Clinical Implications of Plasma-Based Genotyping With the Delivery of Personalized Therapy in Metastatic Non–Small Cell Lung Cancer

Abstract

The clinical implications of adding plasma-based circulating tumor DNA next-generation sequencing (NGS) to tissue NGS for targetable mutation detection in non-small cell lung cancer (NSCLC) have not been formally assessed. OBJECTIVE To determine whether plasma NGS testing was associated with improved mutation detection and enhanced delivery of personalized therapy in a real-world clinical setting. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study enrolled 323 patients with metastatic NSCLC who had plasma testing ordered as part of routine clinical management. Plasma NGS was performed using a 73-gene commercial platform. Patients were enrolled at the Hospital of the University of Pennsylvania from April 1, 2016, through January 2, 2018. The database was locked for follow-up and analyses on January 2, 2018, with a median follow-up of 7 months (range, 1-21 months). MAIN OUTCOMES AND MEASURES The number of patients with targetable alterations detected with plasma and tissue NGS; the association between the allele fractions (AFs) of mutations detected in tissue and plasma; and the association of response rate with the plasma AF of the targeted mutations. RESULTS Among the 323 patients with NSCLC (60.1% female; median age, 65 years [range, 33-93 years]), therapeutically targetable mutations were detected in EGFR, ALK, MET, BRCA1, ROS1, RET, ERBB2, or BRAF for 113 (35.0%) overall. Ninety-four patients (29.1%) had plasma testing only at the discretion of the treating physician or patient preference. Among the 94 patients with plasma testing alone, 31 (33.0%) had a therapeutically targetable mutation detected, thus obviating the need for an invasive biopsy. Among the remaining 229 patients who had concurrent plasma and tissue NGS or were unable to have tissue NGS, a therapeutically targetable mutation was detected in tissue alone for 47 patients (20.5%), whereas the addition of plasma testing increased this number to 82 (35.8%). Thirty-six of 42 patients (85.7%) who received a targeted therapy based on the plasma result achieved a complete or a partial response or stable disease. The plasma-based targeted mutation AF had no correlation with depth of Response Evaluation Criteria in Solid Tumors response (r = −0.121; P = .45). CONCLUSIONS AND RELEVANCE Integration of plasma NGS testing into the routine management of stage IV NSCLC demonstrates a marked increase of the detection of therapeutically targetable mutations and improved delivery of molecularly guided therapy.

Liquid biopsy as a follow‐up tool: Comment on longitudinal monitoring of somatic genetic alterations in circulating cell‐free DNA during treatment with epidermal growth factor receptor–tyrosine kinase inhibitors

“…In the new paradigm, the development of more sensitive detection methods, such as next‐generation sequencing (NGS), allows simultaneous evaluation of multiple somatic mutations; furthermore, the addition of other techniques, such as hybrid capture, makes it possible to determine the presence of other genetic alterations, such as fusions. This approach demonstrated a marked increase in the detection of therapeutically targetable mutations and improved delivery of molecularly guided therapy compared with tissue genotyping, with a shorter turnaround time . These results support a hypothetical change in the upfront management of NSCLC patients from “tissue first” to “blood first.”…”

Evaluation of PCR‐HRM, RFLP, and direct sequencing as simple and cost‐effective methods to detect common EGFR mutations in plasma cell–free DNA of non–small cell lung cancer patients

“…There has been no specific therapeutic recommendation based on T790M appearance alone without evidence of radiological progression. Recent study demonstrates that any positivity of EGFR T790M mutation shows good response to osimertinib independently of MAF . Therefore, patients with positive EGFR mutations detected using the combined methods of DS, PCR‐HRM, and RFLP may also benefit from osimertinib.…”

“…The utility of T790M appearance during TKI therapy to predict progressive disease may be hampered by the dynamics of T790M burden. Quantitative monitoring studies using highly sensitive and sophisticated methods such as NGS and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) have shown that T790M mutation burdens may not necessarily remain elevated up to presentation of frank radiological progression. Indeed, some patients demonstrate only transient elevation of T790M mutations during early phase of TKI treatment, and the mutations eventually disappear near baseline level at later time points prior to disease progression.…”

“…The utility of T790M appearance during TKI therapy to predict progressive disease may be hampered by the dynamics of T790M burden. Quantitative monitoring studies using highly sensitive and sophisticated methods such as NGS [44][45][46] and matrix-assisted laser Indeed, some patients demonstrate only transient elevation of T790M mutations during early phase of TKI treatment, and the mutations eventually disappear near baseline level at later time points prior to disease progression. Using direct sequencing, we also noticed in two of our patients (cases 2 and 4) that the initial presence of T790M in month 3 was not sustained at later follow-ups in months 6 and 9.…”

Highly specific enrichment of rare nucleic acids usingThermus thermophilusArgonaute

“…Detection of mutant alleles is, however, challenging due to their very low concentrations in liquid biopsy samples among the background of highly abundant WT alleles that differ from mutant alleles by as little as a single nucleotide. To improve the sensitivity and specificity of detecting rare alleles that contain valuable diagnostic and therapeutic clues, it is necessary to remove and/or suppress the amplification of WT alleles [31][32][33] . NAVIGATER meets this challenge by selectively and controllably degrading WT alleles in the sample, thereby increasing the fraction of mutant alleles.…”