Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing

摘要

Next‐generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide therapy. In patients with advanced lung cancer, small biopsies such as computed tomography‐guided needle biopsy (CTNB), endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) and transbronchial biopsy (TBB) are less invasive and are preferable to resection to make a pathological diagnosis. However, the quality of DNA/RNA and NGS from small lung tumor biopsy samples is unknown. Between April 2017 and March 2018, 107 consecutive samples were obtained from thoracic tumors or metastatic sites for targeted NGS analysis. Fifteen samples were obtained through CTNB, 11 through EBUS‐TBNA, 11 through TBB and 70 through surgical resection. All samples were formalin‐fixed and paraffin‐embedded. DNA and RNA quality was measured using the ddCq method and the percentage of RNA fragments above 200 nucleotides ( style="fixed-case">DV200), respectively. Our custommade probes were designed to capture exon sequences of 464 cancer‐related genes and transcripts of 463 genes. style="fixed-case">DNA and style="fixed-case">RNA yield from the 3 biopsy methods were similar, and less than the yield obtained from resected samples. The quality of style="fixed-case">DNA and style="fixed-case">RNA was similar across all methods. Overall, 12 of 15 style="fixed-case">CTNB samples (80%), all 11 style="fixed-case">EBUS‐ style="fixed-case">TBNA samples, and 9 of 11 style="fixed-case">TBB samples (82%) underwent successful style="fixed-case">NGS assays from style="fixed-case">DNA. style="fixed-case">NGS analysis from style="fixed-case">RNA was successful in all 12 style="fixed-case">CTNB samples, 9 of 11 style="fixed-case">EBUS‐ style="fixed-case">TBNA samples (82%), and 8 of 11 style="fixed-case">TBB samples (73%). style="fixed-case">CTNB, style="fixed-case"> EBUS‐ style="fixed-case">TBNA and style="fixed-case">TBB mostly resulted in adequate style="fixed-case">DNA and style="fixed-case">RNA quality and enabled high‐quality targeted style="fixed-case">NGS analysis.