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Current Evidence

Poster: Genomic classification of clinically advanced solid tumors based on MTAP genomic loss

Genomic classification of clinically advanced solid tumors based on MTAP genomic loss

Presented at ASCO 2024

Key Finding1:

  • The genomic landscape of MTAP complete and partial loss across more than 540,000 clinical samples shows a frequency pan-cancer of 9.3%
  • Highest frequencies in glioblastoma (43%), bladder cancer (25%), pancreatic cancer (22%), and non-small cell lung cancer (13%)
  • MTAP loss is a frequent genomic alteration of emerging clinical importance as the clinical trials using PRMT5 and MTA-2 inhibitors progress
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Poster: Analytical validation of a homologous recombination deficiency signature (HRDsig) in pan-tumor tissue samples

Analytical validation of a homologous recombination deficiency signature (HRDsig) in pan-tumor tissue samples

Presented at AMP 2024

Key Finding2:

  • HRDsig is a pan-tumor biomarker on FoundationOne®CDx tissue-based test that does not rely on gene alterations and instead uses a DNA scar-based approach to calculate a score based on copy number features to enable detection of both genomic and non-genomic mechanisms of HRD.
  • Analytical validation demonstrated high concordance compared to an independent HRD biomarker, low false-positive rate, and high reproducibility across disease areas.
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New Biomarkers

Poster: Liquid Biopsy Detection of Gene Copy Number Losses Including Existing and emerging clinical targets

Liquid biopsy detection of gene copy number losses including existing and emerging clinical targets

Presented at ISLB 2024

Key Finding3:

  • CN Losses were detected in 5,405 (8.8%) of liquid biopsy and 147,173 (33%) of tissue biopsy samples across solid tumors
  • The most common losses in the liquid biopsy samples were CDKN2A/B, PTEN, MTAP, and RB1
  • Detection of these alterations is possible through robust genomic profiling of tissue and liquid biopsies, however sufficient ctDNA tumor fraction (≥1%) is needed for detection and is critical to distinguish true negatives and inform reflex to tissue testing
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Poster: Targeting clinically advanced breast cancer with conjugated and unconjugated HER2 antibodies: Does copy number matter?

Targeting clinically advanced breast cancer with conjugated and unconjugated HER2 antibodies: Does copy number matter?

Presented at SABCS 2024

Key Finding4:

  • AmpRatio, a new method to quantify copy-number amplifications in tissue or liquid biopsy testing, was significantly associated with clinical outcomes in a cohort of real-world advanced breast cancer patients treated with HER2 antibody therapies. CN amplifications in ERBB2 specifically were correlated with clinical outcomes to HER2 antibody therapies.
  • HER2-low patients treated with the HER2 conjugated antibody T-DXd and with AmpRatio ≤0.5 had significantly worse outcomes, reflecting potential additional predictive value of an NGS-based AmpRatio quantitative biomarker that could be complementary to qualitative IHC status.
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ctDNA Monitoring

Poster: Algorithmic genomic alteration filtering and ctDNA quantification in serial liquid biopsy from patients with prostate cancer

Algorithmic genomic alteration filtering and ctDNA quantification in serial liquid biopsy from patients with prostate cancer

Presented at ISLB 2024

Key Finding5:

  • Filtering of germline and clonal hematopoiesis (CH) is critical to quantify ctDNA change over time and that an algorithmic approach in the absence of paired PBMC sequencing is feasible
  • This method can identify high rates of CH in a subset of actionable genomic alterations in prostate cancer – highlighting the need to identify CH to avoid incorrect therapy selection.
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Poster: Evaluating early changes in ctDNA tumor fraction as a value add to PSA in predicting early progression in metastatic castrate-resistant prostate cancer (mCRPC)

Evaluating early changes in ctDNA tumor fraction as a value add to PSA in predicting early progression in metastatic castrate-resistant prostate cancer (mCRPC)

Presented at ASCO GU 2024

Key Finding6:

  • ctDNA tumor fraction detection at Cycle 3, Day 1 (C3D1) was linked to unfavorable outcomes and identified early progression post-abiraterone, with increased information derived from ctDNA detection at baseline to complement PSA testing, which had a lower positive predictive value (PPV) for identifying early progression than ctDNA tumor fraction.
  • This demonstrates that ctDNA tumor fraction can offer an independent and additive approach to PSA testing and may refine personalized approaches tailored to the individual patient’s risk of progression.
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Video Resources

How ctDNA Can Unveil Early Signs of Molecular Response in Drug Development

Featuring Jon Beer, senior director of diagnostic sciences at Bristol Myers Squibb, and Christine Petersen, PhD and director of business development at Foundation Medicine o This webinar explores ctDNA monitoring applications in biopharmaceutical drug development and examines case studies highlight ctDNA’s impact in clinical trials.

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Homologous Recombination Deficiency and Emerging Biomarkers for Use in Oncology Therapeutic Development

Featuring Kim Reiss of the University of Pennsylvania School of Medicine and David Fabrizio, VP of Partner Innovation at Foundation Medicine. This webinar dives into how genomic advances and patient need drove the evolution of HRD diagnostics and demonstrates clinical insights using Foundation Medicine’s novel pan-tumor HRD biomarker, HRDsig.

View Recording

References

  1. Necchi et al, Genomic classification of clinically advanced solid tumors based on MTAP genomic loss. Presented at ASCO 2024.
  2. Leibowitz et al, Analytical validation of a homologous recombination deficiency signature (HRDsig) in pan-tumor tissue samples. Presented at AMP 2024.
  3. Liquid biopsy detection of gene copy number losses including existing and emerging clinical targets.. Presented at ISLB 2024.
  4. Targeting clinically advanced breast cancer with conjugated and unconjugated HER2 antibodies: Does copy number matter? Presented at SABCS 2024.
  5. Malapelle et al, Algorithmic genomic alteration filtering and ctDNA quantification in serial liquid biopsy from patients with prostate cancer. Presented at ISLB 2024.
  6. Sweeney et al, Evaluating early changes in ctDNA tumor fraction as a value add to PSA in predicting early progression in metastatic castrate-resistant prostate cancer (mCRPC). Presented at ASCO GU 2024.

Additional Notes

FoundationOne®CDx and FoundationOne®Liquid CDx are qualitative next-generation sequencing based in vitro diagnostic tests for advanced cancer patients with solid tumors and are for prescription use only. FoundationOne CDx utilizes FFPE tissue and analyzes 324 genes as well as genomic signatures. FoundationOne Liquid CDx analyzes 324 genes utilizing circulating cell-free DNA and is FDA-approved to report short variants in 311 genes. The tests are companion diagnostics to identify patients who may benefit from treatment with specific therapies in accordance with the therapeutic product labeling. Additional genomic findings may be reported and are not prescriptive or conclusive for labeled use of any specific therapeutic product. Use of the tests does not guarantee a patient will be matched to a treatment. A negative result does not rule out the presence of an alteration. Some patients may require a biopsy for testing with FoundationOne CDx when archival tissue is not available which may pose a risk. When considering eligibility for ROZLYTREK® based on the detection of NTRK1/2/3 and ROS1 fusions, or for TEPMETKO® based on the detection of MET SNVs and indels that lead to MET exon 14 skipping, testing using plasma specimens is only appropriate for patients for whom tumor tissue is not available for testing. Patients who are tested with FoundationOne Liquid CDx and are negative for other companion diagnostic mutations should be reflexed to tumor tissue testing and mutation status confirmed using an FDA-approved tumor tissue test, if feasible. For the complete label, including companion diagnostic indications and important risk information, please visit www.F1CDxLabel.com and www.F1LCDxLabel.com.