Configuration

Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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

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Evaluations and results

1 evaluation · 8 results. Different protocols are not a single leaderboard.

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)

Sorted by F-beta (F2 (beta = 2)) (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	F-beta (F2 (beta = 2))	F1	False negatives (diagnosed variants not flagged)	False positives (non-diagnostic variants flagged for review)	Precision	Recall	True negatives (non-diagnostic variants not flagged)	True positives (diagnosed variants flagged)
Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (Vestito et al. 2024)Evaluation	0.718	0.59	6	37	0.456	0.838	1772	31

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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 0.4, variant score 0.6 (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)	0.59 F1 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'Fscore'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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)	0.718 F-beta (F2 (beta = 2)) 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'F2score'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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)	6 False negatives (diagnosed variants not flagged) 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'FN'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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)	37 False positives (non-diagnostic variants flagged for review) 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'FP'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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)	0.456 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'precision'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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)	0.838 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'recall'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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)	1770 True negatives (non-diagnostic variants not flagged) 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'TN'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.4, variant score 0.6 (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)	31 True positives (diagnosed variants flagged) 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 0.4/0.6: 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 11 (Diff human score 0.4, Var score 0.6), column 'TP'

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

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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-dh4-vs6

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Diff human score 0.4, Var score 0.6
source locator: Supplementary Table 1 line 11
foundation model eligible: false
parameters: Human phenotype score difference 0.4 between database releases; variant score threshold 0.6; 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 0.4/0.6: later-diagnosed 100kGP cases

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