Toward the DNA methylation haplotype map of 11 common solid cancers
Bibliographic record
Abstract
In heterogeneous tumors, adjacent CpG sites form methylation haplotype blocks (MHBs), genomic regions where methylation status reflects local epigenetic concordance. While MHBs have been implicated in gene dysregulation, their pan-cancer dynamics and clinical relevance remain unclear. We profiled 110 primary tumors across 11 common solid cancer types, identifying 81,567 MHBs. These MHBs exhibit high cancer-type specificity, with enrichment in regulatory elements. Integrative bulk and single-cell analyses reveal that MHBs associate with gene expression independently of mean methylation changes. Moreover, pan-cancer prioritization of MHB-associated differentially expressed genes highlights their roles in oncogenic pathways such as the G2/M checkpoint, MYC targets, and E2F signaling. Inter-tumor heterogeneity links MHB discordance to driver mutations and inflammatory pathways. Finally, we demonstrate that MHBs serve as effective biomarkers for cancer detection, performing competitively to existing methods. This resource positions MHBs as multimodal epigenetic regulators, bridging tumor heterogeneity, transcriptional control, and liquid biopsy diagnostics.
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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 | 0.000 | 0.000 |
| 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 | 0.000 | 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".