Next-generation sequencing (NGS) of tumor tissue from >4000 men with metastatic castration-resistant prostate cancer (mCRPC): The PROfound phase III study experience.
Bibliographic record
Abstract
195 Background: The PROfound study (NCT02987543) showed that olaparib provides a statistically significant improvement in radiographic progression-free survival versus physician’s choice of enzalutamide or abiraterone in mCRPC patients (pts) with alterations in genes with a direct or indirect role in the homologous recombination repair (HRR) pathway. This is the largest study to date with central, prospective tumor tissue testing in pts with mCRPC. Here, we report learnings during testing in the PROfound study. Methods: An investigational clinical trial assay, based on the FoundationOne CDx NGS test developed in partnership with Foundation Medicine, Inc (FMI), was used to prospectively identify pts with qualifying alterations in ≥1 of 15 prespecified genes, including BRCA1, BRCA2 or ATM. Tumor testing was conducted centrally using archival or recent biopsy from primary or metastatic tissue. Results: Of 4047 pts who submitted tumor samples, 2792 (69%) were successfully sequenced and yielded a biomarker status. Categories for test failure (n=1255; 31%) were pathology review failure in 277 (6.8%) pts (eg estimated tumor fraction <20% or tumor volume <0.2 mm2), DNA extraction failure in 533 (13.2%) pts, and failure after DNA extraction in 280 (6.9%) pts, with 165 (4.1%) pts in >1 category. Regarding the sample disposition, approximately two-thirds of samples were from core needle biopsies, although higher success rates were observed with larger samples (ie prostatectomy). Samples were mainly from the prostate gland, with <5% from bone. Most samples were from archived tissue of primary tumors; only ~10% were from newly collected tissue. Test turnaround time, as well as representation of sample characteristics and country of origin relative to success rate, will be presented. Conclusions: The PROfound study has demonstrated that tissue testing to identify HRR alterations in men with mCRPC is feasible. Careful selection of high-quality tumor tissue samples is key to ensure success both at pathology review and during downstream steps of the NGS tissue testing process. Clinical trial information: NCT02987543.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".