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Evidence claim

Relevance of target-level detection against routine multiplex PCR, validation set (Sanderson et al. 2026) to "Select an RNA pathogen-detection workflow for diagnostic testing"

Use case
Select an RNA pathogen-detection workflow for diagnostic testing
Assessed by
Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026)
Relevance
Proxy evidence
Endpoint
Target-level sensitivity and specificity of a nanopore RNA metagenomic workflow against routine multiplex PCR in 344 prospectively collected nasopharyngeal swabs (273 passing QC), overall, by pathogen and by viral load, under pre-specified and post-hoc detection criteria

A prospective validation of one RNA metagenomic workflow on respiratory swabs, scored as target-level sensitivity and specificity against the original clinical PCR, with thresholds fixed on a separate derivation set, matches the use case's inputs (nuclease-treated respiratory RNA, reverse-transcribed) and its output (sensitivity against original clinical testing for one respiratory mNGS assay). It is proxy evidence for the same reason as the UCSF anchor: agreement with the clinical PCR panel is not sensitivity against all infections, and samples were selected by PCR result. It compares detection criteria within one workflow, not different workflows.

2 reviewed evaluations

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Citation locations
1 values
  • source id
    rna-pathogen-20261011-sanderson2026-source
    locator
    Results 'Validation Set: Diagnostic performance', 'Performance by pathogen', 'Performance by viral load (Cn,Ct)'
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison group
sanderson2026-nanopore-nps
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.comparison_group

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison title
Nanopore RNA metagenomics on nasopharyngeal swabs against multiplex PCR (Sanderson et al. 2026)
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.comparison_title

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Constraints
3 values
  • Inspect every linked evaluation's source locator and preserved limitations before citing a result.
  • Do not combine these results with another protocol's results; specimens, reference assays and scoring units differ between sources.
  • Cite the pre-specified criteria as the validation result; the alternative criterion is post-hoc.
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.constraints

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Endpoint
Target-level sensitivity and specificity of a nanopore RNA metagenomic workflow against routine multiplex PCR in 344 prospectively collected nasopharyngeal swabs (273 passing QC), overall, by pathogen and by viral load, under pre-specified and post-hoc detection criteria
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.endpoint

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Claimed field
links:assessed_by:rna-pathogen-20261011-sanderson2026-protocol-validation
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.field

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Headline metric
recall
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.headline_metric

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Limitations
9 values
  • Preprint (medRxiv v2); the Journal of Infection version was not retrieved or compared.
  • Developers' own workflow (author_reported).
  • The Abstract and Results give different specificity counts for the pre-specified criteria (3836/3845 against 3901/3910).
  • Upper respiratory swabs with high host background; sensitivity 51% overall, 19% for rhinovirus/enterovirus.
  • Nine false positives, attributed by the authors to barcode crossover in multiplexed runs.
  • 71 of 344 samples failed QC and are not scored.
  • Tables 1 to 3 are images in the preprint and were not transcribed; only values printed in the text are recorded.
  • Spectrum bias: inclusion required a pathogen detected at Ct or Cn 30 or below on the four-target assays, or FilmArray testing, with about one FilmArray-negative sample collected per eight positive samples; sensitivity and specificity are not estimates for unselected swabs.
  • Reads were mapped only to a curated database of the 23 PCR-panel pathogens, so the study does not measure detection of organisms outside the panel or false calls outside it.
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.limitations

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Pinned records
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Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.pins

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Rationale
A prospective validation of one RNA metagenomic workflow on respiratory swabs, scored as target-level sensitivity and specificity against the original clinical PCR, with thresholds fixed on a separate derivation set, matches the use case's inputs (nuclease-treated respiratory RNA, reverse-transcribed) and its output (sensitivity against original clinical testing for one respiratory mNGS assay). It is proxy evidence for the same reason as the UCSF anchor: agreement with the clinical PCR panel is not sensitivity against all infections, and samples were selected by PCR result. It compares detection criteria within one workflow, not different workflows.
Context-only references		Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Original source ↗

rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'

Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML
Retrieved: 2026-10-11T21:38:13Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.rationale

Source artifact SHA-256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: use-case-mapping-rna-pathogen-20261011-sanderson2026-validation

field
links:assessed_by:rna-pathogen-20261011-sanderson2026-protocol-validation
value
rna-pathogen-20261011-sanderson2026-protocol-validation
relevance
proxy
endpoint
Target-level sensitivity and specificity of a nanopore RNA metagenomic workflow against routine multiplex PCR in 344 prospectively collected nasopharyngeal swabs (273 passing QC), overall, by pathogen and by viral load, under pre-specified and post-hoc detection criteria
rationale
A prospective validation of one RNA metagenomic workflow on respiratory swabs, scored as target-level sensitivity and specificity against the original clinical PCR, with thresholds fixed on a separate derivation set, matches the use case's inputs (nuclease-treated respiratory RNA, reverse-transcribed) and its output (sensitivity against original clinical testing for one respiratory mNGS assay). It is proxy evidence for the same reason as the UCSF anchor: agreement with the clinical PCR panel is not sensitivity against all infections, and samples were selected by PCR result. It compares detection criteria within one workflow, not different workflows.
constraints
Inspect every linked evaluation's source locator and preserved limitations before citing a result.; Do not combine these results with another protocol's results; specimens, reference assays and scoring units differ between sources.; Cite the pre-specified criteria as the validation result; the alternative criterion is post-hoc.
limitations
Preprint (medRxiv v2); the Journal of Infection version was not retrieved or compared.; Developers' own workflow (author_reported).; The Abstract and Results give different specificity counts for the pre-specified criteria (3836/3845 against 3901/3910).; Upper respiratory swabs with high host background; sensitivity 51% overall, 19% for rhinovirus/enterovirus.; Nine false positives, attributed by the authors to barcode crossover in multiplexed runs.; 71 of 344 samples failed QC and are not scored.; Tables 1 to 3 are images in the preprint and were not transcribed; only values printed in the text are recorded.; Spectrum bias: inclusion required a pathogen detected at Ct or Cn 30 or below on the four-target assays, or FilmArray testing, with about one FilmArray-negative sample collected per eight positive samples; sensitivity and specificity are not estimates for unselected swabs.; Reads were mapped only to a curated database of the 23 PCR-panel pathogens, so the study does not measure detection of organisms outside the panel or false calls outside it.
citation locators
source id: rna-pathogen-20261011-sanderson2026-source; locator: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen', 'Performance by viral load (Cn,Ct)'
source locator
rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance'
revision
1
reason
Recorded from the 2026-10-11 RNA pathogen-detection literature pass (data/omics/use-case-coverage-rna-pathogen-20261011-sanderson2026). Independently reviewed in docs/reviews/use-cases/pathogen-use-cases-2026-10-11.md.
comparison group
sanderson2026-nanopore-nps
comparison title
Nanopore RNA metagenomics on nasopharyngeal swabs against multiplex PCR (Sanderson et al. 2026)
headline metric
recall
stratum label
Validation set
stratum order
1
review
method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Separate Claude review agent (reviewer-path), independent of the extractor; no human review claimed; date: 2026-10-11; artifact sha256: c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2; retrieval url: https://www.medrxiv.org/content/early/2026/02/26/2026.02.06.26345651.source.xml; method note: Judgement drafted by the extracting agent from the pinned preprint.; note: Re-downloaded the pinned artifact and matched its SHA-256; compared every value with a separate stdlib parser written for this review (the extractor's script was not run) and checked a stratified sample by hand against the rendered table.
reviewed evaluations
rna-pathogen-20261011-sanderson2026-eval-alternative; rna-pathogen-20261011-sanderson2026-eval-prespecified
pins
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