rewirebio.iobenchmarks

Use caseDNA and genomesResearch and clinical research

Select a DNA pathogen-identification workflow for diagnostic testing

Which DNA sequencing classification workflow detects clinically relevant pathogens and handles contamination or organisms absent from the reference?

In this release 1 evaluated endpoint · 1 tested configuration · Proxy evidence only · 3 recorded evidence gaps

Question and applicability

Inspect the Karius plasma microbial cfDNA positive-percent-agreement evidence against initial blood culture before selecting a workflow and reference standard for the intended specimen population.

Who this is for
  • Clinical researchers scoping the available diagnostic-genomics evidence
  • Computational researchers comparing exact evaluated configurations
Research setting

Research and clinical research. See Clinical research scope for what the evidence does not establish.

Biological setting
The Karius 2019 plasma microbial cfDNA sequencing assay achieves 93.7% (59 of 63) positive percent agreement with initial blood culture in a prospective 350-patient sepsis-alert cohort (348 paired results).

Outside this use case

  • Sensitivity against a composite/adjudicated reference standard (a separate, excluded endpoint in the source due to a printed CI conflict)
  • RNA viral pathogen detection (this is a DNA-only assay)

Inputs and expected output

Inputs you need

  • Plasma microbial cell-free DNA sequencing reads
  • The reference standard available for agreement/sensitivity comparison (e.g. blood culture, composite adjudication)

Expected output

A sourced positive-percent-agreement figure against one reference standard, with the reference standard's own detection limits explicit; no general sensitivity claim against all true infections.

Clinical research scope

Clinical applicability is bounded to agreement with initial blood culture, a reference standard that does not identify every true infection; this is not an estimate of sensitivity against all infections in the cohort.

Evaluated evidence

Evidence is grouped by its protocol. Relevance refers to the stated endpoint and context; it is separate from clinical validation and from the review method. Limits specific to each evaluation are listed with it.

Karius 2019 plasma microbial cfDNA positive agreement with initial blood culture protocol

Current source-reviewed mapping

Proxy evidence: transfer to this question is limited

Positive percent agreement against initial blood culture is a proxy for sensitivity against all true infections, since initial blood culture does not identify every infection.

Assessed endpoint
Positive percent agreement with initial blood culture for plasma microbial cfDNA sequencing in a prospective sepsis-alert cohort (59/63 initial-blood-culture-positive subset)
Evaluation protocol
Karius 2019 plasma microbial cfDNA positive agreement with initial blood culture protocol
Computational task
A reviewed task relationship is not recorded for this protocol.
Input and population constraints
  • Inspect every linked evaluation's source locator and preserved conflicts before citing a result.
  • Do not combine this mapping's evaluations with any other protocol's results.

Limits on interpretation

  • Positive agreement uses initial blood culture as reference, which does not identify all infections. It is not sensitivity against all true infections.
  • Exact executable/software/database revision is not established; no foundation model and no new execution.
  • Composite-reference outcomes and estimates are separate endpoints; Table 2 negative composite CI54.8–70.0 conflicts with narrative55.2–70.4 and is excluded.
  • DNA-only plasma microbial cfDNA assay; no RNA viral detection or RNA sensitivity implied.
  • Primary article hosted on third-party rious168 mirror; DOI/title match publisher. Public redistribution licence absent; only compact factual table excerpt retained, original PDF retrieval hash preserved.

Automated source review · 2026-10-07 · Claude Sonnet AMP-integration worker, bounded transcription of Codex-checked primary values; independently reviewed by Codex (workbench/amp-supervision/primary-review.md, integration-review-corrections.md)

Bounded primary-source transcription, independently Codex-checked. No new model execution, independent experimental reproduction, qualified human scientific review or clinical validation.

Evaluated configurations

Each configuration below belongs to this protocol. Inspect its inputs, population and scoring conditions before comparing it with another evaluation.

Karius 2019 plasma microbial cfDNA positive agreement with initial blood culture configuration

Author-reported evaluation · Source checked

Karius 2019 plasma microbial cfDNA positive agreement with initial blood culture evaluation; bounded primary-source candidate.

Inspect results, conditions and reproduction (1 recorded result)
Population and split
SEP-SEQ: 350 prospectively enrolled patients presenting to emergency department with sepsis alert; 348 had both sequencing and initial blood-culture results; initial blood-culture-positive subset n=63. · Prospective SEP-SEQ clinical cohort, not a model training/test split
Inputs and adaptation
Plasma microbial cell-free DNA · Not reported
Evaluation budget
Not reported
Runtime and memory

Runtime and memory measurements are not reported in this evaluation. A study budget is not a runtime or memory measurement.

Recorded results for this configuration
MetricValueCoverageUncertainty and source
positive_percent_agreement_initial_blood_culture93.7%

percent · higher

Not reported scored / Not reported eligible

95% CI 84.5–98.2%

Result provenance

Evaluation methods, evidence and reproduction

No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.

Open the protocol's results and comparison checks →

Mapping sources and review metadata

Mapping use-case-mapping-amp-20261007-issue13 · revision 1

Add Codex-checked primary-source protocol evidence from the bounded AMP intake (rewire.it#365).

Reviewed evidence fingerprint 2f8f6df06e1984966961023a929212ba443fba549e5ea12cb8f5592004ce552b

Limitations and missing evidence

These gaps apply to the question as a whole. Absence of evidence is not a zero score.

  • The composite-reference negative-percent-agreement CI is internally conflicting in the source (54.8-70.0 vs 55.2-70.4) and is excluded from this intake.
  • The exact executable/database version is not pinned in the inspected primary text.
  • The primary article's public redistribution licence is absent; only a compact factual table excerpt is archived.

Planned work

These plans do not contribute measured results or evaluated winners above.

Contribute evidence or propose a correction

Evidence collection plan

Collecting evidence

Mapped evidence already covers 1 evaluated endpoint, in the evaluated evidence above. The status above describes only the specific comparison in this plan, which remains open; it does not mean no evidence has been collected. The plan defines a comparison to investigate; it does not establish model performance or suitability.

Comparison question

Which DNA sequencing classification workflow detects clinically relevant pathogens and handles contamination or organisms absent from the reference?

Baselines, outcomes and validation requirements

Baselines to include

  • The conventional/author-introduced workflow measured in the linked primary source(s).

Outcomes to measure

  • The declared endpoint in this use case's active mapping(s); see evidence_gaps for what remains open.

Validation requirements

  • Independent held-out population matched to the intended clinical setting.
  • Qualified human scientific review before any clinical-validation claim.

Next collection task

A dedicated rewire-benchmarks protocol/run task with a prospectively adjudicated composite reference standard, not solely initial blood culture.

Sources and review

Automated source review · 2026-10-07 · Claude Sonnet AMP-integration worker, bounded transcription of Codex-checked primary values; independently reviewed by Codex (workbench/amp-supervision/primary-review.md, integration-review-corrections.md)

Bounded primary-source transcription, independently Codex-checked. No new model execution, independent experimental reproduction, qualified human scientific review or clinical validation.

Release provenance and downloads

Release 2026-10-07-1448159e6a81

Use-case input digest d60fd7f669bfec7bd34ec6e5080d8e1cb4e8186f8286ead60888848f1e20e001

Download questions, collection plans and review metadata (JSON) · Verify release checksums

Question use-case-diagnostic-dna-pathogen-identification. Any numerical results on this page come from this release's existing evaluation records.