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

Abstract

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.

Conflict of interest statement

Scott A. Tomlins Employment: Strata Oncology Leadership: Strata Oncology Stock and Other Ownership Interests: Strata Oncology, Javelin Oncology Consulting or Advisory Role: Janssen, Astellas Medivation, Strata Oncology Research Funding: Astellas Medivation Patents, Royalties, Other Intellectual Property: I am a coinventor on a patent issued to the University of Michigan on ETS gene fusions in prostate and am included in the royalty stream. The diagnostic field of use was licensed to Hologic/Gen-Probe (who sublicensed some rights to Ventana/Roche) and is licensed to LynxDx. I am a coinventor on a patent issued to Strata Oncology related to MSI determination and checkpoint inhibitor benefit Travel, Accommodations, Expenses: Strata Oncology, Genzyme Daniel H. Hovelson Employment: Strata Oncology Elizabeth C. Dees Consulting or Advisory Role: Novartis, Strata Oncology, G1 Therapeutics Research Funding: Novartis, Genentech/Roche, Pfizer, Merck, H3 Biomedicine, Meryx Pharmaceuticals Travel, Accommodations, Expenses: G1 Therapeutics Mark E. Burkard Consulting or Advisory Role: Pointcare genomics, Strata Oncology, Novartis Research Funding: AbbVie, Strata Oncology, Puma Biotechnology, Loxo, Merck, Arcus Ventures, Apollomics, Elevation Oncology, Genentech Patents, Royalties, Other Intellectual Property: I have a patent for implantable/localized drug delivery device that can sample the tumor microenvironment and deliver drug, I have a patent for a method to detect recombination events with CRISPR-mediated editing, and I have a patent for conducting expansion microscopy without specialized equipment Michael Guarino Stock and Other Ownership Interests: Johnson and Johnson, Johnson and Johnson Travel, Accommodations, Expenses: McKesson, ARMO BioSciences, AstraZeneca, BMS, De Novo Pharmaceuticals Marc R. Matrana Consulting or Advisory Role: Strata Oncology Speakers' Bureau: Bristol Myers Squibb, AstraZeneca, Merck, Eisai, Genentech, Janssen, Exelixis Eddy S. Yang Consulting or Advisory Role: Strata Oncology, AstraZeneca, Bayer, Clovis Oncology, Lilly Research Funding: Lilly, Novartis, Clovis Oncology, Puma Biotechnology Benjamin M. Parsons Consulting or Advisory Role: Celgene, Amgen, AstraZeneca Speakers' Bureau: Amgen, Celgene, AstraZeneca Open Payments Link: https://openpaymentsdata.cms.gov/physician/795031 Michael A. Thompson Stock and Other Ownership Interests: Doximity Consulting or Advisory Role: Celgene, VIA Oncology, Takeda, GlaxoSmithKline, Strata Oncology, Syapse, Adaptive Biotechnologies, AbbVie, GRAIL, Epizyme, Janssen Oncology Research Funding: Takeda, Bristol Myers Squibb, TG Therapeutics, Cancer Research and Biostatistics, AbbVie, PrECOG, Strata Oncology, Lynx Biosciences, Denovo Biopharma, ARMO BioSciences, GlaxoSmithKline, Amgen Patents, Royalties, Other Intellectual Property: UpToDate, Peer Review for Plasma Cell Dyscrasias (Editor: Robert Kyle) Travel, Accommodations, Expenses: Takeda, GlaxoSmithKline, Syapse Other Relationship: Doximity Open Payments Link: https://openpaymentsdata.cms.gov/physician/192826/summary William J. Edenfield Consulting or Advisory Role: Chimerix Suresh Nair Stock and Other Ownership Interests: Moderna Therapeutics, Novavax, Biontech, Gilead Sciences Research Funding: Bristol Myers Squibb, Merck, Nektar Adedayo Onitilo Consulting or Advisory Role: Kite, a Gilead company, Envision Communications Speakers' Bureau: GlaxoSmithKline, Puma Biotechnology, Kite/Gilead, AbbVie Robert Siegel Research Funding: Merck, Mirati Therapeutics, GRAIL, Altor BioScience, Galera Therapeutics, Apollomics, Strata Oncology, Arcus Biosciences, Bristol Myers Squibb, Cancer Insight, Puma Biotechnology, Conjupro Biotherapeutics, Razor Genomics, Sanofi, Seattle Genetics Other Relationship: American Board of Internal Medicine (ABIM) William J. Irvin Research Funding: Merck, Altor BioScience, Odonate Therapeutics, Boston Biomedical, Novartis, Pfizer, Seattle Genetics, Altor BioScience, AstraZeneca Arvinda Padmanabhan Speakers' Bureau: Clovis Oncology, Roche Anneliese Gonzalez Research Funding: Novartis, Radius Health, Astellas Pharma Paul Harms Research Funding: Q32 Bio Jennifer Hipp Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology Consulting or Advisory Role: PathAI Kat Kwiatkowski Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology, Epizyme, Loxo, Editas Medicine, Intuitive Surgical Khalis Mitchell Employment: Strata Oncology Stock and Other Ownership Interests: Mirati Therapeutics Javed Siddiqui Consulting or Advisory Role: Strata Oncology, LynxDx Hana Vakil Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology D. Bryan Johnson Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology Daniel R. Rhodes Employment: Strata Oncology, Javelin Oncology Leadership: Strata Oncology, Javelin Oncology Stock and Other Ownership Interests: Strata Oncology, Javelin Oncology Patents, Royalties, Other Intellectual Property: I am paid royalties from the University of Michigan on license revenues related to a patent on prostate cancer gene fusions No other potential conflicts of interest were reported. Scott A. Tomlins Employment: Strata Oncology Leadership: Strata Oncology Stock and Other Ownership Interests: Strata Oncology, Javelin Oncology Consulting or Advisory Role: Janssen, Astellas Medivation, Strata Oncology Research Funding: Astellas Medivation Patents, Royalties, Other Intellectual Property: I am a coinventor on a patent issued to the University of Michigan on ETS gene fusions in prostate and am included in the royalty stream. The diagnostic field of use was licensed to Hologic/Gen-Probe (who sublicensed some rights to Ventana/Roche) and is licensed to LynxDx. I am a coinventor on a patent issued to Strata Oncology related to MSI determination and checkpoint inhibitor benefit Travel, Accommodations, Expenses: Strata Oncology, Genzyme Daniel H. Hovelson Employment: Strata Oncology Elizabeth C. Dees Consulting or Advisory Role: Novartis, Strata Oncology, G1 Therapeutics Research Funding: Novartis, Genentech/Roche, Pfizer, Merck, H3 Biomedicine, Meryx Pharmaceuticals Travel, Accommodations, Expenses: G1 Therapeutics Mark E. Burkard Consulting or Advisory Role: Pointcare genomics, Strata Oncology, Novartis Research Funding: AbbVie, Strata Oncology, Puma Biotechnology, Loxo, Merck, Arcus Ventures, Apollomics, Elevation Oncology, Genentech Patents, Royalties, Other Intellectual Property: I have a patent for implantable/localized drug delivery device that can sample the tumor microenvironment and deliver drug, I have a patent for a method to detect recombination events with CRISPR-mediated editing, and I have a patent for conducting expansion microscopy without specialized equipment Michael Guarino Stock and Other Ownership Interests: Johnson and Johnson, Johnson and Johnson Travel, Accommodations, Expenses: McKesson, ARMO BioSciences, AstraZeneca, BMS, De Novo Pharmaceuticals Marc R. Matrana Consulting or Advisory Role: Strata Oncology Speakers' Bureau: Bristol Myers Squibb, AstraZeneca, Merck, Eisai, Genentech, Janssen, Exelixis Eddy S. Yang Consulting or Advisory Role: Strata Oncology, AstraZeneca, Bayer, Clovis Oncology, Lilly Research Funding: Lilly, Novartis, Clovis Oncology, Puma Biotechnology Benjamin M. Parsons Consulting or Advisory Role: Celgene, Amgen, AstraZeneca Speakers' Bureau: Amgen, Celgene, AstraZeneca Open Payments Link: https://openpaymentsdata.cms.gov/physician/795031 Michael A. Thompson Stock and Other Ownership Interests: Doximity Consulting or Advisory Role: Celgene, VIA Oncology, Takeda, GlaxoSmithKline, Strata Oncology, Syapse, Adaptive Biotechnologies, AbbVie, GRAIL, Epizyme, Janssen Oncology Research Funding: Takeda, Bristol Myers Squibb, TG Therapeutics, Cancer Research and Biostatistics, AbbVie, PrECOG, Strata Oncology, Lynx Biosciences, Denovo Biopharma, ARMO BioSciences, GlaxoSmithKline, Amgen Patents, Royalties, Other Intellectual Property: UpToDate, Peer Review for Plasma Cell Dyscrasias (Editor: Robert Kyle) Travel, Accommodations, Expenses: Takeda, GlaxoSmithKline, Syapse Other Relationship: Doximity Open Payments Link: https://openpaymentsdata.cms.gov/physician/192826/summary William J. Edenfield Consulting or Advisory Role: Chimerix Suresh Nair Stock and Other Ownership Interests: Moderna Therapeutics, Novavax, Biontech, Gilead Sciences Research Funding: Bristol Myers Squibb, Merck, Nektar Adedayo Onitilo Consulting or Advisory Role: Kite, a Gilead company, Envision Communications Speakers' Bureau: GlaxoSmithKline, Puma Biotechnology, Kite/Gilead, AbbVie Robert Siegel Research Funding: Merck, Mirati Therapeutics, GRAIL, Altor BioScience, Galera Therapeutics, Apollomics, Strata Oncology, Arcus Biosciences, Bristol Myers Squibb, Cancer Insight, Puma Biotechnology, Conjupro Biotherapeutics, Razor Genomics, Sanofi, Seattle Genetics Other Relationship: American Board of Internal Medicine (ABIM) William J. Irvin Research Funding: Merck, Altor BioScience, Odonate Therapeutics, Boston Biomedical, Novartis, Pfizer, Seattle Genetics, Altor BioScience, AstraZeneca Arvinda Padmanabhan Speakers' Bureau: Clovis Oncology, Roche Anneliese Gonzalez Research Funding: Novartis, Radius Health, Astellas Pharma Paul Harms Research Funding: Q32 Bio Jennifer Hipp Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology Consulting or Advisory Role: PathAI Kat Kwiatkowski Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology, Epizyme, Loxo, Editas Medicine, Intuitive Surgical Khalis Mitchell Employment: Strata Oncology Stock and Other Ownership Interests: Mirati Therapeutics Javed Siddiqui Consulting or Advisory Role: Strata Oncology, LynxDx Hana Vakil Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology D. Bryan Johnson Employment: Strata Oncology Stock and Other Ownership Interests: Strata Oncology Daniel R. Rhodes Employment: Strata Oncology, Javelin Oncology Leadership: Strata Oncology, Javelin Oncology Stock and Other Ownership Interests: Strata Oncology, Javelin Oncology Patents, Royalties, Other Intellectual Property: I am paid royalties from the University of Michigan on license revenues related to a patent on prostate cancer gene fusions No other potential conflicts of interest were reported.

© 2021 by American Society of Clinical Oncology.

Figures

FIG 1.

(A) Breakdown of consecutive PCR-CGP tests ordered from a single commercial clinical sequencing provider between February 13, 2017, and June 25, 2020, including the number of samples rejected before testing, the number of tests performed, the number of samples with evaluable input characteristics, and the number of PCR-CGP tests successfully reported. Samples were grouped into those meeting (pass) or not meeting (exception) PCR-CGP input requirements. (B) For all samples with evaluable input characteristics (n = 31,101), the distribution of samples per characteristic is shown. For samples passing all input requirements (pass), samples are stratified by TSA; exception samples were stratified by indicated sample attribute (TC 2; age > 5 years: specimen collected > 5 years before PCR-CGP; and DNA and/or RNA concentration < 1 ng/µL). For each sample characteristic category, the proportion of the total number of samples with evaluable input characteristics is shown within the bar; the percentage of successfully reported samples is indicated by darker shading in the stacked bar chart and displayed numerically in the gray box at right. (C) Representative successfully reported samples received for PCR-CGP across a TSA range (small [< 25 mm2] and large [≥ 25 mm2] samples indicated). Cancer types and selected prioritized alterations are shown. CGP, comprehensive genomic profiling; NSCLC, non–small-cell lung cancer; PCR-CGP, multiplex polymerase chain reaction–based comprehensive genomic profiling; QC, quality control; TC, tumor content; TSA, tumor surface area.

FIG 2.

Pan-cancer assessment of potential actionability from PCR-CGP testing. All sample QC input-evaluable samples profiled between January 1 and June 25, 2020 (n = 8,241), were stratified by tumor type and assigned to one actionability class on the basis of MSI-H status, presence of an FDA-approved (within cancer type) biomarker, presence of an NCCN guideline–recommended (within cancer type) biomarker, and other TMB-H (≥ 10 mutations/megabase as TMB-H) using the associated therapy logic used in current StrataNGS reporting. Samples without one of these biomarkers were considered informative if at least one prioritized biomarker was reported or the sample passed all sequencing QC metrics with ≥ 20% TC. All other samples were considered test failures. CGP, comprehensive genomic profiling; FDA, US Food and Drug Administration; MSI-H, microsatellite instability–high; NCCN, National Comprehensive Cancer Network; NSCLC, non–small-cell lung cancer; PCR-CGP, multiplex polymerase chain reaction–based comprehensive genomic profiling; QC, quality control; TC, tumor content; TMB, tumor mutation burden; TSA, tumor surface area.

FIG 3.

Underlying genomic data supporting a reported ERBB2 amplification in a breast cancer TC and tumor size exception sample. (A) Hematoxlyin and eosin slide from a 1.5-mm2 TSA lung biopsy from a patient with metastatic breast cancer submitted for PCR-CGP. The inked region indicates the region for microdissection, and a scale bar is shown. Sample QC and sequencing QC metrics are shown, with sample exception and failing QC metrics in red. As the overall molecular profile supports a TC of 15%, below the PCR-CGP's overall limit of detection of TC ≥ 20%, positive results can be reported by expert review; however, negative results cannot be asserted and hence the test is partially reported. (B) Genome-wide copy number profiles from DNA panel 1 (top) and DNA panel 2 (bottom) are shown. Individual amplicon-level log2 copy-number ratio (v a pseudomatched normal profile) is plotted for each targeted gene, with data colored by chromosome (chromosome 1 to X from left to right). TC correction has not been applied. Thresholds for calling amplifications and deep deletions are shown by gray dashed lines. The ERBB2 amplification is indicated. (C) Read-level support for reported prioritized TP53 and PIK3CA mutations is shown from DNA panel 1 (left) and DNA panel 2 (right). Reference nucleotides and amino acids are shown on top, with coverage and nonreference allele distributions below. Forward and reverse strand reads are shown in pink and purple, respectively (randomly downsampled reads are shown; nonvariant-containing reads are compressed). Nonreference bases are colored (black = deletion, light purple = insertion, A = green, C = blue, G = orange, and T = red). Variant and total reads are shown, along with the VAF. CGP, comprehensive genomic profiling; chr, chromosome; CNA, copy number alteration; MSI, microsatellite instability; PCR-CGP, multiplex polymerase chain reaction–based comprehensive genomic profiling; QC, quality control; TC, tumor content; TMB, tumor mutation burden; TSA, tumor surface area; VAF, variant allele frequency.

FIG 4.

(A) Donut plot characterizing the composition of consecutively tested, sample input characteristic-evaluable prostate cancer samples (n = 1,344) from the overall PCR-CGP test cohort. The outer ring indicates the percentage of samples meeting (pass: dark red or not meeting (exception: orange) PCR-CGP input requirements. In the inner pie chart, samples passing all input requirements are stratified by TSA; exception samples are stratified by indicated sample attribute (TC 2; age > 5 years: specimen collected > 5 years before PCR-CGP; and DNA and/or RNA concentration < 1 ng/µL). (B) The proportion of tested samples (overall and by sample input requirement category) for which an informative result (able to rule in or out actionable alterations) was reported. To be considered informative (total of light and dark blue), the test must have reported (1) either MSI-H or a deleterious mutation and/or copy number deep deletion in MSH2/6, BRCA1/2, or ATM (dark blue) or (2) tested definitively negative for these biomarkers by meeting all sequencing QC metrics and having TC ≥ 20%, the PCR-CGP test's overall limit of detection (light blue). The percent of total informative and informative rule in are indicated. (C) Potential real-world prostate cancer testing paradigm on the basis of sample characteristics and PCR-CGP performance characteristics observed in this cohort. Patients with noninformative test results in this cohort were not followed to determine whether rebiopsy or liquid biopsy testing was pursued. CGP, comprehensive genomic profiling; FFPE, formalin-fixed paraffin-embedded; MSI-H, microsatellite instability–high; PCR-CGP, multiplex polymerase chain reaction–based comprehensive genomic profiling; QC, quality control; TC, tumor content; TSA, tumor surface area.

FIG 5.

(A) Donut plot characterizing the composition of consecutively tested, sample input characteristic-evaluable NSCLC adenocarcinoma samples (n = 1,142) from the overall PCR-CGP test cohort. The outer ring indicates the percentage of samples meeting (pass: dark red) or not meeting (exception: orange) PCR-CGP input requirements. In the inner pie chart, samples passing all input requirements are stratified by TSA; exception samples are stratified by indicated sample attribute (TC 2; age > 5 years: specimen collected > 5 years before PCR-CGP; and DNA and/or RNA concentration < 1 ng/µL). (B) The proportion of tested samples (overall and by sample input requirement category) for which an informative result (able to rule in or out actionable alterations) was reported. To be considered informative, the test must have either reported a therapy selection and/or mutually exclusive biomarker (as in C and the Data Supplement) or tested definitively negative for all such biomarkers by meeting all sequencing QC metrics and having TC ≥ 20% (the PCR-CGP test's overall limit of detection). (C) Reported actionable biomarker frequencies from this PCR-CGP NSCLC adenocarcinoma cohort (overall) are shown along with those from an external single-institution cohort (MSK-IMPACT; MSK: light red). The color bar at right indicates whether testing positive for each corresponding biomarker is associated with an FDA-approved (green) or NCCN-recommended (orange) targeted therapy or thought to be mutually exclusive (purple) with known LUAD therapy selection biomarkers. TMB frequencies are presented separately from gene-specific biomarkers given the expected overlap between TMB-high and some therapy selection or actionable biomarkers (for this analysis, samples with more than one biomarker were counted in each group). (D) Potential real-world NSCLC adenocarcinoma testing paradigm on the basis of sample characteristics and PCR-CGP performance characteristics observed in this cohort. Patients with noninformative test results in this cohort were not followed to determine whether rebiopsy or liquid biopsy testing was pursued. CGP, comprehensive genomic profiling; FDA, US Food and Drug Administration; FFPE, formalin-fixed paraffin-embedded; LUAD, lung adenocarcinoma; MSK, Memorial Sloan Kettering; NCCN, National Comprehensive Cancer Network; NGS, next-generation sequencing; NSCLC, non–small-cell lung cancer; PCR-CGP, multiplex polymerase chain reaction–based comprehensive genomic profiling; QC, quality control; TC, tumor content; TMB, tumor mutation burden; TSA, tumor surface area.