Concordance between formalin-fixed paraffin-embedded biopsy samples and surgically resected snap-frozen samples in multiplexed molecular profiling of lung cancers.

Abstract

e18556 Background: The results of comprehensive genome-wide characterization of lung cancer have recently been reported. However, the concordance of driver mutations between formalin-fixed paraffin-embedded (FFPE) and surgically resected snap-frozen samples is unclear. We conducted the Shizuoka Lung Cancer Mutation Study to analyze driver mutations in patients with lung cancer. Methods: Based on the biobanking system in conjunction with the clinic including the pathology lab, we developed a multiplexed mutational panel designed to assess 23 mutations in 9 genes (EGFR, KRAS, BRAF, PIK3CA, NRAS, MEK1, AKT1, PTEN and HER2), EGFR, MET, PIK3CA, FGFR1 and FGFR2 amplifications, and EML4-ALK translocations, using pyrosequencing plus capillary electrophoresis, qRT-PCR, and RT-PCR, respectively.DNA concentration in FFPE samples was analyzed by measuring absorbance at 260 nm (A260) in a spectrophotometer. Results: Between July 2011 and July 2012, sixty-five lung cancer patients with both FFPE and snap-frozen samples were included in this study. Patient characteristics were as follows: median age (range) 70 (38-92) years; female 68%; never-smoker 34%; histology adenocarcinoma/squamous cell carcinoma/small cell carcinoma/other 52/29/6/13 %. FFPE samples included 64 transbronchial biopsies and one pleural biopsy. We detected driver mutations in 58% of all cases. Mutations found: EGFR 28%, KRAS 12%, PIK3CA 6%, NRAS 2%, HER2 5%, EGFR amplification 5%, PIK3CA amplification 12%, FGFR1amplification 2%. Complete concordance of driver mutations between FFPE and snap-frozen samples was shown in 65%. Median DNA concentration in FFPE samples was 72.7 ng/ul (range; 2.4 - 472.4 ng/ul). Exploratory analyses using an ROC curve, done to evaluate the useful cutoff of DNA concentration in FFPE samples, showed low AUC (AUC; 0.5326). Conclusions: These results suggest that the rate of complete concordance of driver mutations between FFPE and snap-frozen samples might be acceptable, and DNA concentration in FFPE samples might not be correlated with concordance.