Short-range, orientation-reversing template-switching events occur at a high frequency in the human and yeast genomes
Bibliographic record
Abstract
ABSTRACT The identification of structural variations in genomes using next-generation sequencing approaches greatly facilitates the study of genetic and genomic diseases. The data generated using these approaches also provide interesting new means to examine DNA repair, recombination, and replication to better understand sources of genomic instability. To better utilize this data, we developed SCARR (Systematic Combination of Alignments to Recreate Rearrangements) to identify DNA rearrangements, and used it to examine the occurrence of orientation-reversing events in human and budding yeast genomes. SCARR exceeds the sensitivity of previous genome sequencing approaches, and identifies rearrangements genome-wide with base-pair resolution, which helps provide insights into the mechanisms involved in their formation. We find that short-range orientation-reversing events occur at high rates in both human and yeast genomes. We quantified these rearrangements in yeast strains lacking various DNA repair factors, and propose that these short-range events often occur through template-switching events within a replication fork. We hypothesize that this mechanism may act as an error-prone alternative to fork reversal to restart stalled replication forks.
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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 | 0.001 |
| 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 | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".