CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
Three origin classifiers, one per assay, scored on the 127 validation cancers detected by all three representative detection classifiers.
Overview
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3 recorded evaluations, 3 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
3 evaluations · 3 results. Different protocols are not a single leaderboard.
Protocol: 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)
Sorted by Accuracy (cancer signal origin among 127 jointly detected validation cancers) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Accuracy (cancer signal origin among 127 jointly detected validation cancers) |
|---|---|
| Whole-genome methylation classifier (GRAIL prototype), CCGA substudy 1Evaluation | 75% (best in column) |
| Somatic copy number classifier (GRAIL prototype), CCGA substudy 1Evaluation | 41% |
| Small somatic variant classifier with matched white-blood-cell background removal (GRAIL prototype), CCGA substudy 1Evaluation | 35% |
All 3 result rows with coverage, uncertainty and sources
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Source checking is not independent reproduction. Release 2026-10-10-cbb3da59bc08.
Methods and evaluation design
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Recorded evaluations
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- SCNA on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
- SNV-WBC on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
- WG methylation on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
Baseline coverage
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- Author-reported evaluations
- 3
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Regularised classifier on simple permitted features, or protocol's conventional reference
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
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Strengths, limitations and unresolved questions
Evidence
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Sources and history
Release 2026-10-10-cbb3da59bc08 · Record review: source checked
1 source record and release history
- Evaluation of cell-free DNA approaches for multi-cancer early detection · Original source · 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
Technical metadata and extraction receipts
Stable ID: ctdnajam-20261010-protocol-ccga1-validation-cso-accuracy
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- Each origin classifier predicts one of 13 labels (breast; cervix; colon/rectum; oesophagus; head/neck; liver/bile duct/gallbladder; lung; lymphoma; plasma cell neoplasm; ovary; pancreas; kidney; other) for the 127 jointly detected validation cancers. Accuracy is the share of correct labels.
- version
- Jamshidi et al. 2022, Results (cancer signal origin prediction), Figure 4; STAR Methods, CSO prediction
- metric
- accuracy
- metric direction
- higher
- unit
- percent
- metric definition
- Share of the 127 cancers whose predicted origin label matches the clinical diagnosis; a prediction of 'other' counts as correct for anus, unknown primary, melanoma, stomach, thyroid and uterus cancers.
- limitations
- Developer study; origin classifiers were developed after validation blinding was lifted and are described as post hoc.; Scored only on cancers detected by all three detection classifiers, so the set favours high tumour fraction and contains no non-cancer participants.; The label 'other' covers six cancer types and counts as correct for them.; The Results and the Methods name different classifier triples for defining the jointly detected set (SCNA and SNV-WBC against SNV and SCNA-WBC).; No confidence interval is printed for these accuracies.; McNemar tests: WG methylation against SCNA p = 8 x 10^-9 and against SNV-WBC p = 6.5 x 10^-12; SCNA against SNV-WBC p = 0.35 (Results).
- source locator
- Results, cancer signal origin prediction; Figure 4; STAR Methods, CSO prediction
Related records
- uses data: CCGA substudy 1 validation cancers detected by all three representative classifiers (127)
- assessment: SCNA on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
- assessment: SNV-WBC on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
- assessment: WG methylation on CCGA substudy 1 validation set: cancer signal origin accuracy among jointly detected cancers
- assessed by: Select a plasma ctDNA methylation detection workflow