SEQC2 HCC1395 tumour WGS used tumour-only; truth is the SEQC2 high-confidence call set (about 39,000 SNVs).
18 evaluations · 18 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.
Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified
Exact outcomes, predictions, identifiers and evaluator are connected.
Missing or unresolved evidence
Verified: Not verified
Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.
Missing or unresolved evidence
Verified: Not verified
A pinned recipe describes the inputs, environment and resource requirements.
Missing or unresolved evidence
Verified: Not verified
Separate data and exposure records support an independent test.
Missing or unresolved evidence
Verified: Not verified
Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.
No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
24 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Accession SRA SRX4728512 and related (Data availability) Context-only references | Improved tumor-only variant calling and mutation burden estimation with VarNet-T Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Accession SRA SRX4728512 and related (Data availability) Context-only references | VarNet-T Source Data workbook Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Accession SRA SRX4728512 and related (Data availability) Context-only references | VarNet-T Supplementary Information Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Assay Illumina WGS aligned with BWA-MEM (bcbio-nextgen) to GRCh38 Context-only references | Improved tumor-only variant calling and mutation burden estimation with VarNet-T Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Assay Illumina WGS aligned with BWA-MEM (bcbio-nextgen) to GRCh38 Context-only references | VarNet-T Source Data workbook Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Assay Illumina WGS aligned with BWA-MEM (bcbio-nextgen) to GRCh38 Context-only references | VarNet-T Supplementary Information Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Population SEQC2 HCC1395 tumour WGS Context-only references | Improved tumor-only variant calling and mutation burden estimation with VarNet-T Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Population SEQC2 HCC1395 tumour WGS Context-only references | VarNet-T Source Data workbook Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Population SEQC2 HCC1395 tumour WGS Context-only references | VarNet-T Supplementary Information Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Scope note Truth: SEQC2 consortium reference call set in its high-confidence regions, about 39,000 SNVs. Context-only references | Improved tumor-only variant calling and mutation burden estimation with VarNet-T Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: somatic-varnet-t-20261011-data-seqc2