Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin‐fixed, paraffin‐embedded tissue

Abstract

Molecular oncology testing is important for patient management, and requests for the molecular analysis of cytology specimens are increasingly being made. Formalin-fixed, paraffin-embedded (FFPE) cell blocks of such specimens have been routinely used for molecular diagnosis. However, the inability to assess cellularity before cell block preparation is a pitfall of their use. In this study, various cytologic preparations were tested with several molecular test platforms, and the results were compared with paired FFPE tissue. Seventy-seven cytology cases, including fine-needle aspiration smears, touch preparations, and SurePath thin-layer preparations, were selected from the archives. Areas of interest were removed from the slide with a matrix capture solution. DNA extracted from the cells was evaluated by mutation analysis for BRAF, epidermal growth factor receptor (EGFR), RAS, and a 50-gene panel with various testing platforms (single-nucleotide primer extension assay, Sanger sequencing, and next-generation sequencing). Thirty-eight tumors with available FFPE tissue were tested in parallel. The average DNA concentration was 299 ng/µL for the cytology specimens and 171 ng/µg for the paired FFPE tissue. Point mutations and large deletions were detected in BRAF, KRAS, NRAS, HRAS, and EGFR genes. In comparison with FFPE tissue, 5- to 8-fold less input DNA was needed when cytology preparations were used. The concordance between cytology specimens and FFPE tissue was 100%. Cytologic preparations were found to be a reliable source for molecular oncology testing. DNA derived from cytology specimens performed well on multiple platforms, and 100% concordance was observed between cytology specimens and FFPE tissue.