50. Molecular profiling of Cytolyt-Fixed FNA washes to improve diagnostic yield in lung cancer

Abstract

For therapeutic purpose, tumor molecular profiling (MP) of both DNA and RNA is standard-of-care in lung cancer patients. With increased use of fine needle aspiration (FNA) to assist in diagnosis, MP can be challenging given the limited cell block material. At our institution, only 40% of 309 FNA with lung cancer diagnosis over 2 years were successful for DNA and RNA MP as a send out, compared with 90% of surgically-resected specimens. To improve the diagnostic yield, we salvaged left over FNA washes (FW, 30-40mL) from the Cytology Laboratory within a median of 10 days from collection. For 211 FW with a malignant diagnosis, DNA/RNA extraction from 4 mL FW was performed using QIAamp ccfDNA kit (QIAGEN), where 97% and 83% yielded adequate levels for MP of DNA and RNA respectively. MP of DNA only (48) or DNA/RNA (35) workflows were performed using a 50-gene Hotspot, OCAV3, or OCAplus NGS panels (ThermoFisher). For 67 cases with a concurrent or other profiled specimen, 94% concordance for SNVs/indels and 77% for CNVs detection was observed, and expected EML4-ALK and FGFR3-TACC fusions detected. Discordance of 21 variants calls in 13 FW was due to low VAF, low coverage, or failure of CNV QC metrics. Importantly, 7 relevant variants and fusions were detected in 4 specimens previously reported as insufficient and one with prior DNA results only. Thus, the use of FW as a source of nucleic acids afforded increased diagnostic yield of FNAs for MP in lung cancer and timely targeted therapeutic intervention.