Protocol

Causal-gene rank in 305 DDD 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.

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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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All evaluations

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

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)

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	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)
Exomiser 13.1.0, Protocol D (Yuan et al. 2024)Evaluation	61.6% (best in column)	91.1%	95.1% (best in column)	96.7% (best in column)	97.4% (best in column)	86.6% (best in column)	97.4% (best in column)
Exomiser 13.1.0, Protocol B (Yuan et al. 2024)Evaluation	53.1%	87.9%	91.8%	94.1%	94.8%	83.3%	95.7%
AMELIE 3.1.0, Protocol C (Yuan et al. 2024)Evaluation	50.5%	90.5%	91.8%	92.8%	92.8%	83.3%	93.1%
AMELIE 3.1.0, Protocol D (Yuan et al. 2024)Evaluation	50.5%	90.5%	91.8%	92.8%	92.8%	83%	93.1%
PhenIX 1.16, Protocol D (Yuan et al. 2024)Evaluation	49.5%	91.8% (best in column)	94.8%	96.1%	96.4%	80%	97.4% (best in column)
Exomiser 13.1.0, Protocol C (Yuan et al. 2024)Evaluation	48.5%	91.8% (best in column)	93.8%	95.7%	96.4%	85.6%	97.4% (best in column)
AMELIE 3.1.0, Protocol A (Yuan et al. 2024)Evaluation	46.6%	86.2%	91.1%	92.8%	93.1%	81.3%	93.1%
AMELIE 3.1.0, Protocol B (Yuan et al. 2024)Evaluation	46.6%	85.9%	91.5%	92.8%	93.4%	81.3%	93.4%
LIRICAL 1.3.4 (Yuan et al. 2024)Evaluation	46.6%	83.3%	91.8%	93.8%	95.7%	75.4%	95.7%
PhenIX 1.16, Protocol C (Yuan et al. 2024)Evaluation	46.2%	89.8%	94.8%	96.1%	96.4%	77.7%	96.7%
PhenIX 1.16, Protocol B (Yuan et al. 2024)Evaluation	37%	79%	88.9%	93.8%	94.8%	67.9%	96.1%
Exomiser 13.1.0, Protocol A (Yuan et al. 2024)Evaluation	31.8%	85.2%	92.8%	94.4%	95.4%	73.1%	96.1%
PhenIX 1.16, Protocol A (Yuan et al. 2024)Evaluation	31.1%	75.1%	87.2%	92.5%	94.8%	60%	94.8%

All 91 result rows with coverage, uncertainty and sources

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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 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	46.6% 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 AMELIE Protocol A 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, AMELIE, PROT A), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	86.2% 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 AMELIE Protocol A 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, AMELIE, PROT A), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	91.1% 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 AMELIE Protocol A 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, AMELIE, PROT A), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	92.8% 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 AMELIE Protocol A 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, AMELIE, PROT A), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	93.1% 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 AMELIE Protocol A 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, AMELIE, PROT A), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	81.3% 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 AMELIE Protocol A 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, AMELIE, PROT A), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, Protocol A (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)	93.1% 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 AMELIE Protocol A 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, AMELIE, PROT A), column 'Top50 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	46.6% 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 AMELIE Protocol B 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, AMELIE, PROT B), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	85.9% 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 AMELIE Protocol B 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, AMELIE, PROT B), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	91.5% 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 AMELIE Protocol B 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, AMELIE, PROT B), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	92.8% 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 AMELIE Protocol B 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, AMELIE, PROT B), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	93.4% 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 AMELIE Protocol B 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, AMELIE, PROT B), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	81.3% 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 AMELIE Protocol B 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, AMELIE, PROT B), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, Protocol B (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)	93.4% 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 AMELIE Protocol B 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, AMELIE, PROT B), column 'Top50 (%)'
Configuration: AMELIE 3.1.0, 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)	50.5% 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 AMELIE 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, AMELIE, PROT C), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, 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)	90.5% 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 AMELIE 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, AMELIE, PROT C), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, 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)	91.8% 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 AMELIE 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, AMELIE, PROT C), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, 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)	92.8% 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 AMELIE 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, AMELIE, PROT C), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, 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)	92.8% 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 AMELIE 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, AMELIE, PROT C), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, 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)	83.3% 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 AMELIE 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, AMELIE, PROT C), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, 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)	93.1% 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 AMELIE 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, AMELIE, PROT C), column 'Top50 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	50.5% 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 AMELIE Protocol D 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, AMELIE, PROT D), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	90.5% 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 AMELIE Protocol D 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, AMELIE, PROT D), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	91.8% 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 AMELIE Protocol D 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, AMELIE, PROT D), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol D (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)	92.8% 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 AMELIE Protocol D 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, 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-ddd-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 'DDD'
source locator: Table 1 rows 'DDD'; 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: DDD 305 solved probands (Yuan et al. selection)
subject: reported_finding: rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols
assessment: AMELIE Protocol A on DDD
assessment: AMELIE Protocol B on DDD
assessment: AMELIE Protocol C on DDD
assessment: AMELIE Protocol D on DDD
assessment: Exomiser Protocol A on DDD
assessment: Exomiser Protocol B on DDD
assessment: Exomiser Protocol C on DDD
assessment: Exomiser Protocol D on DDD
assessment: LIRICAL on DDD
assessment: PhenIX Protocol A on DDD
assessment: PhenIX Protocol B on DDD
assessment: PhenIX Protocol C on DDD
assessment: PhenIX Protocol D on DDD
assessed by: Rank rare-disease variants for review

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