Recognizing false positives: synthetic oligonucleotide controls for environmental <scp>DNA</scp> surveillance
Bibliographic record
Abstract
Summary Environmental DNA (eDNA) is increasingly used for surveillance and detection of species of interest in aquatic and soil samples. A significant risk associated with eDNA methods is potential false‐positive results due to laboratory contamination. To minimize and quantify this risk, we designed and validated a set of synthetic oligonucleotides for use as species‐specific positive PCR controls for several high‐profile aquatic invasive species. The controls consist of species‐specific sequences for the species of interest, with the addition of a synthetic insert containing recognition sites for several restriction enzymes. Following PCR, the presence of the synthetic insert can be detected using gel electrophoresis, restriction enzyme digests or DNA sequencing. For quantitative PCR (qPCR), false positives in environmental samples can also be detected using a fluorescent probe designed to detect the synthetic insert. The generation of synthetic controls is a cost‐effective, reproducible method that increases the power and reliability of eDNA testing by eliminating misinterpretation of false‐positive results from laboratory contamination.
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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 | 0.015 | 0.024 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.003 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 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".