• Evaluation of single-nucleotid...

Treffer: Evaluation of single-nucleotide variants in bladder cancer using prediction algorithms.

Title:
Evaluation of single-nucleotide variants in bladder cancer using prediction algorithms.
Transliterated Title:
Evaluation von Punktmutationen bei Blasenkrebs mittels Prädiktionsalgorithmen.
Authors:
Möller J; Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany., Seillier L; Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany., Fürstberger A; Institute of Pathology, University Hospital Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany., Rose M; Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany.; Institute of Pathology, University Hospital Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany., Jonigk DD; Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany.; Biomedical Research in Endstage and Obstructive Lung Disease Hanover (BREATH), Member of the German Center for Lung Research (DZL), Hanover, Germany., Ortiz-Brüchle N; Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany., Gaisa NT; Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany. Nadine.Gaisa@uniklinik-ulm.de.; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany. Nadine.Gaisa@uniklinik-ulm.de.; Institute of Pathology, University Hospital Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany. Nadine.Gaisa@uniklinik-ulm.de.
Source:
Pathologie (Heidelberg, Germany) [Pathologie (Heidelb)] 2026 Jan; Vol. 47 (Suppl 1), pp. 9-17. Date of Electronic Publication: 2025 Dec 03.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Springer Medizin Country of Publication: Germany NLM ID: 9918384887506676 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2731-7196 (Electronic) Linking ISSN: 27317188 NLM ISO Abbreviation: Pathologie (Heidelb) Subsets: MEDLINE
Imprint Name(s):
Original Publication: [Heidelberg, Germany] : Springer Medizin, [2022]-
MeSH Terms:
Urinary Bladder Neoplasms*/genetics , Urinary Bladder Neoplasms*/pathology , Algorithms* , Polymorphism, Single Nucleotide*/genetics, Humans ; Sensitivity and Specificity ; Prediction Algorithms
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Contributed Indexing:
Keywords: Cancer of the upper urinary tract; Next-generation sequencing; Pathogenicity prediction; Urothelial Carcinoma; Variant interpretation
Local Abstract: [Publisher, German] HINTERGRUND: Harnblasen- und Harnwegskarzinome weisen eine schlechte Überlebensrate auf und erfordern neue therapeutische Ansätze. Fortschritte im Omics-Bereich haben die genetische Analyse erweitert, wobei Prädiktionstools eine potenzielle Unterstützung darstellen. Ihre Leistung kann jedoch zwischen Tumorentitäten variieren. [Publisher, German] Ziel der Studie war die Bewertung der Leistungsfähigkeit von Prädiktionstools bei der Analyse genetischer Daten von Harnblasen- und Harnwegskarzinomen. [Publisher, German] Variantendaten wurden aus den Datenbanken ClinVar und cBioPortal für Blasenkarzinome (n = 441), PanCancer (n = 361) und aus benignen Varianten (n = 357) extrahiert. Einzeln sowie in Kombinationen von 2 und 3 Tools wurden 16 Algorithmen getestet; Onkogene und Tumorsuppressorgene wurden verglichen. Zusätzlich wurde ein PanCancer-Datensatz von Suybeng et al. einbezogen. [Publisher, German] Die Prädiktionsleistung variiert zwischen den Datensätzen. Kombinationen aus 3 Tools erzielten die höchste Sensitivität (100 %: MutationTaster/MetaSVM/LIST-S2) und Spezifität (97,45 %: MutationTaster/DEOGEN2/FATHMM.XF). Unterschiede zwischen Entitäten sowie zwischen Onkogenen und Tumorsupressoren wurden beobachtet. [Publisher, German] Kombinationen von Algorithmen können genetische Analysen verbessern. Die Auswahl der Tools sollte im Hinblick auf Entität, Gen und Ziel der Analyse erfolgen.
Entry Date(s):
Date Created: 20251203 Date Completed: 20260119 Latest Revision: 20260119
Update Code:
20260119
DOI:
10.1007/s00292-025-01518-7
PMID:
41335340
Database:
MEDLINE

Weitere Informationen

Background: Bladder and urinary tract cancer show poor survival rates and demand novel therapeutic strategies. Advances in the omics domain have expanded genetic analysis, with prediction tools offering potential support. However, their performance may differ by tumor entity.
Objective: This study aimed to evaluate prediction tool performance using genetic data from bladder and urinary tract cancer.
Methods: Variant data were obtained from ClinVar and cBioPortal for bladder cancer (n = 441), PanCancer (n = 361), and benign variants (n = 357). Sixteen prediction algorithms were assessed individually and in combinations of two or three; oncogenes and tumor suppressors were compared. A PanCancer dataset of Suybeng et al. was also analyzed.
Results: Prediction performance varied across datasets. Combinations of three tools achieved the highest sensitivity (100%: MutationTaster/MetaSVM/List-S2) and specificity (97.45%: MutationTaster/DEOGEN2/FATHMM_XF). Entity-specific and gene-type differences were observed.
Conclusion: Combining prediction tools enhances genetic analysis. Tool selection should depend on cancer entity, gene function, and study objective.
(© 2025. The Author(s), under exclusive licence to Springer Medizin Verlag GmbH, ein Teil von Springer Nature.)

Declarations. Conflict of interest: J. Möller, L. Seillier, A. Fürstberger, M. Rose, D.D. Jonigk, N. Ortiz-Brüchle, and N.T. Gaisa declare that they have no competing interests. Ethics approval and consent to participate: Not applicable, as the study involved use of public data only. Consent for publication: All authors have read and revised the final version of the manuscript. For this article no studies with human participants or animals were performed by any of the authors. All studies mentioned were in accordance with the ethical standards indicated in each case. The supplement containing this article is not sponsored by industry.