Operationalizing a prioritized COVID-19testing strategy at a Canadian tertiary care cancer center
Bibliographic record
Abstract
Background: Available data suggest that cancer patients who contract COVID-19 may have worse outcomes, including a higher mortality compared to noncancer patients In an effort to inform and guide our clinicians in theongoing management of cancer patients during the COVID-19 pandemic, CancerControl Alberta (CCA)implemented targeted fast-track testing for symptomatic, immunocompromised cancer patients in the ambulatorysetting We report the results of the first 7 weeks of testing at the Tom Baker Cancer Centre (TBCC), acomprehensive tertiary cancer center serving southern Alberta (population approximately 2 million) Methods: Referral for prioritized COVID-19 testing (results within 24 hours) was intended for ambulatory cancerpatients who were identified to have symptoms consistent with an influenza-like illness and confirmed to meet atleast one of the following criteria: stem cell transplant recipient, hematologic malignancy, cancer diagnosis receiving>0 5 mg/kg/day of prednisone or equivalent, patients on immunotherapy treatment, patients on active chemotherapy within the last 3 weeks, neutropenia (ANC <500), lung cancer, chronic lung disease (e g , COPD), or patientsreceiving curative radiation Testing occurred on site at the TBCC at a designated drive-through testing area wherestaff, using PPE, tested patients who remained in their cars The assay for COVID-19 was nucleic acid-based test, and patients were also tested for a standard respiratory virus panel Patients received either a nasopharyngeal orthroat swab, for hematologic and solid tumors diagnoses, respectively Descriptive analyses were performed Results: Between April 15th and June 1st, 2020, 80 patients received prioritized testing at the Tom Baker CancerCentre Patients who were tested for COVID-19 had the following characteristics: median age of 60 5 years (range19, 85) and 31% were male The majority of tested patients (80%) met the criteria as outlined to prioritize testing Patients with the following tumor types comprised over 80% of those tested: breast (n=22), hematologic (n=16), lung(n=9), gynecologic (n=9), and GI (n=9) The average time from screening to testing was 26 5 hours, and theaverage time from test to result was 12 8 hours At the time of reporting, only one breast cancer patient, who justfinished chemotherapy, tested positive via the fast-track testing process;this patient received repeat clearancetesting, undergoing a total of 6 tests over one month before achieving 2 negative tests Conclusions: Our experience demonstrates that prioritized testing for COVID-19 among those who are potentiallythe most susceptible, namely immunocompromised cancer patients, is feasible Very few (1%) positive cases ofCOVID-19 were identified, among 80 patients tested in the first 47 days of operationalizing the fast-track testingprocess Expedited testing should be considered as an ongoing strategy to provide guidance to clinicians inmanaging cancer patients during the COVID-19 pandemic
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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 | 0.004 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.006 | 0.001 |
| Scholarly communication | 0.003 | 0.001 |
| Open science | 0.003 | 0.004 |
| Research integrity | 0.001 | 0.001 |
| 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".