Rapid On-Site Next-Generation Sequencing: An Alternative to Single-Gene and Send-Out Testing in Non-Small Cell Lung Cancer and Colorectal Cancer in a Community Pathology Laboratory Setting.

Non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) are malignancies with numerous actionable mutations. Accurate mutation identification is essential for targeted therapies, highlighting the need for next-generation sequencing (NGS). ThermoFisher Oncomine Precision Assay (OPA) as an alternative to single-gene panel (SGP) and send-out NGS (SO-NGS) in NSCLC and CRC was evaluated. Turnaround time (TAT), quantity not sufficient (QNS) rates, and detection of NCCN-recommended alterations were compared.

NSCLC alterations (EGFR, MET exon 14 skipping, ROS1, ALK fusions, RET fusions, ERBB2 mutations, NTRK1/2/3 fusions, BRAF, KRAS p.G12C). CRC alterations included RET fusions, ERBB2 amplification, NTRK1/2/3 fusions, BRAF, KRAS, NRAS, MSI. 74 NSCLC and 72 CRC cases were analyzed concurrently with OPA and SGP; compared with historical SO-NGS data from 163 NSCLC and 49 CRC cases. SGP covered 5/9 NSCLC and 4/7 CRC alterations; OPA covered all NSCLC and 6/7 CRC alterations; SO-NGS covered all NCCN alterations. In NSCLC, mean TAT was 5.0 days (OPA), 7.5 (SGP), and 11.9 (SO-NGS).

QNS was 1.2%, 12.2%, and 11.9%, respectively. Detection rates were 36.5%, 25.7%, and 29.4%. In CRC, TAT was 4.1, 5.3, and 10.2; QNS 0%, 0%, 7.5%; detection 63.9%, 62.5%, and 57.1%. OPA provides faster TAT and lower QNS rates with comparable detection of actionable alterations, supporting its use for community-based molecular testing in NSCLC and CRC.