Utilization of the 21-gene assay for breast cancer treatment decision-making in Alberta.
Bibliographic record
Abstract
e12024 Background: The 21-gene assay (Oncotype DX) was publicly funded in Alberta in March 2014. At the discretion of the consulting oncologist, testing was offered to eligible women to facilitate systemic therapy decision-making. Oncologists recorded their pre-test chemotherapy (CT) recommendation (no, yes, unsure). Methods: Retrospective chart review of patients age ≤ 70 with grade 2 or 3 estrogen receptor positive, HER-2 negative, lymph node negative breast cancer seen at the two tertiary cancer centers in Alberta, Canada (March 2014- June 2015). Patient, tumor, 21-gene assay, and treatment information was recorded. Logistic regression analyses exploring predictors of 21-gene assay use and CT recommendation will be performed. Results: Of 591 eligible patients, 590 were female. Most of the tumors were grade 2 (394; 67%), did not have lymph-vascular invasion (468; 79%) and were 10 to 20 mm in size (T1c; 295; 50%). One hundred and five patients (28%) had 21-gene assay testing completed. In 348 cases (59%) the treating oncologist made treatment recommendations based on patient/tumor characteristics only, 18 (4%) patients were not candidates for CT (3%), 51 (9%) refused CT and 9 (2%) requested CT. For those who had 21-gene assay testing, recurrence risk was low (RS 0-18) in 113 (68%) patients, intermediate (RS 19-30) in 37 (22%), and high ( ≥ 31) in 13 (8%). In two cases, the tissue sample was insufficient for analysis. CT was administered to 1/113 ( < 1%) patients with low risk, 9/37 (24%) with intermediate risk and 13/13 (100%) with high risk. Conclusions: Of eligible patients, 28% had 21-gene assay testing completed. The majority of those tested had a low or intermediate RS and did not receive CT. We will present impact of 21-gene assay results on oncologists’ CT recommendation and regression analyses for predictors of 21-gene assay use, results and CT recommendation. 21-gene assay completed (n = 165) 21-gene assay not done (n = 426) Median age (range) 55 (34-70) 59 (24-70) Local-regional treatment Breast conservation + radiation 99 (60%) 275 (65%) Mastectomy 66 (40%) 151 (35%) Hormonal therapy Yes 159 (96%) 363 (85%) No 6 (4%) 59 (14%) Unknown 0 4 (1%) Chemotherapy Yes 23 (14%) 140 (33%) No 142 (86%) 284 (67%) Unknown 0 2 ( < 1%)
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 | 0.008 |
| 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 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 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".