Protocol

Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3)

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

Overview

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

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

11 recorded evaluations, 77 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

11 evaluations · 77 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-HPO default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	2.4% 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-HPO default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 22 (KMCGD, AMELIE-HPO), column 'TOP 1(%)'
Configuration: AMELIE-HPO default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	16.3% 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-HPO default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 22 (KMCGD, AMELIE-HPO), column 'TOP 10(%)'
Configuration: AMELIE-HPO default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	23% 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-HPO default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 22 (KMCGD, AMELIE-HPO), column 'TOP 20(%)'
Configuration: AMELIE-HPO default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	25.4% 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-HPO default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 22 (KMCGD, AMELIE-HPO), column 'TOP 30(%)'
Configuration: AMELIE-HPO default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	29.2% 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-HPO default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 22 (KMCGD, AMELIE-HPO), column 'TOP 40(%)'
Configuration: AMELIE-HPO default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	9.6% 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-HPO default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 22 (KMCGD, AMELIE-HPO), column 'TOP 5(%)'
Configuration: AMELIE-HPO default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	30.6% 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-HPO default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 22 (KMCGD, AMELIE-HPO), column 'TOP 50(%)'
Configuration: AMELIE default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	57.9% 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 default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 16 (KMCGD, AMELIE), column 'TOP 1(%)'
Configuration: AMELIE default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	78.9% 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 default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 16 (KMCGD, AMELIE), column 'TOP 10(%)'
Configuration: AMELIE default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	81.3% 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 default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 16 (KMCGD, AMELIE), column 'TOP 20(%)'
Configuration: AMELIE default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	81.8% 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 default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 16 (KMCGD, AMELIE), column 'TOP 30(%)'
Configuration: AMELIE default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	81.8% 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 default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 16 (KMCGD, AMELIE), column 'TOP 40(%)'
Configuration: AMELIE default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	73.7% 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 default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 16 (KMCGD, AMELIE), column 'TOP 5(%)'
Configuration: AMELIE default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	82.8% 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 default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 16 (KMCGD, AMELIE), column 'TOP 50(%)'
Configuration: DeepPVP default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	6.2% 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 DeepPVP default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 14 (KMCGD, DeepPVP), column 'TOP 1(%)'
Configuration: DeepPVP default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	12.9% 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 DeepPVP default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 14 (KMCGD, DeepPVP), column 'TOP 10(%)'
Configuration: DeepPVP default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	15.3% 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 DeepPVP default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 14 (KMCGD, DeepPVP), column 'TOP 20(%)'
Configuration: DeepPVP default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	18.2% 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 DeepPVP default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 14 (KMCGD, DeepPVP), column 'TOP 30(%)'
Configuration: DeepPVP default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	18.2% 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 DeepPVP default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 14 (KMCGD, DeepPVP), column 'TOP 40(%)'
Configuration: DeepPVP default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	10.5% 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 DeepPVP default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 14 (KMCGD, DeepPVP), column 'TOP 5(%)'
Configuration: DeepPVP default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	18.7% 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 DeepPVP default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 14 (KMCGD, DeepPVP), column 'TOP 50(%)'
Configuration: Exomiser default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	26.3% 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 Exomiser default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 13 (KMCGD, Exomiser), column 'TOP 1(%)'
Configuration: Exomiser default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	75.1% 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 Exomiser default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 13 (KMCGD, Exomiser), column 'TOP 10(%)'
Configuration: Exomiser default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	78.9% 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 Exomiser default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 13 (KMCGD, Exomiser), column 'TOP 20(%)'
Configuration: Exomiser default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	82.8% 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 Exomiser default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 13 (KMCGD, Exomiser), column 'TOP 30(%)'

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Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases · Original source · Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML
Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · Original source · sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623

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Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default

areas: dna-genomes
contexts: clinical_research
protocol: As for the DDD protocol, on the KMCGD in-house cohort.
version: SM Table 3 rows 'KMCGD'
source locator: SM Table 3; Materials 'Performance evaluation'
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.; Default parameters and singleton mode for every tool.; In-house cohort from the authors' laboratory; not public.

Related records

uses data: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)
assessment: AMELIE default singleton on KMCGD 209
assessment: AMELIE-HPO default singleton on KMCGD 209
assessment: DeepPVP default singleton on KMCGD 209
assessment: Exomiser default singleton on KMCGD 209
assessment: GADO default singleton on KMCGD 209
assessment: HANRD default singleton on KMCGD 209
assessment: LIRICAL default singleton on KMCGD 209
assessment: Phen2Gene default singleton on KMCGD 209
assessment: PhenIX default singleton on KMCGD 209
assessment: Phenolyzer default singleton on KMCGD 209
assessment: Xrare default singleton on KMCGD 209
assessed by: Rank rare-disease variants for review

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