Non-small cell lung cancer (NSCLC) next generation sequencing (NGS) using the Oncomine Comprehensive Assay (OCA) v3: Integrating expanded genomic sequencing into the Canadian publicly funded health care model.
Bibliographic record
Abstract
2620 Background: Standard of care (SOC) molecular diagnostics for stage IV NSCLC patients in Ontario, Canada includes publicly reimbursed EGFR/ ALK, and selected BRAF and ROS-1 testing. Other genomic alterations are not tested routinely; however, enhanced molecular testing may broaden treatment options for patients. This study evaluated costs, identified actionable targets, and determined clinical trial eligibility as a result of using the OCAv3 NGS in stage IV NSCLC patients. Methods: In a prospective study of stage IV NSCLC out-patients at Princess Margaret Cancer Centre (Toronto) without EGFR/ALK/KRAS/BRAF alteration (unless failure of prior targeted therapy), diagnostic samples were tested by OCAv3 (ThermoFisher; 161 genes: hotspots, fusions, and copy number variations). Primary endpoints were incremental actionable targets and clinical trial opportunities as a result of broader OCAv3 testing. Secondary endpoints include feasibility and cost from the Canadian public healthcare perspective, and treatment outcomes. Results: Of 65 enrolled patients (Feb 2018-Jan 2019; 40 (62%) completed/14 (21%) screen fail/ 11 (17%) pending), median age of completed cohort was 65, 60% (N = 24) female, never/light smokers 68% (N = 27), Asian 38% (N = 15), previously treated 33% (N = 13). Actionable targets beyond SOC were identified in 33% (N = 13): ERBB2 (N = 8), BRAFV600 (N = 3), NRG fusion (N = 1), MET exon 14 (N = 1). New clinical trial options were identified in 70%. Failure of NGS was secondary to insufficient tissue [91% (N = 10) of screen failures; usually due to tissue exhaustion from prior SOC molecular testing]. Incremental costs per case beyond EGFR/ALK are estimated at $540 CAD. If ROS-1 and BRAF testing were publicly reimbursed at current rates, the incremental profiling cost with OCAv3 would be $90 CAD per case. Conclusions: Although a key barrier to implementation is lack of funding for NGS in the Canadian publicly funded system, the OCAv3 consolidates genomic testing, identifies additional actionable targets, and substantially increases clinical trial eligibility for patients at a small incremental cost. Clinical trial information: NCT03558165.
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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 | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| 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 | 0.001 |
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".