In everyday practice, it is common for pathology labs to evaluate >50% cytological specimens across solid tumors especially in lung and pancreatic cancers. Many of these cytological specimens require molecular profiling to help confirm diagnoses and guide treatment decisions.
Read why a high quantity not sufficient (QNS) from reference labs is unacceptable for your patients, especially after weeks of waiting, and how you can bring a robust amplicon-based comprehensive genomic profiling (CGP) in-house to ensure that you get answers when it counts.
Samples for molecular testing are getting smaller
When evaluating next-generation sequencing (NGS) technologies, there are many factors to consider that contribute to test performance such as tissue quantity and quality. Amplicon-based NGS assays perform better with cytology and small biopsy samples than hybrid capture-based methods. This is especially important when a high volume of cytological samples are processed within a laboratory.
With a 517 gene amplicon-based NGS panel with input requirements of only 20 ng of DNA/RNA, Geisinger Medical Center was able to obtain an overall sequencing success rate of 97.1% which translates to an impressive QNS of only 2.9% with lung samples despite 81% of the cases coming from cytological samples. Further, more than half of the cytological samples had less than 20 ng of DNA available, highlighting the robustness of amplicon-based sequencing.
Insights in NSCLC NGS testing in a rural population
Using a 517 gene amplicon-based NGS panel, actionable mutations like KRAS G12C were detected in concordance with published data in non-small cell lung cancer (NSCLC). Interestingly, EGFR mutations were detected at a lower level and MET amplifications were detected at a higher level than expected from published literature, possibly reflective of the rural populations in Central Pennsylvania.
Nonetheless, by implementing an amplicon-based NGS assay, Geisinger Medical Center was able to detect actionable alterations in ~58% of lung adenocarcinoma patients and ~37% of lung squamous cell carcinoma patients to give their patients the best chance of the finding the right therapy in a timely manner.
The future of comprehensive genomic profiling
Although there have been improvements in advancing precision medicine from the days of conventional chemotherapy, many unanswered questions remain such as MET amplifications in regards to copy numbers (>10 copies vs <10 copies) and how tumor mutational burden (TMB) medium (10-15 mutations/Mb) and TMB high (>15 mutations/Mb) relate to treatment and response in NSCLC.
As we gain a better understanding of molecular insights from NGS, the hope is that more patients will be able to receive effective biomarker-driven treatments, such as targeted therapy and immunotherapy, while avoiding the toxicity associated with less individualized approaches.
Watch our webinar to learn more: On-Demand Webinar: It’s Hard to Treat What You Can’t See—Molecular Diagnostics Perspective in Oncology
