Real-World Performance of a Comprehensive Genomic Profiling Test Optimized for Small Tumor Samples

Scott A. Tomlins, Daniel H. Hovelson, Jennifer M. Suga, Daniel M. Anderson, Han A. Koh, Elizabeth C. Dees, Brendan McNulty, Mark E. Burkard, Michael Guarino, Jamil Khatri, Malek M. Safa, Marc R. Matrana, Eddy S. Yang, Alex R. Menter, Benjamin M. Parsons, Jennifer N. Slim, Michael A. Thompson, Leon Hwang, William J. Edenfield, Suresh NairAdedayo Onitilo, Robert Siegel, Alan Miller, Timothy Wassenaar, William J. Irvin, William Schulz, Arvinda Padmanabhan, Vallathucherry Harish, Anneliese Gonzalez, Abdul Hai Mansoor, Andrew Kellum, Paul Harms, Stephanie Drewery, Jayson Falkner, Andrew Fischer, Jennifer Hipp, Kat Kwiatkowski, Lorena Lazo de la Vega, Khalis Mitchell, Travis Reeder, Javed Siddiqui, Hana Vakil, D. Bryan Johnson, Daniel R. Rhodes

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


PURPOSE Tissue-based comprehensive genomic profiling (CGP) is increasingly used for treatment selection in patients with advanced cancer; however, tissue availability may limit widespread implementation. Here, we established real-world CGP tissue availability and assessed CGP performance on consecutively received samples. MATERIALS AND METHODS We conducted a post hoc, nonprespecified analysis of 32,048 consecutive tumor tissue samples received for StrataNGS, a multiplex polymerase chain reaction (PCR)–based comprehensive genomic profiling (PCR-CGP) test, as part of an ongoing observational trial (NCT03061305). Sample characteristics and PCR-CGP performance were assessed across all tested samples, including exception samples not meeting minimum input quality control (QC) requirements (, 20% tumor content [TC],, 2 mm2 tumor surface area [TSA], DNA or RNA yield, 1 ng/mL, or specimen age . 5 years). Tests reporting ≥ 1 prioritized alteration or meeting TC and sequencing QC were considered successful. For prostate carcinoma and lung adenocarcinoma, tests reporting ≥ 1 actionable or informative alteration or meeting TC and sequencing QC were considered actionable. RESULTS Among 31,165 (97.2%) samples where PCR-CGP was attempted, 10.7% had, 20% TC and 59.2% were small (, 25 mm2 tumor surface area). Of 31,101 samples evaluable for input requirements, 8,089 (26.0%) were exceptions not meeting requirements. However, 94.2% of the 31,101 tested samples were successfully reported, including 80.5% of exception samples. Positive predictive value of PCR-CGP for ERBB2 amplification in exceptions and/or sequencing QC-failure breast cancer samples was 96.7%. Importantly, 84.0% of tested prostate carcinomas and 87.9% of lung adenocarcinomas yielded results informing treatment selection. CONCLUSION Most real-world tissue samples from patients with advanced cancer desiring CGP are limited, requiring optimized CGP approaches to produce meaningful results. An optimized PCR-CGP test, coupled with an inclusive exception testing policy, delivered reportable results for . 94% of samples, potentially expanding the proportion of CGP-testable patients and impact of biomarker-guided therapies.

Original languageEnglish
Pages (from-to)1312-1324
Number of pages13
JournalJCO Precision Oncology
StatePublished - 2021

Bibliographical note

Publisher Copyright:
Copyright © 2023 American Society of Clinical Oncology. All rights reserved.

ASJC Scopus subject areas

  • Oncology
  • Cancer Research


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