Self-Ligation-Free Next Generation Sequencing Adapters Applied to Methylation Assay
Bibliographic record
Abstract
In developing a bisulfite-free methylation assay with the use of restriction enzymes, self-ligation of next generation sequencing adapters (NGS-adapter) is a technological bottleneck to be overcome. In the experiments of this study, a variety of strategies designed to limit or abolish adapter’s self-ligation has been tested. Experimental data have showed that the three strategies tested can either substantially decrease or completely abolish the self-ligation of NGS-adapters. Minimization or elimination of NGS-adapter’s self-ligation is of importance in increasing the sensitivity, efficiency, and reproducibility of enzyme-mediated methylation assay. The strategies reported in the present study may find applications in some other nanotechnologies. In combination with nanotechnologies, either drop-digit PCR or microarray-based sequencing, the methylation-dependent endonuclease mediated methylation assays will facilitate applications of methylation analysis in both fundamental research and clinical epigenetic studies, particularly in early diagnosis of cancer.
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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 | 0.003 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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".