Training set of the first Circulating Cell-free Genome Atlas substudy, scored by 10-fold cross-validation.
9 evaluations · 9 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Allelic imbalance classifier (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 25% (22%–28%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 22 to 28. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'allelic imbalance', training set, sensitivity and TP/total cancer samples 210/833 |
| Configuration: Clinical risk-factor classifier (no cfDNA), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 2.7% (1.7%–4.1%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 1.7 to 4.1. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'clinical data', training set, sensitivity and TP/total cancer samples 22/815 |
| Configuration: Fragment endpoint classifier (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 22% (19%–25%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 19 to 25. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'fragment endpoints', training set, sensitivity and TP/total cancer samples 181/833 |
| Configuration: Fragment length classifier (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 28% (25%–32%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 25 to 32. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'fragment lengths', training set, sensitivity and TP/total cancer samples 236/833 |
| Configuration: Somatic copy number classifier (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 33% (29%–36%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 29 to 36. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SCNA', training set, sensitivity and TP/total cancer samples 271/833 |
| Configuration: Somatic copy number classifier with matched white-blood-cell correction (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 33% (30%–37%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 30 to 37. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SCNA-WBC', training set, sensitivity and TP/total cancer samples 278/833 |
| Configuration: Small somatic variant classifier on a 507-gene panel (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 19% (16%–22%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 16 to 22. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SNV', training set, sensitivity and TP/total cancer samples 159/833 |
| Configuration: Small somatic variant classifier with matched white-blood-cell background removal (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 36% (33%–39%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 33 to 39. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'SNV-WBC', training set, sensitivity and TP/total cancer samples 299/833 |
| Configuration: Whole-genome methylation classifier (GRAIL prototype), CCGA substudy 1 | Protocol: CCGA substudy 1 training set: cancer signal sensitivity at 98% specificity under 10-fold cross-validation Dataset: CCGA substudy 1 training set (1,414 analysable participants) | 39% (36%–43%) Sensitivity at 98% specificity (training set, post hoc 98% specificity threshold) percent · higher Uncertainty: 95% CI 36 to 43. Clopper-Pearson exact binomial interval (STAR Methods, statistical analysis) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcectdnajam-20261010-protocol-ccga1-training-cv-sens-98spec Aggregation: Not reported Evaluation of cell-free DNA approaches for multi-cancer early detection · Table 3, row 'WG methylation', training set, sensitivity and TP/total cancer samples 328/833 |
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9 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Negatives 560 Context-only references | Evaluation of cell-free DNA approaches for multi-cancer early detection Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| Population 1,414 analysable participants: 854 with cancer and 560 without cancer (Table 1); Table 3 scores 833 cancers and 560 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 Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| Positives 854 Context-only references | Evaluation of cell-free DNA approaches for multi-cancer early detection Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| 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 Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| Source location Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants Context-only references | Evaluation of cell-free DNA approaches for multi-cancer early detection Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| Total 1414 Context-only references | Evaluation of cell-free DNA approaches for multi-cancer early detection Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| Version CCGA (NCT02889978) substudy 1, training set Context-only references | Evaluation of cell-free DNA approaches for multi-cancer early detection Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| Description Training set of the first Circulating Cell-free Genome Atlas substudy, scored by 10-fold cross-validation. Context-only references | Evaluation of cell-free DNA approaches for multi-cancer early detection Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
| Name CCGA substudy 1 training set (1,414 analysable participants) Context-only references | Evaluation of cell-free DNA approaches for multi-cancer early detection Figure 1; Table 1; Table 3 and its footnote a; STAR Methods, study design and participants 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: pdftotext -layout text layer, parsed by extract/extract_ctdna_jamshidi.py |
Release 2026-10-10-cbb3da59bc08 · Record review: source checked
Stable ID: ctdnajam-20261010-data-ccga1-training