Establishment of a National Surgical Tissue Biobank for Pediatric Crohn's Disease: An Implementation Feasibility Study
Bibliographic record
Abstract
BACKGROUND: Crohn's disease (CD) is a lifelong gastrointestinal inflammatory condition that often requires surgery, particularly for patients diagnosed in childhood. CD has been linked to a combination of microbial, genetic, and environmental factors, but pathogenesis remains unknown. We outline a framework for multicenter surgical biobanking across a large geographic area, required to enable meaningful research, and evaluate feasibility using the 2016 Consolidated Standards of Reporting Trials (CONSORT) extension to randomized pilot and feasibility trials. We also share proof-of-concept RNA sequencing and immunohistochemistry results demonstrating adequacy to generate high-quality translational results. METHODS: CD patients (5-17.2 years) scheduled for intestinal resection were included. Intra-abdominal sepsis was excluded. Surgeons from 10 Canadian children's hospitals underwent virtual training on tissue collection. Bowel, mesenteric fat, and lymph nodes were collected intraoperatively, fixed in formalin and RNAlater, and shipped overnight to a single lab. Feasibility was determined by protocol adherence, study recruitment efficacy, and tissue viability. RESULTS: Tissue has been collected from 18 patients at seven sites since the study launched in 2023. The biobank is on track to bank 30-50 % of the total estimated eligible yearly case volume. Adherence to shipping protocols was impacted by the day of the week of the operation and by shipping office closures. Proof-of-concept immunohistochemistry demonstrated high-quality multiplex images. RNA sequencing identified 560 genes discriminating between inflamed and non-inflamed bowel. CONCLUSIONS: Establishing a national biobank for surgically resected pediatric CD is feasible for translational investigations of CD pathogenesis. Preliminary experiments demonstrate functional protocols sufficient to collect research-quality tissue. LEVEL OF EVIDENCE: Prognosis Study - Level IV.
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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 | 0.133 | 0.059 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.003 | 0.003 |
| Scholarly communication | 0.004 | 0.003 |
| Open science | 0.003 | 0.006 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 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".