EP1.01-76 Oncomine Tumor Mutation Load Assay in NSCLC Patients from Argentina: Study Design and Feasibility

Abstract

Listen

Translate article

High throughput next generation sequencing has improved the understanding of the genomic landscape of cancer. Somatic mutations throughout the exome derive in novel peptide sequences that can be recognized by the host immune system and drive immune responses in patients. The tumor mutational load (TML) is the number of somatic mutations per megabase of DNA and is an emerging biomarker to predict response to immune checkpoint inhibitors. The objective of this study was to evaluate the feasibility of assessing TML in tumors from patients with advanced NSCLC, treated with Nivolumab in second with Ion Torrent™ Oncomine™ TML Assay and compare it with TML from WES. The Oncomine TML is a targeted NGS assay that provides quantification of somatic mutations, from limited formalin-fixed, paraffin-embedded (FFPE) samples. DNA was purified with QIAamp DNA FFPE Tissue Kit (QIAGEN). We used a new Ion AmpliSeq targeted panel, derived from the Comprehensive Cancer Panel which covers approximately 1.7 Mb of genomic DNA and 409 genes, OTML in S5, Ion Proton (Life Technologies); and WES were performed in NovaSeq 6000 Sequencing System (Illumina). We included 40 patients with advanced NSCLC. 27 (68%) of patients had both, tumor and normal tissue to perform WES. FFPE samples were obtained from lungs (N=21), lymph nodes (N=11), pleura (N= 3), brain (N=1), skin (N= 1), bone marrow (N = 1), soft tissue (N=1). We used 20 ng of DNA to develop the manual library and templating. We covered a large genomic footprint to accurately measure somatic mutations, replacing the need for whole-exome sequencing (WES). Pipeline for analysis of the NGS output will be presented. TML estimation with low DNA input requirements from FFPE samples is feasible. Up to 8 samples can be sequenced in a Ion 540™ Chip. Mutation load assessment can be done within 2–3 days. This assay was highly reproducible in FFPE samples. A detailed report provides normalized mutation count per MB as well as mutation signatures.