Liquid Biopsy Can Rapidly Detect EGFR Mutations and KRAS mutations with High Specificity

SUMMARY: It has been well established that treatment with EGFR TKIs results in superior outcomes, for patients with tumors harboring exon 19 deletions and exon 21 mutations. The application of precision medicine with targeted therapy, requires detection of molecular abnormalities in a tumor specimen, following progression or recurrence. Archived biopsy specimens may not be helpful as it is important to identify additional mutations in the tumor at the time of recurrence or progression, in order to plan appropriate therapy. Further, recurrent tumors may be inaccessible for a safe biopsy procedure or the clinical condition of the patient may not permit a repeat biopsy. Additionally, the biopsy itself may be subject to sampling error due to tumor heterogeneity. Genotyping cell free DNA in the plasma can potentially overcome the shortcomings of repeat biopsies and tissue genotyping, allowing the detection of many more targetable gene mutations, thus resulting in better evaluation of the tumor genome landscape.

The purpose of this study was to prospectively validate plasma droplet digital PCR (ddPCR) for the rapid detection of common Epidermal Growth Factor Receptor (EGFR) and KRAS mutations, as well as the EGFR T790M acquired resistance mutation. The authors prospectively evaluated the feasibility and accuracy of this assay in patients with newly diagnosed advanced non-squamous Non Small Cell Lung Cancer (NSCLC) who either were newly diagnosed and initial therapy was planned (N=120) or had developed acquired resistance to an EGFR kinase inhibitor and rebiopsy was planned (N=60). The median age was 62 years and 62% were females.

Following initial blood sampling of all patients, plasma droplet digital Polymerase Chain Reaction (ddPCR) for EGFR and KRAS mutations, including EGFR exon 19 deletion, EGFR L858R, KRAS G12X and EGFR T790M acquired resistance mutation, was performed. All patients underwent biopsy for tissue genotyping, and this was used as a reference standard for comparison with the liquid biopsy results. Important study outcomes included sensitivity and specificity of plasma ddPCR assay, as well as test turnaround time, which was defined as the number of business days between blood sampling and test reporting.

Tumor genotypes identified included 80 EGFR exon 19 or L858R mutations, 35 EGFR T790M mutations, and 25 KRAS G12X mutations. The ddPCR assay median turnaround time was 3 days compared with 12 days for tissue genotyping and 27 days for patients with acquired resistance. Plasma ddPCR exhibited a positive predictive value of 100% for EGFR 19 del, 100% for EGFR L858R mutation and 100% for KRAS. The positive predictive value for EGFR T790M was lower at 79%. The sensitivity of plasma ddPCR assay was 82% for EGFR exon19 del, 74% for EGFR L858R mutation, and 77% for EGFR T790M acquired resistance mutation, but lower for KRAS at 64%. Sensitivity for EGFR or KRAS was higher in patients with multiple metastatic sites (P=0.001), specifically in those with bone and hepatic metastases.

The authors concluded that in this first prospective study, plasma ddPCR assay can rapidly detect EGFR and KRAS mutations with high specificity, allowing treatment selection, without repeat biopsies. Additionally, this assay may also detect EGFR T790M mutation, missed by tissue genotyping, due to tumor heterogeneity in resistant disease. Prospective Validation of Rapid Plasma Genotyping for the Detection of EGFR and KRAS Mutations in Advanced Lung Cancer. Sacher AG, Paweletz C, Dahlberg SE, et al. JAMA Oncol. Published online April 07, 2016. doi:10.1001/jamaoncol.2016.0173