Clinical validation of mutational analysis of EGFR and KRAS in fine needle aspiration and small core needle biopsies using a real-time PCR method.

Abstract

e19027 Background: About 75% of NSCLC is diagnosed at an advanced stage, thus analysis is often performed from small samples. There is a growing need for multiple biomarker testing when tissue is limited. We evaluated two real-time PCR based assays to assess EGFR and KRAS mutation status in limited tissue specimens and compared results to a lab validated method. Methods: 117 NSCLC patient samples (46 CNB, 71 FNA) were tested for EGFR and KRAS mutations using a single section. DNA was extracted directly from one stained smear in FNA samples (without pre-processing) and one 5-micron section in CNB using the cobas DNA Sample Preparation Kit. Sixty samples were also analyzed for both genes by direct sequencing using the same DNA. Eleven patients had matched CNB and FNA samples. Results: We tested 68 ADCs, 38 SqCCs, 8 NSCLC-NOS, 2 ADCs in situ non-mucinous, and 1 large cell carcinoma (Table). Median DNA concentrations for CNB and FNA were 14.17 ng/ul and 3.75 ng/ul. The failure rate for the cobas were 1.7% (EGFR), 6.8 % (KRAS) in FNA samples, and 0% for CNB. The failure rate for EGFR sequencing was 13.1% (FNA), 16.4% (CNB), and 0% for KRAS. The 11 patients with FNA and CNB showed concordant results between cobas and sequencing. One patient had two mutations; one (L782F) was detected only by sequencing. No discordant findings were seen other than invalid results comparing both systems. Conclusions: Assessment of mutations in limited tissue samples of CNB and FNA using a single section performed on the cobas EGFR and KRAS test is feasible and reliable. There was a lower invalid rate for EGFR testing on cobas test compared to Sanger sequencing. The cobas tests have rapid turnaround time to results, require limited input DNA, and are easier to use compared to sequencing. Still, it is mandatory that pathologists maintain careful quality control of the samples. [Table: see text]