Protocol

Talos diagnosis recovery and workload: RGP full

Recovery of previously known diagnoses detectable by standardized GATK/GATK-SV/GATK-gCNV calling; default versus strict filtering. Singleton mode removes parental data; full mode uses available family structure. Unresolved families remain in workload denominators.

2 evaluations · 10 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

2 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

2 evaluations · 10 results. Different protocols are not a single leaderboard.

Protocol: Talos diagnosis recovery and workload: RGP full · Dataset: Talos RGP full evaluation cohort

Sorted by Recall (higher 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	Recall	Candidates per case	Candidates per diagnosis	Count (candidate variants flagged)	True positives (known diagnoses)
Talos default filtering, 2026 studyEvaluation	86% (best in column)	1.6	13.7	1,095	80
Talos strict phenotype-match filtering, 2026 studyEvaluation	83%	0.8	7.6	582	77

All 10 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Talos default filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	1,095 Count (candidate variants flagged) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos default: RGP full Not reported Aggregation: total Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, default, Candidate variants
Configuration: Talos default filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	1.6 Candidates per case variants-per-proband · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos default: RGP full Not reported Aggregation: table ratio Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, default, Candidates per proband
Configuration: Talos default filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	13.7 Candidates per diagnosis variants-per-diagnosis · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos default: RGP full Not reported Aggregation: table ratio Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, default, Candidates per diagnoses
Configuration: Talos default filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	80 True positives (known diagnoses) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos default: RGP full Not reported Aggregation: Not reported Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, default, Diagnoses
Configuration: Talos default filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	86% Recall percent · higher Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos default: RGP full Not reported Aggregation: Not reported Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, default, Diagnoses (%)
Configuration: Talos strict phenotype-match filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	582 Count (candidate variants flagged) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos strict: RGP full Not reported Aggregation: total Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, strict, Candidate variants
Configuration: Talos strict phenotype-match filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	0.8 Candidates per case variants-per-proband · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos strict: RGP full Not reported Aggregation: table ratio Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, strict, Candidates per proband
Configuration: Talos strict phenotype-match filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	7.6 Candidates per diagnosis variants-per-diagnosis · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos strict: RGP full Not reported Aggregation: table ratio Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, strict, Candidates per diagnoses
Configuration: Talos strict phenotype-match filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	77 True positives (known diagnoses) count · unknown Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos strict: RGP full Not reported Aggregation: Not reported Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, strict, Diagnoses
Configuration: Talos strict phenotype-match filtering, 2026 study	Protocol: Talos diagnosis recovery and workload: RGP full Dataset: Talos RGP full evaluation cohort	83% Recall percent · higher Uncertainty: Not reported by the source: not reported for this endpoint Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Talos strict: RGP full Not reported Aggregation: Not reported Talos Table 1: complete evaluation cohort outcomes · Table 1, RGP full, strict, Diagnoses (%)

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

Talos 2026 evaluation and reanalysis study

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 2

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-specific valid geometric or structural control

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Upstream conventional structural reference with matched templates and cutoffs

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-11-02-a7f03c9e55a5. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Applicable tests and references

Applicability is distinct from a completed evaluation.

Talos default filtering as comparator for phenotype restriction · source_supported

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Relationship: part of uc-clinical-20260930-benchmark-talos-study Individual claims	Automated reanalysis of genomic data for rare disease diagnostics at scale Original source ↗ Table1; Results comparison with other tools and iterative reanalysis Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Medicine 2026 final publication, 24 June 2026 Retrieved: 2026-09-30T21:24:16Z	source checked ["automated-source-review"] · 2026-09-30 Audit details Transcription from inspected primary source. No execution, independent replication or human scientific review. Field: `links:part_of:uc-clinical-20260930-benchmark-talos-study` Claim: uc-clinical-20260930-membership-talos-rgp-full-protocol Source artifact SHA-256: `629b9578ac42717245256feca69dc9c9d5442deb7d282dd1bdc5a6c1a1efd2ec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: part of uc-clinical-20260930-benchmark-talos-study Individual claims	Talos Table 1: complete evaluation cohort outcomes Original source ↗ Table1; Results comparison with other tools and iterative reanalysis Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Table 1 in final 2026 article Retrieved: 2026-09-30T21:25:04Z	source checked ["automated-source-review"] · 2026-09-30 Audit details Transcription from inspected primary source. No execution, independent replication or human scientific review. Field: `links:part_of:uc-clinical-20260930-benchmark-talos-study` Claim: uc-clinical-20260930-membership-talos-rgp-full-protocol Source artifact SHA-256: `cb86e1a542f458271efdf67464b12faf246ee2f78419e565afe8b87158e77e5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release history

Talos Table 1: complete evaluation cohort outcomes · Original source · Table 1 in final 2026 article

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Technical metadata and extraction receipts

Stable ID: uc-clinical-20260930-talos-rgp-full-protocol

areas: dna-genomes
contexts: clinical_research
protocol: Recovery of previously known diagnoses detectable by standardized GATK/GATK-SV/GATK-gCNV calling; default versus strict filtering. Singleton mode removes parental data; full mode uses available family structure. Unresolved families remain in workload denominators.
review: method: automated-source-review; reviewer: codex; date: 2026-09-30; note: Transcription from inspected primary source. No execution, independent replication or human scientific review.; source id: uc-clinical-20260930-source-talos-table1; reviewer note: role: clinical coverage worker
source locator: Table 1, RGP full
limitations: Not end-to-end diagnostic sensitivity: only callable known diagnoses form recovery denominator.; Not a prospective diagnostic yield comparison.; Candidates per proband is a table ratio; narrative calls fractional values medians and abstract uses average. No median reinterpretation.; Exact software and annotation snapshots remain unextracted.

Related records

part of: Talos 2026 evaluation and reanalysis study
applicable to: Talos default filtering as comparator for phenotype restriction
subject: Published study membership: Talos diagnosis recovery and workload: RGP full
assessment: Talos default: RGP full
assessment: Talos strict: RGP full
assessed by: Rank rare-disease variants for review
assessed by: Reanalyse unresolved rare-disease cases

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