Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026)
Proportion of initially reported variants that Talos prioritised in trio mode and proband-only mode, with failure modes.
Overview
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2 recorded evaluations, 8 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
2 evaluations · 8 results. Different protocols are not a single leaderboard.
Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) · Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026)
Sorted by Proportion (known P/LP variants missed: HPO annotation gaps) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Proportion (known P/LP variants missed: HPO annotation gaps) | Proportion (known P/LP variants missed: large copy-number variants not processed) | Proportion (known P/LP variants missed: out-of-scope variant classes) | Proportion (known P/LP variants missed: pipeline conversion errors) | Proportion (known P/LP variants not prioritised because of trio inheritance filtering) | Recall (known P/LP variants prioritised, proband-only mode) | Recall (known P/LP variants prioritised, trio mode) | Count (known VUS prioritised, trio mode) |
|---|---|---|---|---|---|---|---|---|
| Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026)Evaluation | 6.2% | 2.1% | 2.8% | 6.2% | 7.6% | Not reported | 75.2% | Six |
| Talos 8.2.0, proband-only mode on trio cases (Kaschta et al. 2026)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 82.8% | Not reported | Not reported |
All 8 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | 6.2% Proportion (known P/LP variants missed: pipeline conversion errors) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in trio mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P1, 'nine pipeline conversion errors (6.2%)' |
| Configuration: Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | 6.2% Proportion (known P/LP variants missed: HPO annotation gaps) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in trio mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P1, 'nine HPO annotation gaps (6.2%)' |
| Configuration: Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | 7.6% Proportion (known P/LP variants not prioritised because of trio inheritance filtering) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in trio mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P2, 'An additional 11 P/LP variants (7.6%) were not prioritized' |
| Configuration: Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | 2.1% Proportion (known P/LP variants missed: large copy-number variants not processed) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in trio mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P1, 'three large copy-number variants not processed by the pipeline (2.1%)' |
| Configuration: Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | 2.8% Proportion (known P/LP variants missed: out-of-scope variant classes) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in trio mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P1, 'four out-of-scope variant classes (2.8%)' |
| Configuration: Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | 75.2% Recall (known P/LP variants prioritised, trio mode) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in trio mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P1, 'overall P/LP concordance of 75.2%' |
| Configuration: Talos 8.2.0, proband-only mode on trio cases (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | 82.8% Recall (known P/LP variants prioritised, proband-only mode) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in proband-only mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P3, 'increasing concordance to 82.8%' |
| Configuration: Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026) | Protocol: Talos recovery of known P/LP and VUS variants in 162 trio cases (Kaschta et al. 2026) Dataset: UKSH trio benchmarking cases with known findings (Kaschta et al. 2026) | Six Count (known VUS prioritised, trio mode) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos in trio mode on 162 trio benchmarking cases reanalysis-kaschta-20261010-protocol-talos-trio-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Trio Cases P1, 'Six VUS variants were captured' |
Source checking is not independent reproduction. Release 2026-10-10-cbb3da59bc08.
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Baseline coverage
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-10-cbb3da59bc08 · Record review: source checked
1 source record and release history
- Automated versus manual reanalysis in rare disease genomics · Original source · medRxiv 2026.05.16.26352295 v1, posted 2026-05-19; JATS source XML
Technical metadata and extraction receipts
Stable ID: reanalysis-kaschta-20261010-protocol-talos-trio-benchmark
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- As for singletons; trio cases run with parental genotypes, and again in proband-only mode.
- version
- medRxiv v1
- source locator
- Methods 'Benchmarking of Automated Reanalysis'; Results 'Benchmarking of Automated Reanalysis: Trio Cases' P1-P3
- limitations
- Positive controls are known findings from the initial analysis; recovering them does not establish new diagnostic yield.; Concordance is per variant against the initial report, not per case. Methods 'Benchmarking of Automated Reanalysis' P1 defines the detection rate per case; the Results report concordance per variant (for example 28 of 35 P/LP variants), which is what is stored.; Strict inheritance filtering in trio mode excluded 11 P/LP variants that proband-only mode recovered.