Prospective Trial Shows Utility of Liquid Biopsy for Lung Cancer

Current clinical practice calls for assaying all patients with nonsquamous lung cancer for activating mutations in the EGFR gene and for ALK fusions to identify potential responders to targeted inhibitor therapies. Eventually, though, patients treated with these inhibitors will likely develop treatment resistance. While second- line treatments are available, the molecular mechanism of resistance must be identified and repeat biopsies are necessary.

There is much heralding of the potential for liquid biopsies that use tumor-derived cell-free DNA to revolutionize tumor genotyping, particularly for lung cancer where rapid, noninvasive means could improve care.

“The absence of reliable prospective data on the use of specific plasma genotyping assays in advanced non–small-cell lung cancer has left key aspects of its utility largely undefined and slowed its uptake as a tool for clinical care in patients with both newly diagnosed NSCLC and EGFR acquired resistance,” writes Adrian Sacher, M.D., in an April 7 study published in JAMA Oncology.

The results from this study, the first prospective study of plasma droplet digital polymerase chain reaction (ddPCR), shows that liquid biopsy technology can detect EGFR and KRAS mutations rapidly with high specificity. The authors say the assay is ready to be used for clinical decision making in selecting therapy and avoiding repeat biopsies.

Participants (62 percent female; 84 percent white) were either newly diagnosed planning for initial therapy (n=180) or developed acquired resistance to an EGFR kinase inhibitor and were planning for rebiopsy (n=60). Participants underwent initial blood sampling and immediate plasma ddPCR for EGFR and KRAS hotspot mutations between July 2014 and June 2015. All patients underwent biopsy for tissue genotyping, which was used as the reference standard for comparison. Rebiopsy was required for patients with acquired resistance to EGFR kinase inhibitors and in 22 patients with newly diagnosed NSCLC to obtain sufficient tissue to complete genotyping, highlighting one of the problems with tissue-based genotyping in lung cancer.

The researchers found that median turnaround time (TAT) for plasma ddPCR was 3 days (range one to seven days), while tissue genotyping took a median TAT of 12 days for patients with newly diagnosed NSCLC and 27 days for patients with acquired resistance. Plasma ddPCR demonstrated a positive predictive value of 100 percent for EGFR 19 del, 100 percent for L858R, and 100 percent for KRAS, but a lower 79 percent value for T790M. The sensitivity of plasma ddPCR was 82 percent for EGFR 19 del, 74 percent for L858R, and 77 percent for T790M, but lower (64 percent) for KRAS. Sensitivity for EGFR or KRAS was higher in patients with multiple metastatic sites (specifically for those with hepatic or bone metastases). No false-positive results were seen for driver mutations in EGFR or KRAS.

“Even with a diagnostic sensitivity of less than 100 percent, such a rapid assay with 100 percent positive predictive value carries the potential for immense clinical utility,” writes Sacher and Dana-Farber Cancer Institute (Boston) colleagues. “A key limitation of plasma ddPCR is that although this method is adept at rapidly detecting specific targetable mutations, it cannot easily detect copy number alterations and rearrangements. … This limitation may potentially be addressed by using targeted next-generation sequencing of cfDNA for broad, multiplexed detection of complex genomic alterations including ALK and ROS1 rearrangements.”

The lower limit of detection is 5 to 50 mutant copies in a background of 10,000 wild-type copies, and the assay has a dynamic range of 4 orders of magnitude.

“There are many laboratories and companies working to develop assays that will assess presence or level of ctDNA in plasma, and most have concentrated on disease-specific panels,” writes co-author by P. Mickey Williams, Ph.D., from the Frederick National Laboratory for Cancer Research in Maryland in an accompanying editorial. “At this time, there are no standards or agreed-on approaches for controls and calibrators for assays of ctDNA. Furthermore, there are no agreed-on methods for reporting ctDNA burden (e.g., copies per milliliter of blood versus total copies, or a ratio to wild-type sequence) that would allow results from different assays and laboratories to be compared. The clinical utility of mutation detection in ctDNA relies on accurate quantitation, so these issues must be resolved.”

Takeaway: This is the first prospective study to show that a ddPCR-based liquid biopsy assay can rapidly and accurately detect EGFR and KRAS mutations in a real-world clinical setting so as to direct clinical care.