Evaluating Diff‐Quik cytology smears for large‐panel mutation testing in lung cancer—Predicting DNA content and success with low‐malignant‐cellularity samples

Abstract

Background

Cytology smears are commonly collected during endobronchial ultrasound–guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels.

Methods

A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. All patients had air‐dried, Diff‐Quik cytology smears and formalin‐fixed, paraffin‐embedded cell blocks collected for cytopathology and molecular testing. One hundred eighty‐five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina).

Results

Each microscopy parameter had a significant effect on the DNA yield. An algorithm was developed that predicted a >50‐ng DNA yield of a smear with an area under the curve of 0.86. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. Low‐malignant‐cell content (<25%) and smear area (<15%) were the main reasons for failure. All standard‐of‐care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Tier 1/2 mutations were discovered in two cases where standard‐of‐care specimens were inadequate for sequencing. Smears were scored for tumor mutation burden.

Conclusions

Microscopy of Diff‐Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks.

Abstract

Diff‐Quik cytology smears are a valuable source of material for molecular testing in lung and other cancers. Even smears yielding low‐malignant‐cell content are of great use in high‐depth, targeted gene panel sequencing assays.