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Published on: December 2, 2022
Genomic microarray analysis on formalin-fixed paraffin-embedded material for uveal melanoma prognostication.
Eugen C Minca1, Raymond R Tubbs1, Bryce P Portier1
1Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
Genomic microarray analysis using formalin-fixed paraffin-embedded tissue (FFPET) is a feasible and accurate method for uveal melanoma (UVM) prognostication. This approach provides results highly concordant with frozen tissue analysis and fluorescence in situ hybridization (FISH), enabling reliable outcome prediction.
Area of Science:
- Ophthalmology
- Genetics
- Oncology
Background:
- Cytogenetic alterations are crucial prognostic indicators in uveal melanoma (UVM).
- Standard testing involves fluorescence in situ hybridization (FISH) for specific alterations like monosomy 3 (-3) and MYC amplification.
- Microarray analysis offers comprehensive genomic data but traditionally requires non-fixed frozen tissue, which is not always available.
Purpose of the Study:
- To evaluate the feasibility and accuracy of using formalin-fixed paraffin-embedded tissue (FFPET) for high-resolution genomic microarray analysis in UVM.
- To compare the results of microarray analysis on FFPET with those from frozen tissue (FZT) and FISH.
Main Methods:
- Comparative genomic hybridization and single nucleotide polymorphism (CGH/SNP) analysis were performed on Roche-NimbleGen OncoChip arrays.
- DNA was extracted from both FFPET (n=34) and FZT (n=41) samples from 44 UVM patients.
- CEP3 FISH analysis was conducted on matched cytology ThinPrep material.
Main Results:
- CGH/SNP analysis was successful in 30/34 FFPET and 41/41 FZT samples.
- High concordance (96.3%) was observed between FFPET and FZT for major recurrent abnormalities, including -3.
- CGH/SNP results on FFPET and FZT correlated significantly with clinical outcomes such as metastasis development and survival.
Conclusions:
- Genomic microarray analysis using FFPET is a practical and reliable method for UVM prognostication.
- FFPET-based analysis demonstrates high concordance with FZT and FISH analyses.
- Genome-wide analysis provides valuable data for understanding UVM biology, diagnosis, and prognosis.
