Evidence claim
Relevance of OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020) to "Assess somatic small-variant oncogenicity"
- Use case
- Assess somatic small-variant oncogenicity
- Assessed by
- OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9)
- Relevance
- Proxy evidence
- Endpoint
- Accuracy, sensitivity, specificity, PPV and NPV for 33 predictors on OncoKB benchmark (positive set not stated) using median-score threshold
Somatic missense mutations labelled by expert literature curation (OncoKB), with likely neutral somatic mutations as negatives rather than germline-benign labels. Proxy: the binary metrics use each predictor's median score on the test draw as the threshold, which ranks tools but is not an operating point a reviewer could apply. The authors developed none of the predictors except CanDrA.
33 reviewed evaluations
- CADD on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- CanDrA on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- CHASM on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- CTAT-cancer on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- CTAT-population on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- DANN on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- DEOGEN2 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- Eigen on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- Eigen-PC on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- FATHMM-cancer on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- FATHMM-disease on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- FATHMM-MKL on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- FATHMM-XF on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- GenoCanyon on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- Integrated_fitCons on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- LRT on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- M-CAP on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- MetaLR on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- MetaSVM on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- MPC on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- MutationAssessor on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- MutationTaster2 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- MutPred on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- MVP on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- Polyphen2_HDIV on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- Polyphen2_HVAR on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- PrimateAI on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- PROVEAN on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- REVEL on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- SIFT on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- SIFT4G on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- TransFIC on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
- VEST4 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020)
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.
40 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations2 values
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations2 values
| Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group chen2020-oncokb Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group chen2020-oncokb Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title OncoKB-curated drivers versus likely neutral (Chen et al. 2020) Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title OncoKB-curated drivers versus likely neutral (Chen et al. 2020) Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Accuracy, sensitivity, specificity, PPV and NPV for 33 predictors on OncoKB benchmark (positive set not stated) using median-score threshold Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Accuracy, sensitivity, specificity, PPV and NPV for 33 predictors on OncoKB benchmark (positive set not stated) using median-score threshold Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records and release history
- Comprehensive assessment of computational algorithms in predicting cancer driver mutations · Original source · Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML
- Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) · Original source · 13059_2020_1954_MOESM9_ESM.xlsx
Technical metadata and extraction receipts
Stable ID: use-case-mapping-somatic-oncogenicity-20261009-chen2020-oncokb-median
- field
- links:assessed_by:somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median
- value
- somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median
- relevance
- proxy
- endpoint
- Accuracy, sensitivity, specificity, PPV and NPV for 33 predictors on OncoKB benchmark (positive set not stated) using median-score threshold
- rationale
- Somatic missense mutations labelled by expert literature curation (OncoKB), with likely neutral somatic mutations as negatives rather than germline-benign labels. Proxy: the binary metrics use each predictor's median score on the test draw as the threshold, which ranks tools but is not an operating point a reviewer could apply. The authors developed none of the predictors except CanDrA.
- constraints
- Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; truth sets, negatives, thresholds and predictor versions differ between sources.
- limitations
- Binary metrics are means over 100 random draws of 400 positives and 400 negatives; the bracketed range is the mean plus or minus two standard deviations, not a confidence interval.; Predictor scores date from dbNSFP v4.0 and 2019 web servers; current releases (for example AlphaMissense, CHASMplus, BoostDM) are not included.; The threshold is each algorithm's median score on the benchmark draw, which is not available when classifying a new variant; with balanced draws it makes sensitivity, specificity, PPV and NPV nearly equal, so the table ranks tools rather than measuring a usable operating point.; OncoKB annotations are biased towards known, often actionable cancer genes (Discussion).; Some predictors were trained on known cancer mutations, so performance on literature-curated drivers may be inflated.; The OncoKB set has 421 or 497 likely neutral negatives (Methods and Results disagree) and 400 are drawn per repeat, so the draws overlap heavily and the spread understates sampling uncertainty. Results and Methods also disagree on the positive counts, and which positive set fed the binary metrics is not stated.; Two authors (H. Liang, G.B. Mills) co-developed CanDrA (reference 7), and the cell viability labels come from the same group's assays; CanDrA rows are author_reported.; No linked comparison reports calibrated probabilities, per-criterion evidence strength or indels; all variants are missense SNVs.
- revision
- 1
- reason
- Add primary-source predictor comparison evidence from the somatic oncogenicity use-case pass (2026-10-09).
- citation locators
- source id: somatic-oncogenicity-20261009-source-chen2020-additional-file-9; locator: Additional file 9; source id: somatic-oncogenicity-20261009-source-chen2020; locator: Results 'Benchmark 2'; Methods
- source locator
- somatic-oncogenicity-20261009-source-chen2020-additional-file-9: Additional file 9; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods
- comparison group
- chen2020-oncokb
- comparison title
- OncoKB-curated drivers versus likely neutral (Chen et al. 2020)
- headline metric
- accuracy
- stratum label
- Median-score threshold
- stratum order
- 2
- reviewed evaluations
- somatic-oncogenicity-20261009-eval-chen2020-cadd-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-candra-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-chasm-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-ctat-cancer-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-ctat-population-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-dann-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-deogen2-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-eigen-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-eigen-pc-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-fathmm-cancer-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-fathmm-disease-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-fathmm-mkl-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-fathmm-xf-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-genocanyon-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-integrated-fitcons-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-lrt-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-m-cap-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-metalr-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-metasvm-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-mpc-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-mutationassessor-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-mutationtaster2-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-mutpred-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-mvp-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-polyphen2-hdiv-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-polyphen2-hvar-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-primateai-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-provean-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-revel-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-sift-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-sift4g-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-transfic-oncokb-median; somatic-oncogenicity-20261009-eval-chen2020-vest4-oncokb-median
- review
- method: automated-source-review; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent extracted and judged; a separate Claude review agent checked every value and this judgement against the pinned sources (data/omics/use-case-coverage-somatic-oncogenicity-20261009/review.json); reviewed at: 2026-10-09T21:06:32Z; note: Bounded primary-source transcription with independent automated cell check and relevance review. No execution, reproduction, qualified human scientific review or clinical validation.
- pins
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