Development and Validation of StrataNGS, a Multiplex PCR, Semiconductor Sequencing-Based Comprehensive Genomic Profiling Test

Abstract

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Prediction of pan-solid tumor pembrolizumab benefit by integrating tumor mutation and gene expression profiling

“…Correlation between TTNT and overall survival (OS) was calculated using Spearman's p among patients with both a documented death event and at least two lines of therapy. Throughout this study, TMB-H was defined as ≥10 Muts/Mb by StrataNGS, given the previous validation of TMB by StrataNGS and high concordance with TMB estimates from FoundationOne tissue testing 41 . All analyses were performed in python.…”

“…Thus, there is a need for optimized CPI biomarkers with improved predictive utility that can be developed into a scalable clinical test that is applicable to nearly all cancer patients, including those with limited tumor tissue available. As described herein, IRS addresses these needs by 1) co-isolating DNA and RNA to measure multiple classes of biomarkers from the same tissue sample; 2) optimizing pembrolizumab treatment benefit prediction via explainable model development using highly quantitative gene expression data in a large pan-tumor cohort with real world treatment data; and 3) utilizing a clinically validated and scalable platform developed for real world FFPE samples with minimal tumor size (2 mm 2 tumor surface area) 41,42 . In comparison, only 38.8% of the 25,770 patients in the SCMD used to assess IRS distribution met the minimum tumor surface area requirements (≥25 mm 2 ) for FoundationOne CDx, the FDA approved companion diagnostic device to identify TMB-H tumors 45 , suggesting that the majority of real-world patients with advanced solid tumors have insufficient tumor samples to determine TMB.…”

“…Leveraging a robust clinical molecular database from the StrataTrial (NCT03061305), we developed a highly significant, integrative, multivariate Immune Response Score (IRS) model that combined TMB and quantitative immune gene expression to predict real-world pembrolizumab treatment outcomes in 708 patients from 28 solid tumor types. IRS model inputs were generated from simultaneously performed, clinically validated, multiplex PCR based DNA and RNA NGS (StrataNGS CGP and a separate RNA panel for quantitative gene expression) [40][41][42] . These assays were performed on co-isolated DNA and RNA and share the same key sample input requirements defined from over 30,000 consecutively received FFPE tumor samples for CGP testing: ≥20% tumor content and 2mm 2 tumor surface area (from 10 x 5um FFPE sections) 41,42 .…”

“…Data completeness, consistency, and quality assurance checks were performed across the Strata electronic data capture (EDC) system per an approved Data Management Plan. Additional details on the Strata Trial experience and Strata molecular profiling have been described [40][41][42] .…”

“…Multiplex PCR-based comprehensive genomic profiling (PCR-CGP), including TMB assessment, was performed on FFPE solid tumor tissue using StrataNGS (Strata Oncology, Ann Arbor, MI). The current version of StrataNGS is a 437 gene laboratory-developed test (LDT) for FFPE tumor tissue samples performed on co-isolated DNA and RNA, which has been validated on over 1,900 FFPE tumor samples, and is covered for Medicare beneficiaries 41 . While earlier StrataNGS versions were also used during the study period, all had similar performance for the TMB assessment (and MSI) used herein 42 .…”