Evidence claim

Relevance of organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026) to "Select a DNA pathogen-identification workflow for diagnostic testing"

Use case: Select a DNA pathogen-identification workflow for diagnostic testing
Assessed by: Organism-level agreement with composite reference standard (CRS), 62 BALF specimens (Hu et al. 2026)
Relevance: Proxy evidence
Endpoint: Organism-level PPA and NPA (with 2x2 counts) of a short-read MGI workflow and a host-depleted ONT workflow against composite reference standard (CRS) in 62 BALF specimens, for all organisms, bacteria and fungi

Two complete clinical DNA mNGS workflows are compared on the same patient specimens against a stated reference standard, which bears on the use case's question of which workflow detects clinically relevant pathogens. It is proxy evidence: the specimens are BALF rather than plasma cell-free DNA, agreement is counted per organism rather than per patient, and the two workflows differ in platform, host depletion, aligner and threshold together.

2 reviewed evaluations

Evidence

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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.

40 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Citation locations 2 values source id dna-pathogen-20261011-hu2026-source locator Table 2; Methods 'Clinical performance evaluation and reference standards' source id dna-pathogen-20261011-hu2026-source-supp locator Supplemental Tables S6 and S7 Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id dna-pathogen-20261011-hu2026-source locator Table 2; Methods 'Clinical performance evaluation and reference standards' source id dna-pathogen-20261011-hu2026-source-supp locator Supplemental Tables S6 and S7 Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group hu2026-balf-ngs-tgs Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group hu2026-balf-ngs-tgs Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Short-read versus host-depleted nanopore mNGS on 62 BALF specimens (Hu et al. 2026) Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Short-read versus host-depleted nanopore mNGS on 62 BALF specimens (Hu et al. 2026) Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 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; reference standards, specimens and scoring units differ between sources. Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 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; reference standards, specimens and scoring units differ between sources. Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Organism-level PPA and NPA (with 2x2 counts) of a short-read MGI workflow and a host-depleted ONT workflow against composite reference standard (CRS) in 62 BALF specimens, for all organisms, bacteria and fungi Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Organism-level PPA and NPA (with 2x2 counts) of a short-read MGI workflow and a host-depleted ONT workflow against composite reference standard (CRS) in 62 BALF specimens, for all organisms, bacteria and fungi Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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

2 source records and release history

Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Original source · Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML
Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Original source · spectrum.03993-25-s0001.docx as distributed with PMC13339908

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-dna-pathogen-20261011-hu2026-crs

field: links:assessed_by:dna-pathogen-20261011-hu2026-protocol-crs
value: dna-pathogen-20261011-hu2026-protocol-crs
relevance: proxy
endpoint: Organism-level PPA and NPA (with 2x2 counts) of a short-read MGI workflow and a host-depleted ONT workflow against composite reference standard (CRS) in 62 BALF specimens, for all organisms, bacteria and fungi
rationale: Two complete clinical DNA mNGS workflows are compared on the same patient specimens against a stated reference standard, which bears on the use case's question of which workflow detects clinically relevant pathogens. It is proxy evidence: the specimens are BALF rather than plasma cell-free DNA, agreement is counted per organism rather than per patient, and the two workflows differ in platform, host depletion, aligner and threshold together.
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; reference standards, specimens and scoring units differ between sources.
limitations: Organism-level agreement in 62 residual BALF specimens from lower respiratory tract infection; not plasma cell-free DNA and not patient-level diagnosis.; The two workflows differ in platform, library preparation, host depletion, aligner and positivity threshold together (MGISEQ-200 with BWA-MEM and RP20M >= 3; host-depleted ONT GridION with minimap2 and RP10K >= 1), so the comparison is of whole workflows, not of classifiers.; Both workflows used the same curated 20,484-genome reference database and lowest-common-ancestor assignment.; Eight of the listed authors, including co-corresponding author Lifeng Li, are affiliated with Genskey Medical Technology (Beijing), a clinical mNGS provider; the article states that the authors declare no conflict of interest. The workflows are the authors' own, so the evaluations are author_reported.; Organism-level agreement; a specimen contributes one comparison per organism detected by either side.; Incorporation bias: organisms detected by both sequencing workflows were added to the reference, so PPA and NPA against the CRS favour the sequencing workflows by construction.; The use case's exclusion of sensitivity against a composite or adjudicated reference was recorded for the Karius source's composite endpoint; this composite reference from a different source is recorded as proxy evidence only, because it is built partly from the scored workflows' own calls.
citation locators: source id: dna-pathogen-20261011-hu2026-source; locator: Table 2; Methods 'Clinical performance evaluation and reference standards'; source id: dna-pathogen-20261011-hu2026-source-supp; locator: Supplemental Tables S6 and S7
source locator: dna-pathogen-20261011-hu2026-source: Table 2; dna-pathogen-20261011-hu2026-source-supp: Supplemental Tables S6 and S7
revision: 1
reason: Recorded from the 2026-10-11 DNA pathogen-identification literature pass (data/omics/use-case-coverage-dna-pathogen-20261011-hu2026). Independently reviewed in docs/reviews/use-cases/pathogen-use-cases-2026-10-11.md.
comparison group: hu2026-balf-ngs-tgs
comparison title: Short-read versus host-depleted nanopore mNGS on 62 BALF specimens (Hu et al. 2026)
headline metric: recall
stratum label: Composite reference standard (CRS)
stratum order: 3
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: 555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13339908/fullTextXML; method note: Judgement drafted by the extracting agent from the pinned article and supplement.; 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: dna-pathogen-20261011-hu2026-eval-crs-hdont; dna-pathogen-20261011-hu2026-eval-crs-mgi
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subject: Select a DNA pathogen-identification workflow for diagnostic testing

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