Dataset

DDD 305 solved probands (Yuan et al. selection)

305 Deciphering Developmental Disorders probands with one 'definitely pathogenic' causal SNV or indel, HPO terms and exome VCF; parents' VCFs and disease status added in Yuan et al. 2024.

Research readiness

These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

Release 2026-10-10-6e93f504adfc · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
metric replay: verification is missing

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
metric replay: verification is missing
annotations: verification is missing
dependence: verification is missing

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
recipe pinned: verification is missing
resource estimate: verification is missing

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
independent validation: verification is missing
overlap checked: verification is missing

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Read reviewed discrepancy investigations

Evaluation results

24 evaluations · 168 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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 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-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 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 11 (DDD, AMELIE-HPO), column 'TOP 1(%)'
Configuration: AMELIE-HPO 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)	14.4% 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 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 11 (DDD, AMELIE-HPO), column 'TOP 10(%)'
Configuration: AMELIE-HPO 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)	23.9% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 20(%)'
Configuration: AMELIE-HPO 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)	29.8% 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-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 30(%)'
Configuration: AMELIE-HPO 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)	34.4% 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 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 11 (DDD, AMELIE-HPO), column 'TOP 40(%)'
Configuration: AMELIE-HPO 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)	10.8% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 5(%)'
Configuration: AMELIE-HPO 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)	37.7% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 50(%)'
Configuration: AMELIE 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)	47.9% 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 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 5 (DDD, AMELIE), column 'TOP 1(%)'
Configuration: AMELIE 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)	86.2% 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 AMELIE 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 5 (DDD, AMELIE), column 'TOP 10(%)'
Configuration: AMELIE 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)	90.5% 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 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 5 (DDD, AMELIE), column 'TOP 20(%)'
Configuration: AMELIE 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)	92.8% 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 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 5 (DDD, AMELIE), column 'TOP 30(%)'
Configuration: AMELIE 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)	93.1% 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 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 5 (DDD, AMELIE), column 'TOP 40(%)'
Configuration: AMELIE 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)	81.3% 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 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 5 (DDD, AMELIE), column 'TOP 5(%)'
Configuration: AMELIE 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)	93.1% 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 AMELIE 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 5 (DDD, AMELIE), column 'TOP 50(%)'
Configuration: DeepPVP 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)	1.6% 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 DeepPVP 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 3 (DDD, DeepPVP), column 'TOP 1(%)'
Configuration: DeepPVP 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)	5.6% 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 DeepPVP 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 3 (DDD, DeepPVP), column 'TOP 10(%)'
Configuration: DeepPVP 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)	7.2% 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 DeepPVP 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 3 (DDD, DeepPVP), column 'TOP 20(%)'
Configuration: DeepPVP 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)	8.2% 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 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 3 (DDD, DeepPVP), column 'TOP 30(%)'
Configuration: DeepPVP 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)	8.9% 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 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 3 (DDD, DeepPVP), column 'TOP 40(%)'
Configuration: DeepPVP 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)	3.9% 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 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 3 (DDD, DeepPVP), column 'TOP 5(%)'
Configuration: DeepPVP 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)	8.9% 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 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 3 (DDD, DeepPVP), column 'TOP 50(%)'
Configuration: Exomiser 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)	15.1% 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 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 2 (DDD, Exomiser), column 'TOP 1(%)'
Configuration: Exomiser 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)	53.1% 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 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 2 (DDD, Exomiser), column 'TOP 10(%)'
Configuration: Exomiser 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)	70.5% 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 Exomiser 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 2 (DDD, Exomiser), column 'TOP 20(%)'
Configuration: Exomiser 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)	79% 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 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 2 (DDD, Exomiser), column 'TOP 30(%)'

Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
attributes.access Controlled access through the European Genome-phenome Archive Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.access` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.access Controlled access through the European Genome-phenome Archive Context-only references	Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML Retrieved: 2026-10-09T21:20:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.access` Source artifact SHA-256: `a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.accession EGAD00001001355; EGAD00001001413 Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.accession` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.accession EGAD00001001355; EGAD00001001413 Context-only references	Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML Retrieved: 2026-10-09T21:20:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.accession` Source artifact SHA-256: `a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.patient_count 305 Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.patient_count` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.patient_count 305 Context-only references	Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML Retrieved: 2026-10-09T21:20:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.patient_count` Source artifact SHA-256: `a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population Neurodevelopmental disorders and congenital anomalies; mean 7.5 HPO terms and 100,033 variants per proband; 156 cases are in HGMD (published) Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population Neurodevelopmental disorders and congenital anomalies; mean 7.5 HPO terms and 100,033 variants per proband; 156 cases are in HGMD (published) Context-only references	Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML Retrieved: 2026-10-09T21:20:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Context-only references	Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases Original source ↗ Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML Retrieved: 2026-10-09T21:20:19Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

All evidence (JSONL) (gzip)How to read the evidence

Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

2 source records and release history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-data-ddd-305-solved

areas: dna-genomes
contexts: clinical_research
version: EGAD00001001355 (VCF) and EGAD00001001413 (HPO), as selected by Yuan et al.
patient count: 305
accession: EGAD00001001355; EGAD00001001413
population: Neurodevelopmental disorders and congenital anomalies; mean 7.5 HPO terms and 100,033 variants per proband; 156 cases are in HGMD (published)
split: No split; whole set is the benchmark
access: Controlled access through the European Genome-phenome Archive
source locator: Yuan 2022 Materials 'Datasets curation' and Results paragraph 1; Yuan 2024 Methods 'DDD and KGD trio dataset'

Related records

data: AMELIE default singleton on DDD 305
data: AMELIE-HPO default singleton on DDD 305
data: DeepPVP default singleton on DDD 305
data: Exomiser default singleton on DDD 305
data: GADO default singleton on DDD 305
data: HANRD default singleton on DDD 305
data: LIRICAL default singleton on DDD 305
data: Phen2Gene default singleton on DDD 305
data: PhenIX default singleton on DDD 305
data: Phenolyzer default singleton on DDD 305
data: Xrare default singleton on DDD 305
data: AMELIE Protocol A on DDD
data: AMELIE Protocol B on DDD
data: AMELIE Protocol C on DDD
data: AMELIE Protocol D on DDD
data: Exomiser Protocol A on DDD
data: Exomiser Protocol B on DDD
data: Exomiser Protocol C on DDD
data: Exomiser Protocol D on DDD
data: LIRICAL on DDD
data: PhenIX Protocol A on DDD
data: PhenIX Protocol B on DDD
data: PhenIX Protocol C on DDD
data: PhenIX Protocol D on DDD
uses data: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3)
uses data: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1)

Suggest a correction