Evidence claim

Relevance of CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026) to "Assess somatic small-variant oncogenicity"

Use case: Assess somatic small-variant oncogenicity
Assessed by: CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv)
Relevance: Proxy evidence
Endpoint: AUROC and average precision (labelled AUPRC) of 49 predictor and conservation scores on CGC missense variants, tumour suppressors (loss of function)

Compares 49 predictor and conservation scores, including AlphaMissense, ESM1b and popEVE, separately for oncogene and tumour-suppressor variants, the mechanism split the use case asks for. Proxy: its negatives are germline-benign labels (ClinVar benign or likely benign and gnomAD common variants), which the use case does not accept as somatic controls, and it is a single-author preprint. The author developed none of the scored tools.

49 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-lee2026-oncocal-tool-performance locator group 'TSG' source id somatic-oncogenicity-20261009-source-lee2026 locator Results first section; Methods 'Labels' and 'Features' Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
Citation locations 2 values source id somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance locator group 'TSG' source id somatic-oncogenicity-20261009-source-lee2026 locator Results first section; Methods 'Labels' and 'Features' Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group lee2026-cgc-mechanism Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
Comparison group lee2026-cgc-mechanism Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Predictors by gene mechanism on CGC missense variants (Lee 2026 preprint) Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
Comparison title Predictors by gene mechanism on CGC missense variants (Lee 2026 preprint) Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` 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	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. 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	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint AUROC and average precision (labelled AUPRC) of 49 predictor and conservation scores on CGC missense variants, tumour suppressors (loss of function) Context-only references	An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page Retrieved: 2026-10-09T20:48:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `1b4dfadc861c6b8dbecde6ebb5efdb5ab7203bcf6f1b4e06edc70e167e7050e9` Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Inspected artifact
Endpoint AUROC and average precision (labelled AUPRC) of 49 predictor and conservation scores on CGC missense variants, tumour suppressors (loss of function) Context-only references	OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) Original source ↗ somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11) Retrieved: 2026-10-09T20:48:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `8f5a81078482c8010b83bba6225e9707980a3a7cebbb2ca00ed8b155ad34c3b5` 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

An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers · Original source · bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page
OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) · Original source · commit 40b7770f2a768ba800c4f4c6b48e2bfe967ed14a (2026-07-11)

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-somatic-oncogenicity-20261009-lee2026-tsg

field: links:assessed_by:somatic-oncogenicity-20261009-protocol-lee2026-tsg
value: somatic-oncogenicity-20261009-protocol-lee2026-tsg
relevance: proxy
endpoint: AUROC and average precision (labelled AUPRC) of 49 predictor and conservation scores on CGC missense variants, tumour suppressors (loss of function)
rationale: Compares 49 predictor and conservation scores, including AlphaMissense, ESM1b and popEVE, separately for oncogene and tumour-suppressor variants, the mechanism split the use case asks for. Proxy: its negatives are germline-benign labels (ClinVar benign or likely benign and gnomAD common variants), which the use case does not accept as somatic controls, and it is a single-author preprint. The author developed none of the scored tools.
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: Negatives are ClinVar benign or likely benign and gnomAD common variants, that is germline-benign labels; the use case does not accept these as automatic somatic negatives.; Many supervised tools were trained on ClinVar labels, so the ClinVar-benign negatives overlap their training data.; Single-author bioRxiv preprint (v1, posted 2026-07-23), not peer reviewed; the analysis code is in the linked repository.; Scores are dbNSFP 5.3.1a rank scores; tool coverage differs, so each row has its own n and positives.; No uncertainty is printed in this table. The preprint Results give VARITY_R 0.874 and AlphaMissense 0.868, matching the table; the OncoCal section gives 0.871 and 0.870, probably on the unique protein-level set used to train OncoCal.; Gene role uses CGC gene-level roles where variant-level CIViC mechanism is missing, so some variants may be assigned the wrong mechanism.; The table cannot be regenerated from the repository alone: its script (src/evaluation/part_b.py) needs dbNSFP 5.3.1a and COSMIC v104, which are not redistributed. It was added in the first commit (b17e658d6b) and is unchanged at the pinned commit, whose message credits an AI coding assistant but does not touch the table or its script.; 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-lee2026-oncocal-tool-performance; locator: group 'TSG'; source id: somatic-oncogenicity-20261009-source-lee2026; locator: Results first section; Methods 'Labels' and 'Features'
source locator: somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: group 'TSG'; somatic-oncogenicity-20261009-source-lee2026: Results first section; Methods 'Labels' and 'Features'
comparison group: lee2026-cgc-mechanism
comparison title: Predictors by gene mechanism on CGC missense variants (Lee 2026 preprint)
headline metric: auroc
stratum label: Tumour suppressors (LOF)
stratum order: 3
reviewed evaluations: somatic-oncogenicity-20261009-eval-lee2026-alphamissense-tsg; somatic-oncogenicity-20261009-eval-lee2026-bayesdel-addaf-tsg; somatic-oncogenicity-20261009-eval-lee2026-bayesdel-noaf-tsg; somatic-oncogenicity-20261009-eval-lee2026-bstatistic-tsg; somatic-oncogenicity-20261009-eval-lee2026-cadd-raw-tsg; somatic-oncogenicity-20261009-eval-lee2026-clinpred-tsg; somatic-oncogenicity-20261009-eval-lee2026-dann-tsg; somatic-oncogenicity-20261009-eval-lee2026-deogen2-tsg; somatic-oncogenicity-20261009-eval-lee2026-eigen-pc-raw-coding-tsg; somatic-oncogenicity-20261009-eval-lee2026-eigen-raw-coding-tsg; somatic-oncogenicity-20261009-eval-lee2026-esm1b-tsg; somatic-oncogenicity-20261009-eval-lee2026-fathmm-xf-coding-tsg; somatic-oncogenicity-20261009-eval-lee2026-gerp-92-mammals-tsg; somatic-oncogenicity-20261009-eval-lee2026-gerppp-rs-tsg; somatic-oncogenicity-20261009-eval-lee2026-gmvp-tsg; somatic-oncogenicity-20261009-eval-lee2026-list-s2-tsg; somatic-oncogenicity-20261009-eval-lee2026-m-cap-tsg; somatic-oncogenicity-20261009-eval-lee2026-metalr-tsg; somatic-oncogenicity-20261009-eval-lee2026-metarnn-tsg; somatic-oncogenicity-20261009-eval-lee2026-metasvm-tsg; somatic-oncogenicity-20261009-eval-lee2026-misfit-d-tsg; somatic-oncogenicity-20261009-eval-lee2026-misfit-s-tsg; somatic-oncogenicity-20261009-eval-lee2026-mpc-tsg; somatic-oncogenicity-20261009-eval-lee2026-mutationassessor-tsg; somatic-oncogenicity-20261009-eval-lee2026-mutationtaster-tsg; somatic-oncogenicity-20261009-eval-lee2026-mutformer-tsg; somatic-oncogenicity-20261009-eval-lee2026-mutpred2-tsg; somatic-oncogenicity-20261009-eval-lee2026-mutscore-tsg; somatic-oncogenicity-20261009-eval-lee2026-mvp-tsg; somatic-oncogenicity-20261009-eval-lee2026-phactboost-tsg; somatic-oncogenicity-20261009-eval-lee2026-phastcons100way-vertebrate-tsg; somatic-oncogenicity-20261009-eval-lee2026-phastcons17way-primate-tsg; somatic-oncogenicity-20261009-eval-lee2026-phastcons470way-mammalian-tsg; somatic-oncogenicity-20261009-eval-lee2026-phylop100way-vertebrate-tsg; somatic-oncogenicity-20261009-eval-lee2026-phylop17way-primate-tsg; somatic-oncogenicity-20261009-eval-lee2026-phylop470way-mammalian-tsg; somatic-oncogenicity-20261009-eval-lee2026-polyphen2-hdiv-tsg; somatic-oncogenicity-20261009-eval-lee2026-polyphen2-hvar-tsg; somatic-oncogenicity-20261009-eval-lee2026-popeve-tsg; somatic-oncogenicity-20261009-eval-lee2026-primateai-tsg; somatic-oncogenicity-20261009-eval-lee2026-provean-tsg; somatic-oncogenicity-20261009-eval-lee2026-revel-tsg; somatic-oncogenicity-20261009-eval-lee2026-sift-tsg; somatic-oncogenicity-20261009-eval-lee2026-sift4g-tsg; somatic-oncogenicity-20261009-eval-lee2026-varity-er-loo-tsg; somatic-oncogenicity-20261009-eval-lee2026-varity-er-tsg; somatic-oncogenicity-20261009-eval-lee2026-varity-r-loo-tsg; somatic-oncogenicity-20261009-eval-lee2026-varity-r-tsg; somatic-oncogenicity-20261009-eval-lee2026-vest4-tsg
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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record id: somatic-oncogenicity-20261009-eval-lee2026-clinpred-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: 3f05d90e4b89855c44bf1c041b07b0915543fe0cd8201cb039137879debcfabf; record id: somatic-oncogenicity-20261009-eval-lee2026-dann-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: f7499a46ee6a742220b46a840757b636e7cf6ff7ceca9e1777e052c0ec6b194e; record id: somatic-oncogenicity-20261009-eval-lee2026-deogen2-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: c9c91d8659df2fe1020f6c79ad1833fbb850aafecdf2fbfd8e1f179653985770; record id: somatic-oncogenicity-20261009-eval-lee2026-eigen-pc-raw-coding-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: 2ad6a453f00929f300fd11ea03bc0423d93492fb718ae3d2632cf410e83a72b1; record id: somatic-oncogenicity-20261009-eval-lee2026-eigen-raw-coding-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: 9441544c8e6856341fae8edbe55b40e76c1ad8d82f03148252dddcc276cf8f77; record id: somatic-oncogenicity-20261009-eval-lee2026-esm1b-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: 59b5ce90d3224c16a263794bdd68e9eeabb0d6f2f12e7f7f7bb5c5c81920f491; record id: somatic-oncogenicity-20261009-eval-lee2026-fathmm-xf-coding-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: ab4ad53576889288b1084a88cd74d167bc421f12d19a81bb495ec142ed654633; record id: somatic-oncogenicity-20261009-eval-lee2026-gerp-92-mammals-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: 93edd627b17f05a9ff1bf44c45b674dd58fc88a8cc216c8644c62f411d1c34b9; record id: somatic-oncogenicity-20261009-eval-lee2026-gerppp-rs-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: ce641d4a1f5c0a25261614b49f73db7fc782aff12e8abe0688b80d8adfba17e8; record id: somatic-oncogenicity-20261009-eval-lee2026-gmvp-tsg; fields: status; links; attributes.origin; attributes.comparison; sha256: 1aba0a960368bf4f94dc672e73aecc6899e08bcbf1c8c067083d6550fe46ae87; 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subject: Assess somatic small-variant oncogenicity

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