Talos recovery of known P/LP and VUS variants in 45 singleton cases (Kaschta et al. 2026)
Proportion of initially reported variants that Talos prioritised, with failure modes for missed P/LP variants.
Overview
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1 recorded evaluation, 4 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
1 evaluation · 4 results. Different protocols are not a single leaderboard.
Protocol: Talos recovery of known P/LP and VUS variants in 45 singleton cases (Kaschta et al. 2026) · Dataset: UKSH singleton benchmarking cases with known findings (Kaschta et al. 2026)
Sorted by Proportion (known P/LP variants missed because of 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 because of HPO annotation gaps) | Proportion (known P/LP variants missed because of pipeline conversion errors) | Recall (known P/LP variants prioritised) | Count (known VUS prioritised) |
|---|---|---|---|---|
| Talos 8.2.0 on archived DRAGEN v3.7.5 VCFs, pedigree where available (Kaschta et al. 2026)Evaluation | 11.4% | 8.6% | 80% | two |
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| 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 45 singleton cases (Kaschta et al. 2026) Dataset: UKSH singleton benchmarking cases with known findings (Kaschta et al. 2026) | 8.6% Proportion (known P/LP variants missed because of 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 on 45 singleton benchmarking cases reanalysis-kaschta-20261010-protocol-talos-singleton-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Singleton Cases P3, 'pipeline conversion errors (8.6%)' |
| 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 45 singleton cases (Kaschta et al. 2026) Dataset: UKSH singleton benchmarking cases with known findings (Kaschta et al. 2026) | 11.4% Proportion (known P/LP variants missed because of 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 on 45 singleton benchmarking cases reanalysis-kaschta-20261010-protocol-talos-singleton-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Singleton Cases P3, 'HPO annotation gaps (11.4%)' |
| 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 45 singleton cases (Kaschta et al. 2026) Dataset: UKSH singleton benchmarking cases with known findings (Kaschta et al. 2026) | 80% Recall (known P/LP variants prioritised) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos on 45 singleton benchmarking cases reanalysis-kaschta-20261010-protocol-talos-singleton-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Singleton Cases P2, 'Talos prioritized 28 out of 35 P/LP variants (80.0% concordance)' |
| 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 45 singleton cases (Kaschta et al. 2026) Dataset: UKSH singleton benchmarking cases with known findings (Kaschta et al. 2026) | two Count (known VUS prioritised) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTalos on 45 singleton benchmarking cases reanalysis-kaschta-20261010-protocol-talos-singleton-benchmark Aggregation: Not reported Automated versus manual reanalysis in rare disease genomics · Results, Benchmarking of Automated Reanalysis: Singleton Cases P2, 'only two out of 21 VUS were captured' |
Source checking is not independent reproduction. Release 2026-10-10-cbb3da59bc08.
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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-singleton-benchmark
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- Track each reported variant in the benchmarking set; concordance is the share of known P/LP variants prioritised by Talos; misses grouped into error categories.
- version
- medRxiv v1
- source locator
- Methods 'Benchmarking of Automated Reanalysis'; Results 'Benchmarking of Automated Reanalysis: Singleton 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.; The pipeline conversion share for singletons is 8.6% in the text but 9.6% in the Figure 2 legend; the text value is stored (3 of 35 is 8.6%).