Evidence claim

Relevance of COLO829 tumour-only, indels (Krishnamachari et al. 2026) to "Select a tumour DNA somatic variant-calling workflow"

Use case: Select a tumour DNA somatic variant-calling workflow
Assessed by: COLO829 tumour-only, indels, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1)
Relevance: Proxy evidence
Endpoint: AUPRC of tumour-only callers (VarNet-T, five DeepSom models, DeepSomatic, Mutect2, ClairS-TO): COLO829 tumour-only, indels

Proxy, not direct: per-caller AUPRC on real tumour and cell-line WGS with tumour-normal-derived truth sets is close to the use case's endpoint, but the callers used tumour reads only, whereas this use case's inputs include a matched normal and its exclusions list tumour-only calling; precision, recall and F1 are not extracted. Linked as the closest evidence for users without a matched normal.

9 reviewed evaluations

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.

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 3 values source id somatic-varnet-t-20261011-source-krishnamachari2026-supplementary locator Supplementary Tables 1, 2 and 4 source id somatic-varnet-t-20261011-source-krishnamachari2026-source-data locator Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4' source id somatic-varnet-t-20261011-source-krishnamachari2026 locator Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Context-only references	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 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: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 3 values source id somatic-varnet-t-20261011-source-krishnamachari2026-supplementary locator Supplementary Tables 1, 2 and 4 source id somatic-varnet-t-20261011-source-krishnamachari2026-source-data locator Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4' source id somatic-varnet-t-20261011-source-krishnamachari2026 locator Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Context-only references	VarNet-T Source Data workbook Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2026_71705_MOESM6_ESM.xlsx) Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `4a2deae733ff93a9ae0001053816d82fb60787b01646183c8d37fbc5a764cd17` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 3 values source id somatic-varnet-t-20261011-source-krishnamachari2026-supplementary locator Supplementary Tables 1, 2 and 4 source id somatic-varnet-t-20261011-source-krishnamachari2026-source-data locator Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4' source id somatic-varnet-t-20261011-source-krishnamachari2026 locator Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Context-only references	VarNet-T Supplementary Information Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `c808b4361e17a64911a59ded81d9db04c7a3dd5ba95fb3e1e060a293182f2842` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group krishnamachari2026-varnet-t Context-only references	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 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: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group krishnamachari2026-varnet-t Context-only references	VarNet-T Source Data workbook Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2026_71705_MOESM6_ESM.xlsx) Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `4a2deae733ff93a9ae0001053816d82fb60787b01646183c8d37fbc5a764cd17` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group krishnamachari2026-varnet-t Context-only references	VarNet-T Supplementary Information Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `c808b4361e17a64911a59ded81d9db04c7a3dd5ba95fb3e1e060a293182f2842` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Tumour-only callers on Illumina WGS (Krishnamachari et al. 2026, VarNet-T developers) Context-only references	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 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: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Tumour-only callers on Illumina WGS (Krishnamachari et al. 2026, VarNet-T developers) Context-only references	VarNet-T Source Data workbook Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2026_71705_MOESM6_ESM.xlsx) Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `4a2deae733ff93a9ae0001053816d82fb60787b01646183c8d37fbc5a764cd17` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Tumour-only callers on Illumina WGS (Krishnamachari et al. 2026, VarNet-T developers) Context-only references	VarNet-T Supplementary Information Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `c808b4361e17a64911a59ded81d9db04c7a3dd5ba95fb3e1e060a293182f2842` 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	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 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: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` 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

Improved tumor-only variant calling and mutation burden estimation with VarNet-T · Original source · Nature Communications, published 2026-04-09; PMC13243554 full-text XML
VarNet-T Supplementary Information · Original source · Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages
VarNet-T Source Data workbook · Original source · Source Data file (41467_2026_71705_MOESM6_ESM.xlsx)

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-somatic-varnet-t-20261011-colo829-indel

field: links:assessed_by:somatic-varnet-t-20261011-protocol-colo829-indel
value: somatic-varnet-t-20261011-protocol-colo829-indel
relevance: proxy
endpoint: AUPRC of tumour-only callers (VarNet-T, five DeepSom models, DeepSomatic, Mutect2, ClairS-TO): COLO829 tumour-only, indels
rationale: Proxy, not direct: per-caller AUPRC on real tumour and cell-line WGS with tumour-normal-derived truth sets is close to the use case's endpoint, but the callers used tumour reads only, whereas this use case's inputs include a matched normal and its exclusions list tumour-only calling; precision, recall and F1 are not extracted. 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 VarNet-T (and earlier VarNet); its rows are author_reported. Comparators were run by the authors.; Tumour-only calling: the matched normal was used only to build the truth sets, not by the callers.; Only AUPRC is extracted; the threshold-optimised best F1 values are shown in figures only.; No interval estimates.; DeepSom's developers describe it as a caller of somatic SNVs (github.com/sergeyvilov/DeepSom repository description, checked 2026-10-11; not a pinned source); this source prints indel AUPRC for its models without explanation.; COLO829 truth is the TGen reference set and the reads are EGA EGAD00001002142; Chen et al. 2025 used the NYGC truth set and other COLO829 sequencing, so COLO829 values from the two papers are not comparable (ClairS-TO Illumina SSRS v0.4.0 SNV AUPRC 0.6500 there, 0.270 here).
citation locators: source id: somatic-varnet-t-20261011-source-krishnamachari2026-supplementary; locator: Supplementary Tables 1, 2 and 4; source id: somatic-varnet-t-20261011-source-krishnamachari2026-source-data; locator: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; source id: somatic-varnet-t-20261011-source-krishnamachari2026; locator: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests
source locator: somatic-varnet-t-20261011-source-krishnamachari2026-supplementary: Supplementary Tables 1, 2 and 4; somatic-varnet-t-20261011-source-krishnamachari2026-source-data: Sheets 'Supplementary Table 1', 'Supplementary Table 2', 'Supplementary Table 4'; somatic-varnet-t-20261011-source-krishnamachari2026: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG'; Methods 'Implementation of tumor-only variant callers', 'PCAWG benchmark samples'; Competing interests
headline metric: auprc
reason: Add a relevance judgement from the 2026-10-11 oncology use-case literature pass.
comparison group: krishnamachari2026-varnet-t
comparison title: Tumour-only callers on Illumina WGS (Krishnamachari et al. 2026, VarNet-T developers)
stratum label: COLO829 tumour-only, indels
stratum order: 4
reviewed evaluations: somatic-varnet-t-20261011-eval-clairs-to-colo829-indel; somatic-varnet-t-20261011-eval-deepsom-blca-colo829-indel; somatic-varnet-t-20261011-eval-deepsom-esad-colo829-indel; somatic-varnet-t-20261011-eval-deepsom-gaca-colo829-indel; somatic-varnet-t-20261011-eval-deepsom-laml-colo829-indel; somatic-varnet-t-20261011-eval-deepsom-linc-colo829-indel; somatic-varnet-t-20261011-eval-deepsomatic-tumor-only-colo829-indel; somatic-varnet-t-20261011-eval-mutect2-tumor-only-colo829-indel; somatic-varnet-t-20261011-eval-varnet-t-colo829-indel
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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subject: Select a tumour DNA somatic variant-calling workflow

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