billion and is expected to reach USD 16.35 billion by the year 2024. This represents a compound annual growth rate (CAGR) of 19.2%. Contributing to this growth are the following critical factors:

1. An increase in the number of disease treatment options, accompanied by the adoption of precision medicine & molecular diagnostics
2. Advancements in NGS platforms, with sequencers providing increased throughput and improved data quality
3. A decline in NGS capital requirements – while the sequencing technology itself improves, there are reduced capital requirements across multiple sequencing platform providers
4. Changes in the regulatory environment, with an increase in acceptance of utilization of NGS-based tests in the clinic
5. Changes in reimbursement, with payors increasingly willing to pay for these tests
6. Funding for large-scale sequencing projects from both government & private sources

These developments constitute a significant dilemma for the industry. We have on one hand a labor-intensive diagnostic process that requires expertise and attention to detail, while on the other hand, a rapidly growing demand for NGS-based tests. Clinical laboratories in this space can expect to multiply their workload within the next four years, with similar if not greater growth anticipated beyond that. At the same time, there is already a shortage of clinical experts in the field of genetics with specific expertise in the NGS area. Automation is the only way to solve this dilemma. The process of final variant classification and reporting often requires adjudicating multiple lines of evidence, following decision trees and evidence weighing systems. Automation of this process will help to eliminate the problems associated with human error and individual subjectivity. In addition, the automation of the informatics and creation of guided workflows will reduce the time and effort required for molecular pathologists and medical geneticists to sign off on clinical reports.  Over the last few years, we have had extensive dialogues with users (our customers) who work in this clinical setting, to identify the processes, optimized workflows, and challenges, which led up to the initial launch of our VSClinical product.

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