Clinical Utility of Rapid EGFR Genotyping in Advanced Lung Cancer

Abstract

Purpose: Targeted therapy is the cornerstone of treatment of advanced EGFR-mutant non-small-cell lung cancer (NSCLC). Next-generation sequencing (NGS), the preferred method for genotyping, typically requires several weeks. Here, we assessed workflows designed to rapidly identify patients with actionable EGFR mutations and reduce time to initiation (TTI) of epidermal growth factor receptor (EGFR)-directed therapy.

Patients and methods: We performed rapid testing for EGFR L858R mutations and exon 19 deletions on paraffin-embedded or frozen section biopsy specimens from newly diagnosed patients with metastatic NSCLC by using an EGFR-specific assay (rapid test). To determine clinical utility, we assessed concordance with NGS results, turnaround time, and TTI of EGFR therapy, and we evaluated reimbursement data.

Results: Between January 2015 and September 2017, we performed 243 rapid EGFR tests and identified EGFR mutations in 43 patients (18%). With NGS results as a reference, sensitivity and specificity of the rapid EGFR polymerase chain reaction assay were 98% and 100%, respectively. The median turnaround time for NGS was 14 days, compared with 7 days for rapid testing (P < .001). In the rapid group, 95% of patients received an EGFR inhibitor in the first-line setting. The median TTI of EGFR therapy was significantly shorter in the rapid cohort when compared with 121 historical cases (22 v 37 days; P = .01). Escalation of the initiative into an interdisciplinary ultra-rapid next-day frozen-section workflow for highly symptomatic patients (n = 8) resulted in a reduction in the median (± standard deviation) turnaround time to 1 ± 0.4 days and allowed several patients to initiate therapy within 1 week of biopsy. An extended 9-month clinical evaluation phase confirmed operational sustainability (turnaround times: ultra-rapid, 0.81 ± 0.4 days; rapid, 3 ± 1.5 days), and a 63% reimbursement rate indicated financial sustainability.

Conclusion: Rapid genotyping facilitates earlier initiation of EGFR-directed therapies without compromising NGS workflows.

Fig 1.

Rapid EGFR testing approach. We implemented rapid EGFR testing in parallel to genotyping using next-generation sequencing (NGS; compare pathway A v B). As a result of differences in reporting times, detection of an actionable EGFR mutation with rapid testing might lead to a treatment decision before NGS results are obtained. Note that there is a (variable) delay from reporting to treatment decision and initiation of therapy because of cost-coverage determination, preauthorization requirements, etc.The ultra-rapid EGFR testing pathway (pathway C) is a multidisciplinary workflow designed to improve turnaround time using fresh tissue (frozen sections) to extract nucleic acids. Note that ultra-rapid testing combines preanalytical improvements with the optimized rapid workflow and allows coupling with NGS (Data Supplement). Dx, diagnosis; FNA, fine-needle aspiration; Neg, negative; PCR, polymerase chain reaction; Pos, positive; QC, quality control; TKI, tyrosine kinase inhibitor.

Fig 2.

Rapid EGFR assay and turnaround times compared with next-generation sequencing (NGS)–based genotyping. (A) The rapid EGFR assay consists of three separate reactions: a sizing assay to identify exon 19 (ELREA sequence) deletions and two single-nucleotide extension reactions to identify p.T790M and p.L858R missense mutations. (B) After validation (last quarter of 2014), we implemented rapid EGFR genotyping in January 2015. Scatter plots portray turnaround times of all 243 rapid EGFR samples (Jan 2015 to May 2017; black, EGFR wild type [WT]; red, EGFR mutation [mut] detected) and all specimens that underwent NGS (gray dots) during this period. Note that process improvements have led to a reduction in average turnaround times for both assays (lines).

Fig 3.

Integration of molecular-genetic testing in 243 patients with non–small-cell lung cancer who underwent rapid EGFR genotyping. The heatmap portrays clinicopathologic features (top three rows), rapid EGFR results, and key molecular drivers along with the results of next-generation sequencing (NGS)–based fusion detection, fluorescence in-situ hybridization (FISH), and NGS panel results. Key findings include (1) an isolated false-negative rapid EGFR result (arrow), (2) the inability of the rapid EGFR test to detect EGFR mutations at other residues, (3) identification of at least one underlying driver mutation in more than 50% of all tested cases by using the integrated molecular diagnostic approach, and (4) the association between clinicopathologic features and certain key drivers (eg, never-smoking women with adenocarcinoma and EGFR v > 10 pack-year smoking history and KRAS). Adeno, adenocarcinoma; AdSQ, adenosquamous; Delins, insertion/deletion; Ex19del, exon 19 deletion; Ex20ins, exon 20 insertion; GCCa, giant cell carcinoma; LCNEC, large-cell neuroendocrine carcinoma; N/A, not applicable; Non-syn, nonsynonymous; PM, point mutation; py, pack year; SarcCa, sarcomatoid carcinoma; SQ, squamous.

Fig 4.

Therapeutic and clinical utility of rapid EGFR genotyping. (A) Event curve that shows rapid EGFR test reporting times and a comparison of the tyrosine kinase inhibitor (TKI) initiation times (relative to date of diagnosis) for patients in the rapid and historical cohorts. (B) Timeline of 43 patients with EGFR-mutant lung cancer. The top three patients did not receive epidermal growth factor receptor (EGFR)–directed therapy during the follow-up period. The second block shows the 49% of patients (n = 17 of 35 patients) with EGFR-mutant disease who started a TKI before next-generation sequencing (NGS) results were available. The third block shows patients who initiated EGFR-directed therapy after NGS results were available. (C) Response to the EGFR inhibitor osimertinib in a patient with non–small-cell lung cancer who underwent ultra-rapid EGFR testing: (left) pretreatment image and (right) response after 3 weeks; arrow indicates primary tumor. (D) Comparison of rapid test times (average) and the eight patients tested with the ultra-rapid protocol (Fig 1C); inset shows event curve comparison of time to initiation of TKI between the rapid and ultra-rapid subsets. (E) Turnaround times for rapid (gray) and ultra-rapid (blue) workflows in a 9-month extended standard-of-care evaluation phase; red, cases with an EGFR mutation. Outliers in reporting times are due to delays in block retrieval or repeated testing. (F) Reimbursement analysis: pie chart depicts the overall frequency of reimbursement; columns illustrate the payor-based number of reimbursed encounters. mut, mutated; WT, wild type.