Configuration

PhenIX default, singleton (Yuan et al. 2022)

PhenIX default, singleton (Yuan et al. 2022) as evaluated in the cited comparison.

Overview

PhenIX default, singleton (Yuan et al. 2022) as evaluated in the cited comparison.

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.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: PhenIX default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	15.7% 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 PhenIX default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-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 1 (DDD, PhenIX), column 'TOP 1(%)'
Configuration: PhenIX default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	41.6% 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 PhenIX default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-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 1 (DDD, PhenIX), column 'TOP 10(%)'
Configuration: PhenIX default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	54.8% 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 PhenIX default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-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 1 (DDD, PhenIX), column 'TOP 20(%)'
Configuration: PhenIX default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	61.3% 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 PhenIX default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-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 1 (DDD, PhenIX), column 'TOP 30(%)'
Configuration: PhenIX default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	69.5% 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 PhenIX default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-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 1 (DDD, PhenIX), column 'TOP 40(%)'
Configuration: PhenIX default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	33.8% 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 PhenIX default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-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 1 (DDD, PhenIX), column 'TOP 5(%)'
Configuration: PhenIX default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	74.1% 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 PhenIX default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-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 1 (DDD, PhenIX), column 'TOP 50(%)'
Configuration: PhenIX 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)	42.6% 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 PhenIX 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 12 (KMCGD, PhenIX), column 'TOP 1(%)'
Configuration: PhenIX 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)	73.2% 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 PhenIX 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 12 (KMCGD, PhenIX), column 'TOP 10(%)'
Configuration: PhenIX 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)	79.9% 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 PhenIX 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 12 (KMCGD, PhenIX), column 'TOP 20(%)'
Configuration: PhenIX 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 PhenIX 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 12 (KMCGD, PhenIX), column 'TOP 30(%)'
Configuration: PhenIX 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)	84.2% 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 PhenIX 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 12 (KMCGD, PhenIX), column 'TOP 40(%)'
Configuration: PhenIX 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)	64.6% 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 PhenIX 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 12 (KMCGD, PhenIX), column 'TOP 5(%)'
Configuration: PhenIX 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)	87.1% 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 PhenIX 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 12 (KMCGD, PhenIX), column 'TOP 50(%)'

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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-config-yuan2022-phenix

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: PhenIX default, singleton (Yuan et al. 2022)
foundation model eligible: false
version: 1.16
parameters: Default parameters; input HPO + VCF; singleton proband analysis
source locator: Table 2 row 'PhenIX'; SM Table 3 row 'PhenIX'

Related records

configuration of: PhenIX
system: PhenIX default singleton on DDD 305
system: PhenIX default singleton on KMCGD 209

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