Association Between Plasma Genotyping and Outcomes of Treatment With Osimertinib (AZD9291) in Advanced Non-Small-Cell Lung Cancer

Abstract

Purpose: Third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have demonstrated potent activity against TKI resistance mediated by EGFR T790M. We studied whether noninvasive genotyping of cell-free plasma DNA (cfDNA) is a useful biomarker for prediction of outcome from a third-generation EGFR-TKI, osimertinib.

Methods: Plasma was collected from all patients in the first-in-man study of osimertinib. Patients who were included had acquired EGFR-TKI resistance and evidence of a common EGFR-sensitizing mutation. Genotyping of cell-free plasma DNA was performed by using BEAMing. Plasma genotyping accuracy was assessed by using tumor genotyping from a central laboratory as reference. Objective response rate (ORR) and progression-free survival (PFS) were analyzed in all T790M-positive or T790M-negative patients.

Results: Sensitivity of plasma genotyping for detection of T790M was 70%. Of 58 patients with T790M-negative tumors, T790M was detected in plasma of 18 (31%). ORR and median PFS were similar in patients with T790M-positive plasma (ORR, 63%; PFS, 9.7 months) or T790M-positive tumor (ORR, 62%; PFS, 9.7 months) results. Although patients with T790M-negative plasma had overall favorable outcomes (ORR, 46%; median PFS, 8.2 months), tumor genotyping distinguished a subset of patients positive for T790M who had better outcomes (ORR, 69%; PFS, 16.5 months) as well as a subset of patients negative for T790M with poor outcomes (ORR, 25%; PFS, 2.8 months).

Conclusion: In this retrospective analysis, patients positive for T790M in plasma have outcomes with osimertinib that are equivalent to patients positive by a tissue-based assay. This study suggests that, upon availability of validated plasma T790M assays, some patients could avoid a tumor biopsy for T790M genotyping. As a result of the 30% false-negative rate of plasma genotyping, those with T790M-negative plasma results still need a tumor biopsy to determine presence or absence of T790M.

Trial registration: ClinicalTrials.gov NCT01802632.

Fig 1.

Flow diagram of eligible study population. Of 308 eligible patients, 237 had central tumor genotyping results, 271 had central plasma genotyping results, and 216 had both. EGFR, epidermal growth factor receptor.

Fig 2.

Waterfall plots for best percentage change in target lesion diameter for evaluable patients. Results are presented by (A and B) tumor T790M status and by (C and D) plasma T790M status. Colored bars indicate plasma T790M status in panels A and B and tumor T790M status in panels C and D. Asterisks represent imputed values; if it was known that a patient had died within 14 weeks (96 days) after the start of treatment and had no assessments of the target lesion that could be evaluated, the best change was imputed as 20%. ORR, objective response rate.

Fig 3.

Kaplan-Meier curves of progression-free survival (PFS) in T790M-positive (T790M+) and T790M-negative (T790M−) subpopulations treated with osimertinib. (A) Patients with T790M+ tumors have a dramatically longer PFS than do patients with T790M− tumors (P < .001). (B) Plasma genotyping for T790M fails to identify two subgroups with different PFS (P = .188). (C) Patients with T790M− plasma subdivided into tumor T790M+ (blue) and T790M− (yellow) demonstrate significantly improved PFS in tumor T790M+ patients (P < .001). (D) A similar trend is observed in patients with T790M+ plasma when subdivided by tumor genotyping status, though the T790M+ tumor group is limited to only 18 patients.

Fig 4.

Heterogeneity in patients with T790M-positive (T790M+) plasma/T790M-negative (T790M−) tumors. (A) Objective response rate was 28% (5 of 18; 95% CI, 10% to 53%) in patients with T790M+ plasma but with discordant tumor genotyping. (B) Studying the relative T790M allelic fraction (AF; calculated as the ratio of AF of T790M to AF of the sensitizing mutation), this was significantly lower in 16 patients with a T790M− tumor genotype (yellow) than in 118 patients with a T790M+ tumor genotype (blue; P = .0047). Circles indicate outliers, solid lines indicate medians, and boxes represent interquartile ranges. (C) Studying relative T790M AF and depth of response, no significant association overall is seen (R = -0.183); however, patients with a relative T790M AF > 10% showed a greater depth of response compared with patients with a relative T790M AF < 10% (P = .0407).

Fig 5.

A proposed paradigm for use of plasma genotyping for epidermal growth factor receptor (EGFR) T790M. (A) In the conventional paradigm, all patients undergo a resistance biopsy for T790M genotyping, and this result is used to guide treatment decisions. (B) Our data support an alternate paradigm where plasma genotyping for T790M is used as a screening test before biopsy, which would only be needed for patients with no T790M detected in plasma. FDA, US Food and Drug Administration; FFPE, formalin-fixed, paraffin-embedded; pts, patients; TKI, tyrosine kinase inhibitor.

Fig A1.

AURA phase I cohorts enrolling previously treated patients. Dose escalation cohorts (dark blue) were not preselected by T790M status, and enrolled approximately 6 patients each. Dose expansion cohorts initially enrolled approximately 12 patients each, which was then expanded to approximately 20 patients. Most of these expansion cohorts enrolled patients as locally T790M positive (yellow) or T790M negative (gray), with central T790M testing used for allocation if local testing was unavailable. Additional cohorts included two paired biopsy cohorts enrolling T790M-positive patients (red), and two tablet cohorts (light blue) enrolling patients T790M positive by cytology or T790M unselected. EGFR, epidermal growth factor receptor.

Fig A2.

Test characteristics and dynamic range of central plasma EGFR genotyping using BEAMing. (A) Sensitivity of the assays for exon 19 deletion (19 del), L858R, and T790M, calculated as the proportion of patients positive in plasma for a given mutation out of all patients with positive central tumor genotyping for that mutation. (B) Among patients T790M positive on tumor genotyping, sensitivity of the plasma T790M assay is lower in cases where no EGFR-sensitizing mutation is detected in plasma (P < .001). (C) Specificity of the assays for 19 del, L858R, and T790M, calculated as the proportion of patients negative in plasma for a given mutation out of all patients with negative central tumor genotyping for that mutation. 0.04% allelic fraction is the positive threshold for EGFR exon 19 del and L858R assays, while 0.06% is the positive threshold for the EGFR T790M assay. Turkey box plots of allelic fraction are shown; circles indicate outliers, solid lines indicate medians, and boxes represent interquartile ranges. N/D, not determined.

Fig A3.

Objective response rate (ORR) and progrssion-free survival (PFS) of the plasma T790M negative (T790M−) population using detection of a plasma-sensitizing mutation (sens) as a quality control. (A) Waterfall plots for best percentage change in target lesion size of evaluable patients in the 33 cases whose plasma genotype was T790M−/sens- (yellow dashed) or the 69 patients whose plasma genotype was T790M−/sens+ (yellow dotted) by BEAMing. The dashed lines at 20% represent the boundary for determination of progressive disease, and the dashed line at −30% represents the boundary for determination of partial response. Asterisks represent imputed values: if it was known that a patient had died within 14 weeks (96 days) after the start of treatment and had no assessments of the target lesion that could be evaluated, the best change was imputed as 20%. (B) Kaplan-Meier curves of PFS using detection of a plasma-sensitizing mutation as a quality control for plasma T790M− cases. Three groups can be identified with significant differences in PFS (P = .002). T790M+, T790M-positive.