Evaluation

Exomiser reanalysis flag 0.3/0.8: later-diagnosed 100kGP cases

Published reanalysis method comparison; transcribed, not reproduced.

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

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Evaluation results

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

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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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 0.8 (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)	0.698 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'Fscore'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)	0.761 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'F2score'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)	7 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'FN'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)	19 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'FP'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)	0.612 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'precision'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)	0.811 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'recall'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)	1790 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'TN'
Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)	30 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 0.3/0.8: 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 3 (Diff human score 0.3, Var score 0.8), column 'TP'

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

Evaluation procedure

rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging

Configuration: Exomiser 13.1.0 reanalysis flag: phenotype score increase 0.3, variant score 0.8 (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)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging
dataset version: 37 later-diagnosed 100kGP cases
split: No split
population: 1846 Exomiser candidate variants, 37 diagnosed
inputs: Original 100kGP VCFs; Exomiser 13.1.0 with database releases February 2019 to February 2022
adaptation: Threshold pair as stated per configuration
metric implementation: Variant-level confusion counts in R 4.2.1
aggregation: All 37 cases pooled
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: No split
Adaptation: Threshold pair as stated per configuration
Scoring implementation: Variant-level confusion counts in R 4.2.1

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

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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38 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.comparison.adaptation Threshold pair as stated per configuration Context-only references	Efficient reinterpretation of rare disease cases using Exomiser Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: npj Genomic Medicine 9:65, published 2024-12-18; PMC11655964 full-text XML Retrieved: 2026-10-09T20:36:38Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `b8cd48ed7e4a337ddf954d1b9bb004305ac78c383268592828e6203418d04058` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation Threshold pair as stated per configuration Context-only references	Vestito et al. 2024, Supplementary Table 1 Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages) Retrieved: 2026-10-09T20:36:47Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `d761ccee3944cd762d1c07e5388ed2810bd57634e1fc2c23a054b547a710a5ad` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation All 37 cases pooled Context-only references	Efficient reinterpretation of rare disease cases using Exomiser Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: npj Genomic Medicine 9:65, published 2024-12-18; PMC11655964 full-text XML Retrieved: 2026-10-09T20:36:38Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `b8cd48ed7e4a337ddf954d1b9bb004305ac78c383268592828e6203418d04058` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation All 37 cases pooled Context-only references	Vestito et al. 2024, Supplementary Table 1 Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages) Retrieved: 2026-10-09T20:36:47Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `d761ccee3944cd762d1c07e5388ed2810bd57634e1fc2c23a054b547a710a5ad` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Efficient reinterpretation of rare disease cases using Exomiser Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: npj Genomic Medicine 9:65, published 2024-12-18; PMC11655964 full-text XML Retrieved: 2026-10-09T20:36:38Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `b8cd48ed7e4a337ddf954d1b9bb004305ac78c383268592828e6203418d04058` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Vestito et al. 2024, Supplementary Table 1 Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages) Retrieved: 2026-10-09T20:36:47Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `d761ccee3944cd762d1c07e5388ed2810bd57634e1fc2c23a054b547a710a5ad` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version 37 later-diagnosed 100kGP cases Context-only references	Efficient reinterpretation of rare disease cases using Exomiser Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: npj Genomic Medicine 9:65, published 2024-12-18; PMC11655964 full-text XML Retrieved: 2026-10-09T20:36:38Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `b8cd48ed7e4a337ddf954d1b9bb004305ac78c383268592828e6203418d04058` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version 37 later-diagnosed 100kGP cases Context-only references	Vestito et al. 2024, Supplementary Table 1 Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages) Retrieved: 2026-10-09T20:36:47Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `d761ccee3944cd762d1c07e5388ed2810bd57634e1fc2c23a054b547a710a5ad` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Original 100kGP VCFs; Exomiser 13.1.0 with database releases February 2019 to February 2022 Context-only references	Efficient reinterpretation of rare disease cases using Exomiser Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: npj Genomic Medicine 9:65, published 2024-12-18; PMC11655964 full-text XML Retrieved: 2026-10-09T20:36:38Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `b8cd48ed7e4a337ddf954d1b9bb004305ac78c383268592828e6203418d04058` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Original 100kGP VCFs; Exomiser 13.1.0 with database releases February 2019 to February 2022 Context-only references	Vestito et al. 2024, Supplementary Table 1 Original source ↗ Supplementary Table 1 line 3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41525_2024_456_MOESM1_ESM.pdf from the Europe PMC supplementary bundle (PDF title 'Supplementary_table_S1 copy', 4 pages) Retrieved: 2026-10-09T20:36:47Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `d761ccee3944cd762d1c07e5388ed2810bd57634e1fc2c23a054b547a710a5ad` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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-eval-vestito2024-dh3-vs8

areas: dna-genomes
contexts: clinical_research
origin: author_reported
protocol: rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging
version: Primary source as retrieved 2026-10-09
comparison: protocol id: rare-reanalysis-20261009-protocol-vestito2024-new-candidate-flagging; dataset version: 37 later-diagnosed 100kGP cases; split: No split; population: 1846 Exomiser candidate variants, 37 diagnosed; inputs: Original 100kGP VCFs; Exomiser 13.1.0 with database releases February 2019 to February 2022; adaptation: Threshold pair as stated per configuration; metric implementation: Variant-level confusion counts in R 4.2.1; aggregation: All 37 cases pooled; budget: Not reported
source locator: Supplementary Table 1 line 3
limitations: Exomiser developers evaluating their own tool on retrospectively diagnosed cases.

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