Configuration

PhenIX 1.16, Protocol C (Yuan et al. 2024)

PhenIX 1.16, Protocol C: Trio mode.

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.

Evaluations and results

2 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) (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	Protocol and dataset	Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)
PhenIX 1.16, Protocol C (Yuan et al. 2024)Evaluation	Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1), KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	65.8% (best in column)	90.1% (best in column)	92.1%	92.1%	92.1%	86.2% (best in column)	92.1%
PhenIX 1.16, Protocol C (Yuan et al. 2024)Evaluation	Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1), DDD 305 solved probands (Yuan et al. selection)	46.2%	89.8%	94.8% (best in column)	96.1% (best in column)	96.4% (best in column)	77.7%	96.7% (best in column)

All 14 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: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	46.2% Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, PhenIX, PROT C), column 'Top1 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	89.8% Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, PhenIX, PROT C), column 'Top10 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	94.8% Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, PhenIX, PROT C), column 'Top20 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	96.1% Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, PhenIX, PROT C), column 'Top30 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	96.4% Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, PhenIX, PROT C), column 'Top40 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	77.7% Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, PhenIX, PROT C), column 'Top5 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	96.7% Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, PhenIX, PROT C), column 'Top50 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	65.8% Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT C), column 'Top1 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	90.1% Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT C), column 'Top10 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	92.1% Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT C), column 'Top20 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	92.1% Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT C), column 'Top30 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	92.1% Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT C), column 'Top40 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	86.2% Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT C), column 'Top5 (%)'
Configuration: PhenIX 1.16, Protocol C (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	92.1% Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhenIX Protocol C on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT C), column 'Top50 (%)'

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

Use this configuration

How it works, versions and access

Additional methodological details, versions and access terms have not yet been extracted into a structured profile for this configuration. Consult the linked sources and evaluation records below.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

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

0 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

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

1 source record and release history

Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Original source · Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-config-yuan2024-phenix-protocol-c

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: PhenIX 1.16, Protocol C (Yuan et al. 2024)
foundation model eligible: false
version: 1.16
parameters: Trio mode
source locator: Table 1 rows 'PhenIX', PROT 'C'; Results 'Performance improvement assessment'
limitations: Protocol option tables are in Figure 2 (image, not read); descriptions are from the Results text, and the exact pathogenicity source in Protocols C and D is not stated in the text.
provenance note: PhenIX 1.16, Protocol C (Yuan et al. 2024) as evaluated in the cited comparison.

Related records

configuration of: PhenIX
system: PhenIX Protocol C on DDD
system: PhenIX Protocol C on KGD

Suggest a correction