Configuration

SQUIRLS 2.0.1 (Drost et al.)

SQUIRLS as used by Drost et al.

Overview

SQUIRLS as used by Drost et al.

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

Evaluations and results

3 evaluations · 24 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: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.88 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'CAGI6', cell I10; row Squirls, column AUPRC
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.78 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'CAGI6', cell H10; row Squirls, column AUROC
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.773 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell F23; row Squirls, column F1
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.556 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell H23; row Squirls, column Neg Pred Value
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.763 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell G23; row Squirls, column Pos Pred Value
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.763 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell E23; row Squirls, column Precision
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.784 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell C23; row Squirls, column Sensitivity (Recall)
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.526 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell D23; row Squirls, column Specificity
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.873 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'In House', cell I15; row Squirls, column AUPRC
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.811 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'In House', cell H15; row Squirls, column AUROC
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.792 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell F36; row Squirls, column F1
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.646 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell H36; row Squirls, column Neg Pred Value
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.779 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell G36; row Squirls, column Pos Pred Value
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.779 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell E36; row Squirls, column Precision
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.805 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell C36; row Squirls, column Sensitivity (Recall)
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.609 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell D36; row Squirls, column Specificity
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.881 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Entire Dataset', cell D13; row Squirls, column AUPRC
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.806 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Entire Dataset', cell C13; row Squirls, column AUROC
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.787 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell F10; row Squirls, column F1
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.627 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell H10; row Squirls, column Neg Pred Value
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.775 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell G10; row Squirls, column Pos Pred Value
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.775 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell E10; row Squirls, column Precision
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.8 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell C10; row Squirls, column Sensitivity (Recall)
Configuration: SQUIRLS 2.0.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.591 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell D10; row Squirls, column Specificity

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Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools · Original source · HGG Advances 7(1):100521, published online 2025-09-22; PMC12547740 full-text XML
Drost et al. 2025, Data S1 (Tables S1-S6) · Original source · mmc2.xlsx (Data S1. Tables S1-S6) inside the Europe PMC supplementaryFiles zip for PMC12547740

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261009-config-drost2025-squirls

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: SQUIRLS 2.0.1 (Drost et al.)
foundation model eligible: false
version: 2.0.1
parameters: Binary predictions at the literature threshold 0.018
source locator: Methods 'In silico splice predictions'; Results paragraph 3

Related records

configuration of: SQUIRLS
system: SQUIRLS 2.0.1 on 56 CAGI6 Splicing VUS variants
system: SQUIRLS 2.0.1 on in-house scorable variants (count not printed)
system: SQUIRLS 2.0.1 on 243 scorable variants (in-house plus CAGI6)

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