COLO829 melanoma cell line tumour WGS used tumour-only; truth is the multi-institution TGen reference set (about 35,000 SNVs).
18 evaluations · 18 results. Different protocols are not a single leaderboard.
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24 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Accession EGA EGAD00001002142 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 EGA EGAD00001002142 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 EGA EGAD00001002142 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 COLO829 melanoma cell line 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 COLO829 melanoma cell line 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 COLO829 melanoma cell line 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: TGen multi-institution COLO829 reference set, about 35,000 SNVs (Results 'Benchmarking on somatic reference datasets', 'Challenges in tumor samples with low somatic mutation burden'). This is a different truth set and sequencing run from Chen et al. 2025 (NYGC truth, 42,993 SNVs before filtering). 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-colo829