UCSF respiratory RNA mNGS original-testing sensitivity protocol
UCSF respiratory RNA mNGS original-testing sensitivity protocol; bounded primary-source candidate.
Overview
UCSF respiratory RNA mNGS original-testing sensitivity protocol; bounded primary-source candidate.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
1 recorded evaluation, 1 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: UCSF respiratory RNA mNGS original-testing sensitivity tested configuration | Protocol: UCSF respiratory RNA mNGS original-testing sensitivity protocol Dataset: UCSF respiratory RNA mNGS original-testing sensitivity cohort | 93.6% (103 of 110) sensitivity_against_original_rvp_testing percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUCSF respiratory RNA mNGS original-testing sensitivity amp-20261007-rna-pathogens-protocol Aggregation: Not reported Tan et al., Nature Communications 15, 9016 (2024) · PMC11558004 Results paragraph Par15; Table 1 Tab1 Accuracy / Original testing; Fig. 6A. Methods Par34 and Par38 define reference assays and mixed-target weighting. |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
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Baseline coverage
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- Author-reported evaluations
- 1
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Null control
Proposed control: requires review
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Conventional reference
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Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-10-07-1448159e6a81. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
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Release 2026-10-07-1448159e6a81 · Record review: source checked
1 source records and release history
- Tan et al., Nature Communications 15, 9016 (2024) · Original source · Tan et al., Nature Communications 15, 9016 (2024)
Technical metadata and extraction receipts
Stable ID: amp-20261007-rna-pathogens-protocol
- areas
- rna-transcriptomes
- method types
- conventional_pipeline
- tasks
- pathogen_detection
- missing metadata
- version: No immutable protocol identifier extracted
- scope note
- RNA-only specimen preparation supports RNA pathogen-detection workflow; tested target mix includes adenovirus, a DNA virus detected via transcription. Do not describe the 93.6% as a pure RNA-virus-only subgroup score. Multiple detected targets are weighted so each specimen contributes one observation; out-of-panel mNGS positive calls are not counted as false positives. Positive-specimen BAL/swab count disagreement in Results vs Methods remains unresolved; total 110 positives and 81 negatives agree. No confidence interval extracted for original sensitivity. After selective discrepancy adjudication, report PPA/NPA rather than sensitivity; DTCA measurements must remain separate. No foundation model or independent external replication; clinical residual-sample validation study supplies conventional baseline evidence.
- source locator
- PMC11558004 Results paragraph Par15; Table 1 Tab1 Accuracy / Original testing; Fig. 6A. Methods Par34 and Par38 define reference assays and mixed-target weighting.
- task
- sensitivity_against_original_rvp_testing
- version
- Not reported
- workflow
- RNA isolation with DNase, rRNA depletion and cDNA synthesis; Tecan MagicPrep NGS; Illumina MiniSeq/NextSeq; SURPI+ container v1.0.0, SNAP edit distance 16 against March 2019 NCBI NT viral reference augmented by SARS-CoV-2 NC_045512.