Evidence claim

Relevance of ONT COLO829, SNVs tumour-only calling (Chen et al. 2025) to "Select a tumour DNA somatic variant-calling workflow"

Use case: Select a tumour DNA somatic variant-calling workflow
Assessed by: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a)
Relevance: Proxy evidence
Endpoint: AUPRC, and precision, recall, F1, TP, FP and FN at the best-F1 threshold, for tumour-only somatic SNV calling by the callers in Supplementary Table 2a

Proxy, not direct: the endpoint matches (per-caller precision, recall and F1 on held-out cell lines with consortium truth sets), but the callers used tumour reads only, whereas this use case's inputs include a matched normal and its exclusions list tumour-only calling. Linked as the closest evidence for users without a matched normal.

4 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.

57 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Citation locations 2 values source id somatic-clairs-to-20261011-source-chen2025-supplementary locator Supplementary Table 2a; 'Command lines used' source id somatic-clairs-to-20261011-source-chen2025 locator Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id somatic-clairs-to-20261011-source-chen2025-supplementary locator Supplementary Table 2a; 'Command lines used' source id somatic-clairs-to-20261011-source-chen2025 locator Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Context-only references	ClairS-TO Source Data workbook Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article Retrieved: 2026-10-11T21:38:10Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `4347c74fe0ce2ed04b1ac40d28bd4f8885c77f628e911a7027a275b1234828f8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id somatic-clairs-to-20261011-source-chen2025-supplementary locator Supplementary Table 2a; 'Command lines used' source id somatic-clairs-to-20261011-source-chen2025 locator Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Context-only references	ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article Retrieved: 2026-10-11T21:37:53Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `806cd47423031495bf00543d7e3e3abad3f93fc4ee3ee2a7a570c335227f5603` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group chen2025-clairs-to Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group chen2025-clairs-to Context-only references	ClairS-TO Source Data workbook Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article Retrieved: 2026-10-11T21:38:10Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `4347c74fe0ce2ed04b1ac40d28bd4f8885c77f628e911a7027a275b1234828f8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group chen2025-clairs-to Context-only references	ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article Retrieved: 2026-10-11T21:37:53Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `806cd47423031495bf00543d7e3e3abad3f93fc4ee3ee2a7a570c335227f5603` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Tumour-only callers on cell lines (Chen et al. 2025, ClairS-TO developers) Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Tumour-only callers on cell lines (Chen et al. 2025, ClairS-TO developers) Context-only references	ClairS-TO Source Data workbook Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article Retrieved: 2026-10-11T21:38:10Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `4347c74fe0ce2ed04b1ac40d28bd4f8885c77f628e911a7027a275b1234828f8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Tumour-only callers on cell lines (Chen et al. 2025, ClairS-TO developers) Context-only references	ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article Retrieved: 2026-10-11T21:37:53Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `806cd47423031495bf00543d7e3e3abad3f93fc4ee3ee2a7a570c335227f5603` 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, specimens, sequencing and caller versions differ between sources. Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

3 source records and release history

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling · Original source · Nature Communications, published 2025-10-31; PMC12579226 full-text XML
ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) · Original source · Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article
ClairS-TO Source Data workbook · Original source · Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: use-case-mapping-somatic-clairs-to-20261011-ont-colo829-snv

field: links:assessed_by:somatic-clairs-to-20261011-protocol-ont-colo829-snv
value: somatic-clairs-to-20261011-protocol-ont-colo829-snv
relevance: proxy
endpoint: AUPRC, and precision, recall, F1, TP, FP and FN at the best-F1 threshold, for tumour-only somatic SNV calling by the callers in Supplementary Table 2a
rationale: Proxy, not direct: the endpoint matches (per-caller precision, recall and F1 on held-out cell lines with consortium truth sets), but the callers used tumour reads only, whereas this use case's inputs include a matched normal and its exclusions list tumour-only calling. Linked as the closest evidence for users without a matched normal.
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, specimens, sequencing and caller versions differ between sources.
limitations: Developer paper: the authors developed ClairS-TO and its SS and SSRS models (author_reported); Clair3, also run here, comes from the same group. Comparators were run by the authors with their recommended settings.; Tumour-only calling of cell lines; the truth sets were derived from tumour-normal data and are filtered to variants with coverage at least 4, at least 3 alternative reads and VAF at least 0.05, so very low-VAF variants are not scored.; Precision, recall and F1 are at the best achievable F1 over the caller's quality threshold, chosen on the test data (Figure 2 legend); AUPRC summarises the whole curve. Neither is an operating point fixed in advance.; Clair3 is a germline caller; its calls were treated as somatic after removing those tagged by ClairS-TO's panels of normals.; Single sample per dataset; no interval estimates.; Comparator versions are old relative to the paper (DeepSomatic 1.7.0 run from the 'latest' container; Mutect2 4.2.6.1; Octopus 0.7.4; Pisces 5.3.0).; Competing interests: the senior author (R.L.) receives research funding from ONT.; Whether the DeepSomatic 1.7.0 models were trained with COLO829 data is not stated in the source.; The denominator is TP + FN after the authors' truth filter; it is the same for every caller in this table.
citation locators: source id: somatic-clairs-to-20261011-source-chen2025-supplementary; locator: Supplementary Table 2a; 'Command lines used'; source id: somatic-clairs-to-20261011-source-chen2025; locator: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend
source locator: somatic-clairs-to-20261011-source-chen2025-supplementary: Supplementary Table 2a; 'Command lines used'; somatic-clairs-to-20261011-source-chen2025: Results 'Benchmarking datasets and evaluation', 'Performance on short-read data'; Methods 'Benchmarking'; Figure 2 legend
headline metric: f1-score
reason: Add a relevance judgement from the 2026-10-11 oncology use-case literature pass.
comparison group: chen2025-clairs-to
comparison title: Tumour-only callers on cell lines (Chen et al. 2025, ClairS-TO developers)
stratum label: ONT COLO829, SNVs
stratum order: 1
reviewed evaluations: somatic-clairs-to-20261011-eval-clair3-ont-colo829-snv; somatic-clairs-to-20261011-eval-clairs-to-ss-ont-colo829-snv; somatic-clairs-to-20261011-eval-clairs-to-ssrs-ont-colo829-snv; somatic-clairs-to-20261011-eval-deepsomatic-ont-colo829-snv
review: method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs and output, the relevance rating and the limitations; every evaluation on the protocol had its values checked in the batch review. Corrections listed in review.md were applied by the extractor.; reviewer: claude; reviewer note: Claude research agent reviewer-onc-1, independent of the extractor uc-oncology; no human review claimed; reviewed at: 2026-10-11T23:30:00Z; note: Automated review; not human scientific review. See docs/reviews/use-cases/tumour-dna-somatic-variant-detection-2026-10-11.md.
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