1. A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors.
- Author
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Conroy JM, Pabla S, Glenn ST, Seager RJ, Van Roey E, Gao S, Burgher B, Andreas J, Giamo V, Mallon M, Lee YH, DePietro P, Nesline M, Wang Y, Lenzo FL, Klein R, and Zhang S
- Subjects
- Biomarkers, Tumor genetics, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing instrumentation, Humans, Mutation, Neoplasms pathology, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, RNA, Workflow, Genetic Variation, High-Throughput Nucleotide Sequencing methods, Microsatellite Instability, Neoplasms genetics
- Abstract
Timely and accurate identification of molecular alterations in solid tumors is essential for proper management of patients with advanced cancers. This has created a need for rapid, scalable comprehensive genomic profiling (CGP) systems that detect an increasing number of therapeutically-relevant variant types and molecular signatures. In this study, we assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of somatic alterations from formalin-fixed paraffin-embedded tissue specimens. In parallel, we developed supporting software and automated sample preparation systems designed to process up to 70 clinical samples in a single NovaSeq 6000TM sequencing run with a turnaround time of <7 days from specimen receipt to report. The results demonstrate that the scalable assay accurately and reproducibly detects small variants, copy number alterations, microsatellite instability (MSI) and tumor mutational burden (TMB) from 40ng DNA, and multiple gene fusions, including known and unknown partners and splice variants from 20ng RNA. 717 tumor samples and reference materials with previously known alterations in 96 cancer-related genes were sequenced to evaluate assay performance. All variant classes were reliably detected at consistent and reportable variant allele percentages with >99% overall accuracy and precision. Our results demonstrate that the high-throughput CGP assay is a reliable method for accurate detection of molecular alterations in support of precision therapeutics in oncology. The supporting systems and scalable workflow allow for efficient interpretation and prompt reporting of hundreds of patient cancer genomes per week with excellent analytical performance., Competing Interests: The authors have the following interests. At the time of this research JC, SP, SG, RJS, EVR, SG, BB, JA, VG, MM, YHL, PD, MN, YW, FL, RK and SZ were employed by OmniSeq, Inc., the funder of this study. In addition, JC, SP, SG, PD, MN, RK and SZ were minority OmniSeq shareholders. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.
- Published
- 2021
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