Integration of a bacterial gene sequence into a chronic eosinophilic leukemia patient’s genome as part of a fusion gene linker
Bibliographic record
Abstract
Analysis of databases from the human genome project (HGP), the 1000 Genomes Project (1KGP), and The Cancer Genome Atlas (TCGA) revealed bacterial DNA integration into the human somatic genome, particularly in tumor tissues. Fusion genes have also been associated with tumorigenesis and 34 PDGFR fusion genes are linked to hematological malignancies. Here, we determined that a 17-bp homologous sequence in Marinobacter sp. Hb8, Rhodococcus fascians D188, Rhodococcus sp. PBTS2, Micrococcus luteus strain trpE16 and M. luteus NCTC 2665 integrates into the genome of a chronic eosinophilic leukemia patient as part of the linker for the novel CDK5RAP2-PDGFRα fusion gene. The resulting fusion protein that has CDK5RAP2’s self-activating domain and PDGFRa’s tyrosine kinase domain but lacks PDGFRa’s membrane-binding and ligand-dependent activation properties may act together with the integrated bacterial sequence to readily phosphorylate downstream targets, amplify proliferation signals and promote leukemic cancer progression.
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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 | 0.000 | 0.000 |
| 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".