Evidence claim

Relevance of cell viability drivers versus neutral, default categorical calls (Chen et al. 2020) to "Assess somatic small-variant oncogenicity"

Use case: Assess somatic small-variant oncogenicity
Assessed by: Cell viability drivers versus neutral, default categorical calls (Chen et al. 2020 Additional file 22)
Relevance: Direct evidence
Endpoint: Accuracy, sensitivity, specificity, PPV and NPV for 17 predictors on cell viability drivers versus neutral using default categorical calls

Somatic missense mutations labelled by Ba/F3 and MCF10A cell viability assays, with assay-neutral negatives rather than germline-benign labels; a growth effect is functional evidence, not a full oncogenicity classification. 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

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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-22 locator Additional file 22 source id somatic-oncogenicity-20261009-source-chen2020 locator Results 'Benchmark 5'; Methods Context-only references	Comprehensive assessment of computational algorithms in predicting cancer driver mutations Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; 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-22 locator Additional file 22 source id somatic-oncogenicity-20261009-source-chen2020 locator Results 'Benchmark 5'; Methods Context-only references	Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM22_ESM.xlsx Retrieved: 2026-10-09T20:46:15Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `21ed28f45eee2149e88dff6b75680c99001c4b6daa9805cc9e473d2300ae117a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group chen2020-cell-viability Context-only references	Comprehensive assessment of computational algorithms in predicting cancer driver mutations Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; 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-cell-viability Context-only references	Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM22_ESM.xlsx Retrieved: 2026-10-09T20:46:15Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `21ed28f45eee2149e88dff6b75680c99001c4b6daa9805cc9e473d2300ae117a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Cell viability assay drivers versus 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-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; 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 Cell viability assay drivers versus neutral (Chen et al. 2020) Context-only references	Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM22_ESM.xlsx Retrieved: 2026-10-09T20:46:15Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `21ed28f45eee2149e88dff6b75680c99001c4b6daa9805cc9e473d2300ae117a` 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-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; 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 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM22_ESM.xlsx Retrieved: 2026-10-09T20:46:15Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `21ed28f45eee2149e88dff6b75680c99001c4b6daa9805cc9e473d2300ae117a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Accuracy, sensitivity, specificity, PPV and NPV for 17 predictors on cell viability drivers versus neutral 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-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; 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 cell viability drivers versus neutral using default categorical calls Context-only references	Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) Original source ↗ somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM22_ESM.xlsx Retrieved: 2026-10-09T20:46:15Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `21ed28f45eee2149e88dff6b75680c99001c4b6daa9805cc9e473d2300ae117a` 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

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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 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) · Original source · 13059_2020_1954_MOESM22_ESM.xlsx

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Technical metadata and extraction receipts

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

field: links:assessed_by:somatic-oncogenicity-20261009-protocol-chen2020-viability-default
value: somatic-oncogenicity-20261009-protocol-chen2020-viability-default
relevance: direct
endpoint: Accuracy, sensitivity, specificity, PPV and NPV for 17 predictors on cell viability drivers versus neutral using default categorical calls
rationale: Somatic missense mutations labelled by Ba/F3 and MCF10A cell viability assays, with assay-neutral negatives rather than germline-benign labels; a growth effect is functional evidence, not a full oncogenicity classification. 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.; Functional calls come from the authors' own Ba/F3 and MCF10A screens; a growth effect in either cell model counts as positive.; Activating and inactivating variants are pooled, so oncogene and tumour-suppressor mechanisms are not separated.; The combined cell viability set has 376 positives (Results), yet Methods say 400 positives were drawn per repeat, so positives were drawn with replacement or the counts differ; the source does not say.; 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-22; locator: Additional file 22; source id: somatic-oncogenicity-20261009-source-chen2020; locator: Results 'Benchmark 5'; Methods
source locator: somatic-oncogenicity-20261009-source-chen2020-additional-file-22: Additional file 22; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 5'; Methods
comparison group: chen2020-cell-viability
comparison title: Cell viability assay drivers versus neutral (Chen et al. 2020)
headline metric: accuracy
stratum label: Default categories
stratum order: 1
reviewed evaluations: somatic-oncogenicity-20261009-eval-chen2020-candra-viability-default; somatic-oncogenicity-20261009-eval-chen2020-deogen2-viability-default; somatic-oncogenicity-20261009-eval-chen2020-fathmm-disease-viability-default; somatic-oncogenicity-20261009-eval-chen2020-fathmm-mkl-viability-default; somatic-oncogenicity-20261009-eval-chen2020-fathmm-xf-viability-default; somatic-oncogenicity-20261009-eval-chen2020-lrt-viability-default; somatic-oncogenicity-20261009-eval-chen2020-m-cap-viability-default; somatic-oncogenicity-20261009-eval-chen2020-metalr-viability-default; somatic-oncogenicity-20261009-eval-chen2020-metasvm-viability-default; somatic-oncogenicity-20261009-eval-chen2020-mutationassessor-viability-default; somatic-oncogenicity-20261009-eval-chen2020-mutationtaster2-viability-default; somatic-oncogenicity-20261009-eval-chen2020-polyphen2-hdiv-viability-default; somatic-oncogenicity-20261009-eval-chen2020-polyphen2-hvar-viability-default; somatic-oncogenicity-20261009-eval-chen2020-primateai-viability-default; somatic-oncogenicity-20261009-eval-chen2020-provean-viability-default; somatic-oncogenicity-20261009-eval-chen2020-sift-viability-default; somatic-oncogenicity-20261009-eval-chen2020-sift4g-viability-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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