Dataset

25 Coriell cell lines with documented CNVs, 184-gene virtual panel

Cell-line truth set for the De La Vega et al. virtual-panel evaluation.

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Release 2026-10-09-8eac2440869c · Evidence verified: Not verified

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Evaluation results

2 evaluations · 12 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	8% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	10% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	1% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	100% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	30% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	2% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	100% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS-F (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	81% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS-F (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	68% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS-F (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	100% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS-F (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	89% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS-F (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	74% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS-F (%)' (CNV length block)

Source checking is not independent reproduction. Release 2026-10-09-8eac2440869c.

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6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-8eac2440869c
Property and statement	Original source and location	Review and provenance
attributes.population PCR-free 50x WGS of 25 Coriell cell lines; evaluation limited to coding exons of 184 genes; putative false positives inspected and some added to the truth set; paralogous genes requiring specialised callers excluded. Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Methods 2.1, 2.4 paragraph 4; Results 3.2 Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.population` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Methods 2.1, 2.4 paragraph 4; Results 3.2 Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Methods 2.1, 2.4 paragraph 4; Results 3.2 Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split 25 cell lines Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Methods 2.1, 2.4 paragraph 4; Results 3.2 Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.split` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.version Coriell catalogue annotations curated by the authors (Supplementary Table S1); 184-gene panel (Supplementary Table S2) Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Methods 2.1, 2.4 paragraph 4; Results 3.2 Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.version` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
description Cell-line truth set for the De La Vega et al. virtual-panel evaluation. Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Methods 2.1, 2.4 paragraph 4; Results 3.2 Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
name 25 Coriell cell lines with documented CNVs, 184-gene virtual panel Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Methods 2.1, 2.4 paragraph 4; Results 3.2 Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `name` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-09-8eac2440869c · Record review: source checked

1 source records and release history

Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Original source · Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML

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Technical metadata and extraction receipts

Stable ID: cnv-20261009-data-delavega2025-coriell-virtual-panel

areas: dna-genomes
contexts: clinical_research
version: Coriell catalogue annotations curated by the authors (Supplementary Table S1); 184-gene panel (Supplementary Table S2)
split: 25 cell lines
population: PCR-free 50x WGS of 25 Coriell cell lines; evaluation limited to coding exons of 184 genes; putative false positives inspected and some added to the truth set; paralogous genes requiring specialised callers excluded.
source locator: Methods 2.1, 2.4 paragraph 4; Results 3.2
missing metadata: denominator: reason: unreported; note: Per-stratum truth counts unreported in Table 1

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