Configuration

HANRD default, singleton (Yuan et al. 2022)

HANRD default, singleton: Default parameters; input HPO only; singleton proband analysis.

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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)
HANRD default, singleton (Yuan et al. 2022)Evaluation	Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3), KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	3.3% (best in column)	13.9% (best in column)	19.6% (best in column)	20.6% (best in column)	21.1% (best in column)	7.7% (best in column)	22.5% (best in column)
HANRD default, singleton (Yuan et al. 2022)Evaluation	Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3), DDD 305 solved probands (Yuan et al. selection)	1.3%	6.9%	7.9%	10.5%	13.1%	4.3%	14.1%

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: HANRD 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)	1.3% 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 HANRD 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 8 (DDD, HANRD), column 'TOP 1(%)'
Configuration: HANRD 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)	6.9% 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 HANRD 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 8 (DDD, HANRD), column 'TOP 10(%)'
Configuration: HANRD 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)	7.9% 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 HANRD 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 8 (DDD, HANRD), column 'TOP 20(%)'
Configuration: HANRD 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)	10.5% 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 HANRD 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 8 (DDD, HANRD), column 'TOP 30(%)'
Configuration: HANRD 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)	13.1% 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 HANRD 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 8 (DDD, HANRD), column 'TOP 40(%)'
Configuration: HANRD 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)	4.3% 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 HANRD 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 8 (DDD, HANRD), column 'TOP 5(%)'
Configuration: HANRD 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)	14.1% 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 HANRD 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 8 (DDD, HANRD), column 'TOP 50(%)'
Configuration: HANRD 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)	3.3% 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 HANRD 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 19 (KMCGD, HANRD), column 'TOP 1(%)'
Configuration: HANRD 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)	13.9% 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 HANRD 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 19 (KMCGD, HANRD), column 'TOP 10(%)'
Configuration: HANRD 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)	19.6% 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 HANRD 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 19 (KMCGD, HANRD), column 'TOP 20(%)'
Configuration: HANRD 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)	20.6% 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 HANRD 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 19 (KMCGD, HANRD), column 'TOP 30(%)'
Configuration: HANRD 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)	21.1% 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 HANRD 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 19 (KMCGD, HANRD), column 'TOP 40(%)'
Configuration: HANRD 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)	7.7% 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 HANRD 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 19 (KMCGD, HANRD), column 'TOP 5(%)'
Configuration: HANRD 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)	22.5% 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 HANRD 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 19 (KMCGD, HANRD), column 'TOP 50(%)'

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

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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-hanrd

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: HANRD default, singleton (Yuan et al. 2022)
foundation model eligible: false
missing metadata: version: reason: unreported; note: Table 2 prints a dash for the HANRD version
parameters: Default parameters; input HPO only; singleton proband analysis
source locator: Table 2 row 'HANRD'; SM Table 3 row 'HANRD'
provenance note: HANRD default, singleton (Yuan et al. 2022) as evaluated in the cited comparison.

Related records

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

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