Comparison of FISH and Cytogenomic Microarray Analysis for Detection of Chromosomal Abnormalities in Uveal Melanoma

Abstract

Purpose : Uveal melanoma has high tendency for hematogenous metastasis to the liver. Fluorescence in situ hybridization (FISH) testing is routinely done to detect monosomy 3 and predict the likelihood of metastasis. We compared the sensitivity and specificity of FISH testing with cytogenomic microarray single nucleotide polymorphism (SNP) analysis in detecting chromosomal abnormalities in uveal melanoma specimens.

Methods : Uveal melanoma enucleation specimens were collected from 2014 to 2016. Five patients were included, 4 were male and 1 was female. The age range was from 40 to 80. FISH testing was performed on unstained sections from 4 enucleations. OncoScan cytogenomic microarray SNP analysis was performed on 5 cases, 4 of them from formalin-fixed enucleation tissue extracted, and in 1 case the material was taken from fine needle aspiration of vitreal fluid. FISH and OncoScan results were compared. Formalin fixed, paraffin-embedded tissue blocks from the enucleation specimens were also examined by hematoxylin and eosin (H&E) for histopathologic tumor staging and grading.

Results : Histologically, 3 uveal melanoma cases had mixed spindle and epithelioid type morphology, 1 case was spindle type, and 1 case was epithelioid type. FISH testing showed that 3 cases had <20% of monosomy 3 in tumor cells (normal), and in 1 case, 74.5% of tumor cells showed monosomy 3. OncoScan results revealed abnormality in all 5 cases. One case showed loss of heterozygosity (LOH) involving the BAP1 locus on chromosome 3. The second case showed complete LOH for BAP1, loss of Y chromosome and 6q, gain of 4p (FGFR3, WHSC1, SLC34A2, RHOH and PHOX2B), 6p, 8q, 2p24.3-p24.3 (MYCN) and 9p. The third case had loss 6q, 16q, 17p, 17q and 21q, gain of 6p, 16p, 17q (proximal segment), most of 21q and gain of 4q12-q22.1 (PDGFRA, KIT), 6p22.1-p21.1 (CCND3), 8q (MYC). The fourth case had loss of X chromosome, homozygous deletion 22q11.23 (GSTT1), and gain of 6p. The fifth case showed loss of Y, gain of 9, loss of distal 14q, and low-level loss of 16q/proximal 16p.

Conclusions : Our findings suggest that OncoScan microarray analysis is more sensitive than FISH test in detecting chromosomal abnormalities in uveal melanomas particularly small deletions and duplications. Interestingly, OncoScan can also be performed on small vitreal samples.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.