EPEN-10. Open Sea DNA Hypomethylation/Island Hypermethylation ratio as a Predictor of Chromosomal Instability and Survival in PFA ependymoma
Bibliographic record
Abstract
Abstract Posterior fossa group A ependymoma (PFA) recur in more than 50% of cases. At recurrence a significant number of cases acquire high-risk chromosomal copy number variants (CNV), specifically gain of chromosome 1q (1q+) and/or loss of 6q (6q-). Analysis of DNA methylation profiles at presentation showed a correlation between open sea hypomethylation and island hypermethylation with acquisition of 1q+ and/or 6q- at recurrence. We hypothesize that hypomethylation of open sea DNA methylation sites results in chromosomal instability in PFA, and subsequent acquisition of 1q+ and/or 6q-. Identification of 1q+/6q- predisposed cases at presentation would provide a tool for stratification into a high-risk arm for upcoming clinical trials. Using a training set of 1q+ and/or 6q- predisposed (n = 24) and non-predisposed (“stable”, n = 29) we developed a DNA methylation-based predictive classifier, predominantly based on the ratio of island to open sea methylation sites, that correctly classified 96% (51/53) of training set cases. The performance of this classifier was tested in an independent multi-institutional dataset of approximately 500 PFA for which DNA methylation from presentation samples and survival data were available. Although this dataset did not contain information regarding the CNV status of recurrences thus preventing our ability to test prediction of high-risk CNV acquisition, we could infer acquisition of a high-risk CNV phenotype by outcome analysis. Multivariate analysis of outcome from presentation showed that samples classed as “predisposed” had a significantly shorter overall survival than those classed as “stable”. This result suggests the PFA high-risk DNA methylation classifier will be of utility in identification of those cases that are predisposed to high-risk CNV acquisition. We hope to definitively test the classifier in correlative studies of both the COG ependymoma clinical trial ACNS0831and the European BIOMECA study (SIOP EPN II trial related) for which recurrence CNV status is pending.
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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 | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".