Evidence claim

Relevance of OncoKB benchmark (positive set not stated), default categorical calls (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), default categorical calls (Chen et al. 2020 Additional file 10)
Relevance: Direct evidence
Endpoint: Accuracy, sensitivity, specificity, PPV and NPV for 17 predictors on OncoKB benchmark (positive set not stated) using default categorical calls

Somatic missense mutations labelled by expert literature curation (OncoKB), with likely neutral somatic mutations as negatives rather than germline-benign labels. Direct: each predictor's own default calls are a real operating point. The authors developed none of the predictors except CanDrA.

17 reviewed evaluations

Evidence

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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

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Citation locations 2 values source id somatic-oncogenicity-20261009-source-chen2020-additional-file-10 locator Additional file 10 source id somatic-oncogenicity-20261009-source-chen2020 locator Results 'Benchmark 2'; Methods Context-only references	Comprehensive assessment of computational algorithms in predicting cancer driver mutations Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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 Retrieved: 2026-10-09T20:45:50Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `fef52f70c3a0ff3f82902f87080933c220e12274787de6309b41ee283daf8b8e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id somatic-oncogenicity-20261009-source-chen2020-additional-file-10 locator Additional file 10 source id somatic-oncogenicity-20261009-source-chen2020 locator Results 'Benchmark 2'; Methods Context-only references	Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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_MOESM10_ESM.xlsx Retrieved: 2026-10-09T20:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `b9c41136f45b38533312baa4abfe2923390861c4e49d4d91c6d0275a85222294` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group chen2020-oncokb Context-only references	Comprehensive assessment of computational algorithms in predicting cancer driver mutations Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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 Retrieved: 2026-10-09T20:45:50Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `fef52f70c3a0ff3f82902f87080933c220e12274787de6309b41ee283daf8b8e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group chen2020-oncokb Context-only references	Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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_MOESM10_ESM.xlsx Retrieved: 2026-10-09T20:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `b9c41136f45b38533312baa4abfe2923390861c4e49d4d91c6d0275a85222294` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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 Retrieved: 2026-10-09T20:45:50Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `fef52f70c3a0ff3f82902f87080933c220e12274787de6309b41ee283daf8b8e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title OncoKB-curated drivers versus likely neutral (Chen et al. 2020) Context-only references	Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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_MOESM10_ESM.xlsx Retrieved: 2026-10-09T20:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `b9c41136f45b38533312baa4abfe2923390861c4e49d4d91c6d0275a85222294` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values 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. Context-only references	Comprehensive assessment of computational algorithms in predicting cancer driver mutations Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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 Retrieved: 2026-10-09T20:45:50Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `fef52f70c3a0ff3f82902f87080933c220e12274787de6309b41ee283daf8b8e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values 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. Context-only references	Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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_MOESM10_ESM.xlsx Retrieved: 2026-10-09T20:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `b9c41136f45b38533312baa4abfe2923390861c4e49d4d91c6d0275a85222294` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Accuracy, sensitivity, specificity, PPV and NPV for 17 predictors on OncoKB benchmark (positive set not stated) using default categorical calls Context-only references	Comprehensive assessment of computational algorithms in predicting cancer driver mutations Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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 Retrieved: 2026-10-09T20:45:50Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `fef52f70c3a0ff3f82902f87080933c220e12274787de6309b41ee283daf8b8e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Accuracy, sensitivity, specificity, PPV and NPV for 17 predictors on OncoKB benchmark (positive set not stated) using default categorical calls Context-only references	Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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_MOESM10_ESM.xlsx Retrieved: 2026-10-09T20:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `b9c41136f45b38533312baa4abfe2923390861c4e49d4d91c6d0275a85222294` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) · Original source · 13059_2020_1954_MOESM10_ESM.xlsx

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-somatic-oncogenicity-20261009-chen2020-oncokb-default

field: links:assessed_by:somatic-oncogenicity-20261009-protocol-chen2020-oncokb-default
value: somatic-oncogenicity-20261009-protocol-chen2020-oncokb-default
relevance: direct
endpoint: Accuracy, sensitivity, specificity, PPV and NPV for 17 predictors on OncoKB benchmark (positive set not stated) using default categorical calls
rationale: Somatic missense mutations labelled by expert literature curation (OncoKB), with likely neutral somatic mutations as negatives rather than germline-benign labels. Direct: each predictor's own default calls are a real operating point. 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.; Only 17 algorithms provide default categories, mostly germline deleteriousness tools; cancer-specific tools other than CanDrA and FATHMM-disease are absent.; 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-10; locator: Additional file 10; source id: somatic-oncogenicity-20261009-source-chen2020; locator: Results 'Benchmark 2'; Methods
source locator: somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; 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: Default categories
stratum order: 1
reviewed evaluations: somatic-oncogenicity-20261009-eval-chen2020-candra-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-deogen2-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-fathmm-disease-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-fathmm-mkl-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-fathmm-xf-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-lrt-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-m-cap-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-metalr-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-metasvm-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-mutationassessor-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-mutationtaster2-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-polyphen2-hdiv-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-polyphen2-hvar-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-primateai-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-provean-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-sift-oncokb-default; somatic-oncogenicity-20261009-eval-chen2020-sift4g-oncokb-default
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.
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subject: Assess somatic small-variant oncogenicity

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