title: Genomic microarray analysis on formalin-fixed paraffin-embedded material for uveal melanoma prognostication.
abstract: Cytogenetic alterations are strong outcome prognosticators in uveal melanoma (UVM). Monosomy 3 (-3) and MYC amplification at 8q24 are commonly tested by fluorescence in situ hybridization (FISH). Alternatively, microarray analysis provides whole genome data, detecting partial chromosome loss, loss of heterozygosity (LOH), or abnormalities unrepresented by FISH probes. Nonfixed frozen tissue is conventionally used for microarray analysis but may not always be available. We assessed the feasibility of genomic microarray analysis for high resolution interrogation of UVM using formalin-fixed paraffin-embedded tissue (FFPET) as an alternative to frozen tissue (FZT). Enucleations from 44 patients (clinical trial NCT00952939) yielded sufficient DNA from FFPET (n = 34) and/or frozen tissue (n = 41) for comparative genomic hybridization and select single nucleotide polymorphism analysis (CGH/SNP) on Roche-NimbleGen OncoChip arrays. CEP3 FISH analysis was performed on matched cytology ThinPrep material. CGH/SNP analysis was successful in 30 of 34 FFPET and 41 of 41 FZT samples. Of 27 paired FFPET/FZT samples, 26 (96.3%) were concordant for at least four of six major recurrent abnormalities (-3, +8q, -1p, +6p, -6q, -8p), and 25 of 27 (92.6%) were concordant for -3. Results of CGH/SNP were concordant with the CEP3 FISH results in 27 of 30 (90%) FFPET and 38 of 41 (92.6%) FZT cases; partial -3q was detected in two CEP3 FISH-negative cases and whole chromosome 3, 4, and 6 SNP-LOH in one case. CGH detection of -3, +8q, -8p on FFPET and FZT showed significant correlation with the clinical outcome measures (metastasis development, time to progression, survival). Results of the UVM genotyping by CGH/SNP on FFPET are highly concordant with those of the FZT analysis and with those of the CEP3 FISH analysis, and therefore CGH/SNP is a practical method for UVM prognostication. Genome-wide coverage provides additional data with potential relevance to UVM biology, diagnosis, and prognosis.
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Eugen C
authors.initials: EC
authors.lastname: Minca
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Raymond R
authors.initials: RR
authors.lastname: Tubbs
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Bryce P
authors.initials: BP
authors.lastname: Portier
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Lanigan
authors.affiliation: Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Mary E
authors.initials: ME
authors.lastname: Aronow
authors.affiliation: Tausig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Pierre L
authors.initials: PL
authors.lastname: Triozzi
authors.affiliation: Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Arun
authors.initials: A
authors.lastname: Singh
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Cook
authors.affiliation: Tausig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Yogen
authors.initials: Y
authors.lastname: Saunthararajah
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Plesec
authors.affiliation: Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Lynn
authors.initials: L
authors.lastname: Schoenfield
authors.affiliation: Signature Genomics Laboratories, Perkin Elmer, Spokane, WA, USA.
authors.forename: Victoria
authors.initials: V
authors.lastname: Cawich
authors.affiliation: Signature Genomics Laboratories, Perkin Elmer, Spokane, WA, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Sulpizio
authors.affiliation: Signature Genomics Laboratories, Perkin Elmer, Spokane, WA, USA. Electronic address: Roger.Schultz@PerkinElmer.com.
authors.forename: Roger A
authors.initials: RA
authors.lastname: Schultz
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D002869:Chromosome Aberrations; D055028:Comparative Genomic Hybridization; D005240:Feasibility Studies; D005557:Formaldehyde; D020869:Gene Expression Profiling; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008545:Melanoma / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011379:Prognosis; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014604:Uveal Neoplasms / Q000235:genetics* / Q000473:pathology; D000098943:Uveal Melanoma
chemical_list: D014408:Biomarkers, Tumor; D012333:RNA, Messenger; D005557:Formaldehyde
keywords: FFPE; Uveal melanoma; genomic; microarray; prognostic