Development and Validation of a Scalable Next-Generation Sequencing System for Assessing Relevant Somatic Variants in Solid Tumors

Abstract

Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with < 20 ng of DNA/RNA from formalin-fixed paraffin-embedded (FFPE) tissues], coupled with an informatics pipeline to specifically identify relevant predefined variants and created a knowledge base of related potential treatments, current practice guidelines, and open clinical trials. We validated OCP using molecular standards and more than 300 FFPE tumor samples, achieving >95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts.

Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial

“…The Oncomine Cancer Panel assay 10 using AmpliSeq chemistry and the PGM sequencer was selected and optimized for the NCI-MATCH NGS assay. The NCI-MATCH NGS assay system was designed to detect and report 4066 predefined genomic variations, encompassing 3259 SNVs, 114 indels, 435 large indels, 75 CNVs, and 183 gene fusions (Supplemental Table S2) across 143 unique genes (after removal of genes duplicated in more than one variant type) (Supplemental Table S3) in the Oncomine Cancer Research Panel (Thermo Fisher Scientific).…”

Genomic Profiling of Penile Squamous Cell Carcinoma Reveals New Opportunities for Targeted Therapy

“…Clinicopathologic data was obtained from medical records. DNA isolation was performed as described (11).…”

The integration of genomics testing and functional proteomics in the era of personalized medicine

“…NGS-based platforms for cancer genomic testing, such as FoundationOne and the Oncomine Comprehensive Assay, have been applied as investigational clinical sequencing methods in the field of clinical oncology [6,7]. FoundationOne and the Oncomine Comprehensive Assay cover 315 and 161 cancer-related genes, respectively.…”

“…FGFR inhibitors are classified into FGFR1/2/3 inhibitors, FGFR4 inhibitors, and pan-FGFR inhibitors as a result of the divergence of FGFR4 from other FGFRs [7]. AZD4547, derazantinib, and infigratinib are representative FGFR1/2/3 inhibitors in clinical trials, whereas erdafitinib and LY2874455 are representative pan-FGFR inhibitors in clinical trials.…”