Configuration

Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)

Exomiser reanalysis filter flagging variants whose human phenotype score rose by the stated amount and whose variant score exceeds the stated threshold.

1 evaluation · 8 results

Overview

Exomiser reanalysis filter flagging variants whose human phenotype score rose by the stated amount and whose variant score exceeds the stated threshold.

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

Evaluations and results

1 evaluation · 8 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: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	0.732 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'Fscore'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	0.714 f-beta-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'F2score'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	11 false-negative-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'FN'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	8 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'FP'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	0.765 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'precision'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	0.703 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'recall'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	1800 true-negative-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'TN'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.9 (Vestito et al. 2024)	Protocol: Flagging new reanalysis candidates from Exomiser score changes across database releases (Vestito et al. 2024 Supplementary Table 1) Dataset: 100,000 Genomes Project: 37 cases unsolved in February 2019 and later diagnosed through a new disease-gene association (Vestito et al. 2024)	26 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging Aggregation: Not reported Vestito et al. 2024, Supplementary Table 1 · Supplementary Table 1 line 12 (Diff human score 0.3, Var score 0.9), column 'TP'

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Sources and history

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

2 source records and release history

Efficient reinterpretation of rare disease cases using Exomiser · Original source · npj Genomic Medicine 9:65, published 2024-12-18; PMC11655964 full-text XML
Vestito et al. 2024, Supplementary Table 1 · Original source · 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages)

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Technical metadata and extraction receipts

Stable ID: rare-reanalysis-20261009-config-vestito2024-exomiser-13-1-0-dh3-vs9

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Diff human score 0.3, Var score 0.9
source locator: Supplementary Table 1 line 12
foundation model eligible: false
parameters: Human phenotype score difference 0.3 between database releases; variant score threshold 0.9; other settings for these runs are not stated (Methods 'Analysis of 100kGP samples' gives default settings for the main 24,015-case reanalysis)
version: 13.1.0

Related records

configuration of: Exomiser
system: Exomiser reanalysis flag 0.3/0.9: later-diagnosed 100kGP cases

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