Protocol

Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1)

Proportion of solved cases whose causal gene each tool and parameter protocol ranks within the top k.

Overview

Proportion of solved cases whose causal gene each tool and parameter protocol ranks within the top k.

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13 recorded evaluations, 91 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

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13 evaluations · 91 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AMELIE 3.1.0, Protocol A (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)	50.7% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol A 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, AMELIE, PROT A), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	86.8% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol A 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, AMELIE, PROT A), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	88.2% top-20-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol A 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, AMELIE, PROT A), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	89.5% top-30-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol A 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, AMELIE, PROT A), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	89.5% top-40-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol A 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, AMELIE, PROT A), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	79.6% top-5-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol A 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, AMELIE, PROT A), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	89.5% top-50-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol A 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, AMELIE, PROT A), column 'Top50 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	52% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol B 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, AMELIE, PROT B), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	87.5% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol B 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, AMELIE, PROT B), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	88.8% top-20-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol B 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, AMELIE, PROT B), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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-30-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol B 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, AMELIE, PROT B), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	90.8% top-40-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol B 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, AMELIE, PROT B), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	80.3% top-5-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol B 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, AMELIE, PROT B), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	90.8% top-50-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol B 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, AMELIE, PROT B), column 'Top50 (%)'
Configuration: AMELIE 3.1.0, 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)	54.6% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE 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, AMELIE, PROT C), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, 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)	86.8% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE 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, AMELIE, PROT C), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, 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)	87.5% top-20-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE 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, AMELIE, PROT C), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, 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)	88.2% top-30-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE 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, AMELIE, PROT C), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, 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)	88.2% top-40-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE 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, AMELIE, PROT C), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, 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)	81.6% top-5-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE 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, AMELIE, PROT C), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, 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)	88.2% top-50-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE 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, AMELIE, PROT C), column 'Top50 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	55.9% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol D 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, AMELIE, PROT D), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	86.8% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol D 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, AMELIE, PROT D), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	87.5% top-20-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol D 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, AMELIE, PROT D), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	88.2% top-30-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AMELIE Protocol D 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, AMELIE, PROT D), column 'Top30 (%)'

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

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Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols

areas: dna-genomes
contexts: clinical_research
protocol: Run Exomiser and PhenIX under Protocols A-D (pathogenicity source and trio mode), AMELIE under Protocols A-D (allele-frequency cutoff and filterByCount) and LIRICAL once; record the rank of the causal gene; report the percentage of cases in the top 1 and within top 5, 10, 20, 30, 40 and 50.
version: Table 1 rows 'KGD'
source locator: Table 1 rows 'KGD'; Methods 'Visualization and statistical analysis'
limitations: Ranking of the known causal gene in solved cases; does not establish pathogenicity or a diagnosis.; Each case has a single causal gene; cases with no or several causal genes are not represented.; Only Exomiser and PhenIX Protocols C and D are trio mode. Every other row, including all AMELIE and LIRICAL rows, is singleton (Discussion paragraph 1, item 4). The authors' comparison of optimised settings sets trio-mode Exomiser and PhenIX (Protocol D) against singleton AMELIE (Protocol B) and LIRICAL; compare within mode only.; The authors chose Protocol D for Exomiser and PhenIX and Protocol B for AMELIE on these same cohorts, so those six rows (two cohorts) overstate expected performance on new cases. The values of all rows are as printed.; Same authors as Yuan et al. 2022; none developed the tools compared.; What distinguishes Exomiser and PhenIX Protocol C from Protocol D is shown only in the Figure 2 option table (image, not read); the text says only that both are trio mode. The pathogenicity source for C and D is not stated in the text.

Related records

uses data: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)
assessment: AMELIE Protocol A on KGD
assessment: AMELIE Protocol B on KGD
assessment: AMELIE Protocol C on KGD
assessment: AMELIE Protocol D on KGD
assessment: Exomiser Protocol A on KGD
assessment: Exomiser Protocol B on KGD
assessment: Exomiser Protocol C on KGD
assessment: Exomiser Protocol D on KGD
assessment: LIRICAL on KGD
assessment: PhenIX Protocol A on KGD
assessment: PhenIX Protocol B on KGD
assessment: PhenIX Protocol C on KGD
assessment: PhenIX Protocol D on KGD
assessed by: Rank rare-disease variants for review

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