Supplementary Methods and Data from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
Bibliographic record
Abstract
Supplemental Figures S1-S7, Supplemental Tables S1-S7. Methods and Figures S1-S8; Tables S1-S7. SF1: Heterozygous TP53 deletion in the germline and tumor of patient 1 and expression timelines of DSE. SF2: Mutational signatures in pGBM samples. SF3: Deletions at immune-modulatory loci and their effect on gene expression. SF4: Dynamics of germlines SVs during tumor evolution. SF5: Copy number assays using TaqMan probes confirm the deletion at the ATRX locus. SF6: Genetic heterogeneity at the ATRX locus. SF7: Distribution of allelic frequencies and clonal sizes in pGBM samples. ST1: Calgary pediatric GBM cohort. ST2: Therapeutic approach taken for each pediatric GBM patient in the Calgary cohort. ST3: Toronto pediatric GBM cohort used for WGS with linked reads and bulk RNA-seq. ST4: Features of each sample analyzed by whole-genome sequencing with linked reads. ST5: Genes mutated in diagnostic pGBM samples in more than one patient. ST6: Genes mutated in follow-up resections in more than one patient. ST7: Results of the fits of the first incomplete moment and the negative binomial like distribution to the samples.
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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 | 0.009 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.591 | 0.138 |
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".