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An Optimized NGS Workflow Defines Genetically Based Prognostic Categories for Patients with Uveal Melanoma
Michele Massimino1,2, Elena Tirrò2, Stefania Stella2,3
1Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy.
Biomolecules
|January 25, 2025
Summary
A new standardized workflow using next-generation sequencing (NGS) effectively classifies uveal melanoma (UM) genetic alterations, improving patient risk stratification and survival prediction. This reproducible method offers a reliable tool for clinical application in UM management.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Uveal melanoma (UM) has a high rate of metastasis (50%) and poor survival despite treatment advances.
- Molecular profiling identifies genetic alterations for UM risk stratification.
- Current genetic analyses are fragmented across studies and methods, hindering standardization.
Purpose of the Study:
- To develop a standardized, reproducible workflow for molecular analysis in UM.
- To create a next-generation sequencing (NGS)-based gene panel (UMpanel) for UM classification.
Main Methods:
- Developed an NGS-based gene panel (UMpanel) based on TCGA-UM study findings.
- Classified UM genetic alterations into initiating, prognostic, emergent biomarker, and chromosomal abnormality categories.
- Validated the UMpanel using commercial gene panels, reference DNAs, and Sanger sequencing against the TCGA-UM cohort.
Main Results:
- The UMpanel successfully predicted survival with high specificity and sensitivity.
- Comparative analysis confirmed the methodological approach's reliability.
- The workflow demonstrated reproducibility and effectiveness in stratifying UM patients.
Conclusions:
- A reproducible NGS-based workflow provides a reliable tool for clinical stratification of UM patients.
- Standardized molecular analysis enhances UM patient management and prognostic accuracy.
