Bibliographic record
Abstract
Oropharyngeal squamous cell carcinoma (OpSCC) patients have improved survival when tested positive for high-risk human papillomavirus (HR-HPV). However, tissue assessment of HPV status is currently not standardized and additional factors may influence survival among HPV-positive patients. The main objectives were to evaluate HPV detection methods and to identify possible factors that impact survival of OpSCC patients in British Columbia. We retrospectively analyzed 972 primary OpSCC patients diagnosed between 2000-2008 and referred to the BC Cancer Agency for treatment with curative intents of radiotherapy with or without concurrent chemotherapy. Patient charts were reviewed and collected information for demographics, smoking history, clinical assessments, treatment received, and outcomes. We analyzed two cohorts of Study Cohort, 244 cases with enough formalin-fixed, paraffin-embedded (FFPE) tissues for experiment, and General Cohort, 728 cases without tissues available. Experimental procedures included in situ hybridization (ISH) to detect DNA and RNA HPV and immunohistochemistry (IHC) to detect p16, p53, the retinoblastoma protein (pRB), cyclin D1, and Ki67. We used polymerase chain reaction (PCR) to detect type-specific HPV from cases with enough FFPE tissues for DNA extraction (n=41). Cox proportional hazard (Cox-PH) and Kaplan-Meier (KM) survival analysis were conducted to identify potential clinical and biological factors impacting on 5-year overall survival (OS), disease-specific survival (DSS), and development of loco-regional recurrence (LRR). The incidence rates of males increased from 3.2 to 7.6 per 100,000 whereas females declined from 1.1 to 0.8 per 100,000. The Study Cohort was relatively representative of the General Cohort. The Study Cohort of patients classified as ever-smokers, had tumours staged at T3/4, and received radiotherapy only had poorer 5-year OS, DSS, and LRR (p<0.05). HPV was detected in 77.6% of patients. Using PCR as standard, DNA/RNA ISH to detect HPV was more specific than IHC p16. Stratification of patients by HPV status showed that HPV-positive/p53-positive and HPV-negative/cyclin D1-positive patients had significantly poorer DSS (p=0.03) and 5-year OS (p=0.02), respectively. In conclusion, both HPV burden and its prognostic significance were found in BC. ISH assessment may be used to determine HPV status. IHC assessments of p53 or cyclin D1 status may be prognostic indicators to guide treatment.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 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".