rewirebio.iobenchmarks
Dataset

CCGA substudy 1 validation cancers detected by all three representative classifiers (127)

Validation-set cancers that the three representative detection classifiers all called positive at 98% specificity.

Evaluation results

3 evaluations · 3 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Somatic copy number classifier (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
Dataset: CCGA substudy 1 validation cancers detected by all three representative classifiers (127)
41% Accuracy (cancer signal origin among 127 jointly detected validation cancers)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

SCNA on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers

ctdnajam-20261010-protocol-ccga1-validation-cso-accuracy

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Results, cancer signal origin prediction: 41% (52/127)
Configuration: Small somatic variant classifier with matched white-blood-cell background removal (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
Dataset: CCGA substudy 1 validation cancers detected by all three representative classifiers (127)
35% Accuracy (cancer signal origin among 127 jointly detected validation cancers)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

SNV-WBC on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers

ctdnajam-20261010-protocol-ccga1-validation-cso-accuracy

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Results, cancer signal origin prediction: 35% (44/127)
Configuration: Whole-genome methylation classifier (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
Dataset: CCGA substudy 1 validation cancers detected by all three representative classifiers (127)
75% Accuracy (cancer signal origin among 127 jointly detected validation cancers)
percent · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

WG methylation on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers

ctdnajam-20261010-protocol-ccga1-validation-cso-accuracy

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Results, cancer signal origin prediction: 75% (95/127)

Source checking is not independent reproduction. Release 2026-10-10-cbb3da59bc08.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-10-cbb3da59bc08 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

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Missing or unresolved evidence

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  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

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  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
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Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

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No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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.

7 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-cbb3da59bc08
Property and statementOriginal source and locationReview and provenance
Population
127 cancers, solid and haematologic
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Results, cancer signal origin prediction; STAR Methods, CSO prediction

Version: Cancer Cell 40(12):1537-1549.e12, published 2022-12-12; publisher PDF (1-s2.0-S153561082200513X-main.pdf) as deposited by the Francis Crick Institute on figshare, 10.25418/crick.21731870.v1
Retrieved: 2026-10-10T06:05:17Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.population

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py

Inspected artifact

Scope note
A subset chosen by detection, so it is enriched for high tumour fraction. The Results name the three classifiers as WG methylation, SCNA and SNV-WBC; the Methods name them as WG methylation, SNV and SCNA-WBC. Origin classifiers were rerun with the plasma cell neoplasms and leukaemias that detection had excluded (STAR Methods).
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Results, cancer signal origin prediction; STAR Methods, CSO prediction

Version: Cancer Cell 40(12):1537-1549.e12, published 2022-12-12; publisher PDF (1-s2.0-S153561082200513X-main.pdf) as deposited by the Francis Crick Institute on figshare, 10.25418/crick.21731870.v1
Retrieved: 2026-10-10T06:05:17Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.scope_note

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py

Inspected artifact

Source location
Results, cancer signal origin prediction; STAR Methods, CSO prediction
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Results, cancer signal origin prediction; STAR Methods, CSO prediction

Version: Cancer Cell 40(12):1537-1549.e12, published 2022-12-12; publisher PDF (1-s2.0-S153561082200513X-main.pdf) as deposited by the Francis Crick Institute on figshare, 10.25418/crick.21731870.v1
Retrieved: 2026-10-10T06:05:17Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py

Inspected artifact

Total
127
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Results, cancer signal origin prediction; STAR Methods, CSO prediction

Version: Cancer Cell 40(12):1537-1549.e12, published 2022-12-12; publisher PDF (1-s2.0-S153561082200513X-main.pdf) as deposited by the Francis Crick Institute on figshare, 10.25418/crick.21731870.v1
Retrieved: 2026-10-10T06:05:17Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.total

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py

Inspected artifact

Version
CCGA (NCT02889978) substudy 1, validation set subset
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Results, cancer signal origin prediction; STAR Methods, CSO prediction

Version: Cancer Cell 40(12):1537-1549.e12, published 2022-12-12; publisher PDF (1-s2.0-S153561082200513X-main.pdf) as deposited by the Francis Crick Institute on figshare, 10.25418/crick.21731870.v1
Retrieved: 2026-10-10T06:05:17Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.version

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py

Inspected artifact

Description
Validation-set cancers that the three representative detection classifiers all called positive at 98% specificity.
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Results, cancer signal origin prediction; STAR Methods, CSO prediction

Version: Cancer Cell 40(12):1537-1549.e12, published 2022-12-12; publisher PDF (1-s2.0-S153561082200513X-main.pdf) as deposited by the Francis Crick Institute on figshare, 10.25418/crick.21731870.v1
Retrieved: 2026-10-10T06:05:17Z

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py

Inspected artifact

Name
CCGA substudy 1 validation cancers detected by all three representative classifiers (127)
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Results, cancer signal origin prediction; STAR Methods, CSO prediction

Version: Cancer Cell 40(12):1537-1549.e12, published 2022-12-12; publisher PDF (1-s2.0-S153561082200513X-main.pdf) as deposited by the Francis Crick Institute on figshare, 10.25418/crick.21731870.v1
Retrieved: 2026-10-10T06:05:17Z

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py

Inspected artifact

Sources and history

Release 2026-10-10-cbb3da59bc08 · Record review: source checked

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

Stable ID: ctdnajam-20261010-data-ccga1-validation-jointly-detected

areas
dna-genomes
contexts
clinical_research
version
CCGA (NCT02889978) substudy 1, validation set subset
population
127 cancers, solid and haematologic
total
127
scope note
A subset chosen by detection, so it is enriched for high tumour fraction. The Results name the three classifiers as WG methylation, SCNA and SNV-WBC; the Methods name them as WG methylation, SNV and SCNA-WBC. Origin classifiers were rerun with the plasma cell neoplasms and leukaemias that detection had excluded (STAR Methods).
source locator
Results, cancer signal origin prediction; STAR Methods, CSO prediction
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