Result

92.1% top-40-accuracy

yuan2024-kgd-phenix-protocol-d-top40 top-40-accuracy

Tested configuration: PhenIX 1.16, Protocol D (Yuan et al. 2024)
Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1)
Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)
Procedure: rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols
Evaluation: PhenIX Protocol D on KGD
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedRefined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, PhenIX, PROT D), column 'Top40 (%)'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: No split
Adaptation: Trio mode; chosen as optimal by the authors
Scoring implementation: Rank of the causal gene per case

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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1 evidence row 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
Reported result 92.1 Individual claims	Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases Original source ↗ Table 1 row (KGD, PhenIX, PROT D), column 'Top40 (%)' Version: Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML Retrieved: 2026-10-09T21:20:19Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit details Deterministic parse of the pinned article XML table (extract/extract_rare_ranking.py) with caption, column headers, cohort, prioritizer and protocol labels asserted; row-spanning cells resolved by position. Independent review 2026-10-09: matches Table 1 (table-wrap id 'Tab1'). The row is monotone from top 1 to top 50, and the percentage equals a whole number of cases out of the cohort size (305 DDD or 152 KGD) at the printed precision. Field: `attributes.printed_value` Source artifact SHA-256: `a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45` Extraction artifact

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Sources and history

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

1 source records and release history

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-result-yuan2024-kgd-phenix-protocol-d-top40

metric: top-40-accuracy
metric direction: higher
unit: percent
printed value: 92.1
numeric value: 92.1
source locator: Table 1 row (KGD, PhenIX, PROT D), column 'Top40 (%)'
missing metadata: uncertainty: reason: unreported
metric qualifier: proportion of solved cases with the causal gene within the tool's top-ranked genes
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the artifact and matched its SHA-256. Read the cell with a separate parser written for this review; the extractor script was not imported or run. Checked printed and numeric value, locator, metric, qualifier, unit, direction and the linked evaluation, configuration, protocol and dataset.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: a5dbb24eb1e29ef8fde2832da1ff49a436464210d0e54d2a1fd10ad764a24b45; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10838329/fullTextXML; note: Deterministic parse of the pinned article XML table (extract/extract_rare_ranking.py) with caption, column headers, cohort, prioritizer and protocol labels asserted; row-spanning cells resolved by position. Independent review 2026-10-09: matches Table 1 (table-wrap id 'Tab1'). The row is monotone from top 1 to top 50, and the percentage equals a whole number of cases out of the cohort size (305 DDD or 152 KGD) at the printed precision.

Related records

evaluation: PhenIX Protocol D on KGD

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