Frequency of Chromosome 3 LOH and Partial Loss in Uveal Melanoma by Genomic Microarray Analysis of Frozen Tissue
Eugen C Minca, Raymond R Tubbs, Bryce P Portier, Zhen Wang, Christopher Lanigan, Charles Biscotti, Mary Beth Aronow, Pierre Triozzi, Arun Singh, James R Cook, Yogen Saunthararajah, Lynn Schoenfield, Blake C Baliff, Roger A Schultz. Cleveland Clinic Foundation, Cleveland, OH; Signature Genomics, Spokane, WA
Background: Molecular cytogenetic alterations, especially monosomy of chromosome 3, are strongly correlated with metastases and death in uveal melanoma (UVM). For prognostic stratification, monosomy 3 is frequently assessed by fluorescence in-situ hybridization (FISH). A subset of UVM exhibit only regional chromosome 3 loss or loss of heterozygosity (LOH) resulting from uniparental disomy, that are undetectable by chromosome enumeration probes. Alternatively, CGH/SNP microarray analysis can generate high resolution multi-chromosome data and identify LOH. Here we assessed the frequency of chromosome 3 LOH and partial loss by combined genomic and SNP array analysis of DNA extracted from frozen tissue (FZT) procured from a consecutive series of enucleations performed for UVM.
Design: Sufficient FZT DNA for genomic microarray analysis was obtained from enucleations performed for 28/119 patients on clinical trial NCT00952939 with CEP3-FISH results obtained as described (Invest Opthal Vis Sci 2012 Apr 17 Epub PMID 22511634). DNA was fluorescently labeled (Roche) and microarray analysis was performed using a custom designed Roche® NimbleGen® array (OncoChip®v2) with oligonucleotide coverage biased to >2400 cancer features and backbone SNP coverage affording combined oligo and SNP analysis (CGH/SNP).
Results: CGH/SNP results were technically successful in all cases. 15/28 aCGH samples showed chromosome 3 monosomy (14/15 concordant with FISH). 13/28 aCGH samples showed chromosome 3 eusomy (7/13 concordant with FISH). Of the 13 cases with chromosome 3 eusomy by aCGH, 1 case (3.5%) demonstrated whole chromosome 3 LOH by SNP analysis, and 1 case (3.5%) showed partial 3q loss. In addition, large terminal 6p gains were seen in all cases with chromosome 3 eusomy. Amplifications involving TERT and NEDD9 genes, deletions involving CDKN2A/B and LUM genes, and other whole chromosome LOH were also identified.
Conclusions: Chromosome 3 LOH and partial loss are rare events that can be detected by CGH/SNP genotyping of DNA from FZT of UVM. Genomic microarray analysis may be warranted as second step testing in UVM cases with apparent chromosome 3 eusomy by FISH. The genome-wide coverage of CHG/SNP identifies complex genomic signatures and provides additional data with potential relevance to UVM biology, diagnosis and prognosis.
Tuesday, March 5, 2013 9:30 AM
Poster Session III # 220, Tuesday Morning