Open AccessA scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors
Author(s) -
Jeffrey M. Conroy,
Sarabjot Pabla,
Sean T. Glenn,
R. J. Seager,
Erik Van Roey,
Shuang Gao,
Blake Burgher,
Jonathan Andreas,
Vincent Giamo,
Melissa Mallon,
Yong Hee Lee,
Paul DePietro,
Mary Nesline,
Yirong Wang,
Felicia L. Lenzo,
Roger D. Klein,
Shengle Zhang
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0260089
Subject(s) - computational biology , turnaround time , dna sequencing , biology , scalability , precision oncology , bioinformatics , computer science , cancer , gene , genetics , database , operating system
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 6000 TM 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.