rewirebio.iobenchmarks
Dataset

CCGA substudy 1 validation set (847 analysable participants)

Independent validation set of the first Circulating Cell-free Genome Atlas substudy.

Evaluation results

10 evaluations · 10 results. Different protocols are not a single leaderboard.

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Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Allelic imbalance classifier (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
22% (18%–26%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 18 to 26. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

Coverage: Not reported scored / Not reported eligible

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

allelic imbalance on CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'allelic imbalance', validation set, sensitivity and TP/total cancer samples 101/464
Configuration: Clinical risk-factor classifier (no cfDNA), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
2.6% (1.4%–4.5%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 1.4 to 4.5. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

Coverage: Not reported scored / Not reported eligible

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

clinical data on CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'clinical data', validation set, sensitivity and TP/total cancer samples 12/457
Configuration: Fragment endpoint classifier (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
18% (15%–22%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 15 to 22. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

Coverage: Not reported scored / Not reported eligible

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

fragment endpoints on CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'fragment endpoints', validation set, sensitivity and TP/total cancer samples 84/464
Configuration: Fragment length classifier (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
29% (25%–34%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 25 to 34. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

Coverage: Not reported scored / Not reported eligible

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

fragment lengths on CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'fragment lengths', validation set, sensitivity and TP/total cancer samples 136/464
Configuration: Pan-feature classifier over all cfDNA classifier scores (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
36% (31%–40%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 31 to 40. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

Coverage: Not reported scored / Not reported eligible

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

pan-feature on CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'pan-feature', validation set, sensitivity and TP/total cancer samples 165/464
Configuration: Somatic copy number classifier (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
27% (23%–31%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 23 to 31. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

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 sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SCNA', validation set, sensitivity and TP/total cancer samples 125/464
Configuration: Somatic copy number classifier with matched white-blood-cell correction (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
30% (26%–34%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 26 to 34. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

Coverage: Not reported scored / Not reported eligible

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

SCNA-WBC on CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SCNA-WBC', validation set, sensitivity and TP/total cancer samples 139/464
Configuration: Small somatic variant classifier on a 507-gene panel (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
16% (13%–20%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 13 to 20. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

Coverage: Not reported scored / Not reported eligible

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

SNV on CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SNV', validation set, sensitivity and TP/total cancer samples 75/464
Configuration: Small somatic variant classifier with matched white-blood-cell background removal (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
33% (29%–38%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 29 to 38. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

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 sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SNV-WBC', validation set, sensitivity and TP/total cancer samples 155/464
Configuration: Whole-genome methylation classifier (GRAIL prototype), CCGA substudy 1Protocol: CCGA substudy 1 validation set: cancer signal sensitivity at 98% specificity
Dataset: CCGA substudy 1 validation set (847 analysable participants)
34% (30%–39%) Sensitivity at 98% specificity (validation set, post hoc 98% specificity threshold)
percent · higher

Uncertainty: 95% CI 30 to 39. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis)

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 sensitivity at 98% specificity

ctdnajam-20261010-protocol-ccga1-validation-sens-98spec

Aggregation: Not reported

Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'WG methylation', validation set, sensitivity and TP/total cancer samples 158/464

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

Exact outcomes, predictions, identifiers and evaluator are connected.

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
  • 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

  • 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
  • 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
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

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.

Artifacts and reproduction

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.

9 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
Negatives
362
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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.negatives

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

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

Inspected artifact

Population
847 analysable participants: 485 with cancer and 362 without cancer (Table 1); Table 3 scores 464 cancers and 362 non-cancers; the difference is the 21 plasma cell neoplasms and leukaemias in each set, excluded because detection was restricted to solid cancers (STAR Methods; Table 1 footnote a)
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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

Positives
485
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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.positives

Source artifact SHA-256: 5159294dd203d511dd437837a34555b276e14e0edf615bcb58bae5d9a1246d9a

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

Inspected artifact

Scope note
Case-control: participants with cancer were enrolled before treatment, and non-cancer participants were enrolled from the same centres or regions in a ratio of about 3 to 7. Participants were randomised to training and validation sets in sequencing batches; the first four batches were women only. All assays were run on contemporaneous blood samples from the same participants. Sequencing data are not public.
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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
Figure 1; Table 1; Table 3 and its footnote a
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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
847
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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
Independent validation set of the first Circulating Cell-free Genome Atlas substudy.
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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 set (847 analysable participants)
Context-only references
Evaluation of cell-free DNA approaches for multi-cancer early detection

Original source ↗

Figure 1; Table 1; Table 3 and its footnote a

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

areas
dna-genomes
contexts
clinical_research
version
CCGA (NCT02889978) substudy 1, validation set
population
847 analysable participants: 485 with cancer and 362 without cancer (Table 1); Table 3 scores 464 cancers and 362 non-cancers; the difference is the 21 plasma cell neoplasms and leukaemias in each set, excluded because detection was restricted to solid cancers (STAR Methods; Table 1 footnote a)
total
847
positives
485
negatives
362
scope note
Case-control: participants with cancer were enrolled before treatment, and non-cancer participants were enrolled from the same centres or regions in a ratio of about 3 to 7. Participants were randomised to training and validation sets in sequencing batches; the first four batches were women only. All assays were run on contemporaneous blood samples from the same participants. Sequencing data are not public.
source locator
Figure 1; Table 1; Table 3 and its footnote a
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