Real-world performance of a comprehensive genomic profiling test optimized for small tumor samples


Scott A. Tomlins, Strata Oncology, Ann Arbor, MI.
Daniel H. Hovelson, Strata Oncology, Ann Arbor, MI.
Jennifer M. Suga, Kaiser Permanente, Dept of Medical Oncology, Vallejo, CA.
Daniel M. Anderson, Metro-Minnesota Community Oncology Research Consortium (MMCORC), St Louis Park, MN.
Han A. Koh, Kaiser Permanente, Bellflower, CA.
Elizabeth C. Dees, The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC.
Brendan McNulty, UNC Rex Healthcare, Raleigh, NC.
Mark E. Burkard, University of Wisconsin Carbone Cancer Center, Madison, WI.
Michael Guarino, ChristianaCare's Helen F. Graham Cancer Center & Research Institute, Newark, DE.
Jamil Khatri, ChristianaCare's Helen F. Graham Cancer Center & Research Institute, Newark, DE.
Malek M. Safa, Kettering Cancer Center, Kettering, OH.
Marc R. Matrana, Ochsner Cancer Institute, New Orleans, LA.
Eddy S. Yang, University of Alabama at Birmingham, Birmingham, AL.
Alex R. Menter, Kaiser Permanente Medical Group, Denver, CO.
Benjamin M. Parsons, Gundersen Health System, La Crosse, WI.
Jennifer N. Slim, MultiCare, Auburn, WA.
Michael A. Thompson, Advocate Aurora HealthFollow
Leon Hwang, Kaiser Permanente Mid Atlantic, Rockville, MD.
William J. Edenfield, Prisma Health Cancer Institute, Greenville, SC.
Suresh Nair, Lehigh Valley Health Network, Allentown, PA.
Adedayo Onitilo, Marshfield Clinic, Marshfield WI.
Robert Siegel, Bon Secours St Francis Cancer Center, Greenville, SC.
Alan Miller, SCL Health Colorado, Broomfield, CO.
Timothy Wassenaar, ProHealth Care, Waukesha, WI.
William J. Irvin, Bon Secours St Francis Medical Center Midlothian, Midlothian, VA.
William Schulz, Swedish American, Rockford, IL.
Arvinda Padmanabhan, Baptist Health, Lexington, KY.
Vallathucherry Harish, High Point Medical Center, High Point, NC.
Anneliese Gonzalez, UT Health-Memorial Hermann Cancer Institute, Houston, TX.
Abdul Hai Mansoor, Kaiser Permanente Northwest, Portland, OR.
Andrew Kellum, North Mississippi Medical Center, Tupelo, MS.
Paul Harms, University of Michigan Health Systems, Ann Arbor, MI.


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/µL, 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.



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