Assessing NGS: Pleural fluid cell block with limited tumor content and NGS challenges

Context

B.B., a 62-year-old piano teacher and avid hiker, began experiencing symptoms associated with lung cancer, including sudden shortness of breath and a persistent cough. Concerned, she sought medical help from a pulmonologist referred by her primary care physician. She was found to have a large pleural effusion, and her pulmonologist aspirated 40 mL of fluid, which was sent to pathology. A cell block was prepared, and histology and immunohistochemistry analyses of the cell block confirmed non-small cell lung cancer (NSCLC) with 15% tumor content, making it adequate for molecular testing.

Familiar with the benefits of targeted therapy, her pulmonologist ordered genomic testing with a large next-generation sequencing (NGS) panel to increase the likelihood of identifying an actionable variant. However, after 12 days, the NGS testing was reported as failed due to quantity not sufficient (QNS).