title: High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.
abstract: We have used prostate cancer, the most commonly diagnosed noncutaneous neoplasm among men, to investigate the feasibility of performing genomic array analyses of archival tissue. Prostate-specific antigen and a biopsy Gleason grade have not proven to be accurate in predicting clinical outcome, yet they remain the only accepted biomarkers for prostate cancer. It is likely that distinct spectra of genomic alterations underlie these phenotypic differences, and that once identified, may be used to differentiate between indolent and aggressive tumors. Array comparative genomic hybridization allows quantitative detection and mapping of copy number aberrations in tumors and subsequent associations to be made with clinical outcome. Archived tissues are needed to have patients with sufficient clinical follow-up. In this report, 20 formalin-fixed and paraffin-embedded prostate cancer samples originating from 1986 to 1996 were studied. We present a straightforward protocol and demonstrate the utility of archived tissue for array comparative genomic hybridization with a 2400 element BAC array that provides high-resolution detection of both deletions and amplifications.
authors.affiliation: Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94115, USA.
authors.forename: Pamela L
authors.initials: PL
authors.lastname: Paris
authors.forename: Donna G
authors.initials: DG
authors.lastname: Albertson
authors.forename: Janneke C
authors.initials: JC
authors.lastname: Alers
authors.forename: Armann
authors.initials: A
authors.lastname: Andaya
authors.forename: Peter
authors.initials: P
authors.lastname: Carroll
authors.forename: Jane
authors.initials: J
authors.lastname: Fridlyand
authors.forename: Ajay N
authors.initials: AN
authors.lastname: Jain
authors.forename: Sherwin
authors.initials: S
authors.lastname: Kamkar
authors.forename: David
authors.initials: D
authors.lastname: Kowbel
authors.forename: Pieter-Jaap
authors.initials: PJ
authors.lastname: Krijtenburg
authors.forename: Daniel
authors.initials: D
authors.lastname: Pinkel
authors.forename: Fritz H
authors.initials: FH
authors.lastname: Schröder
authors.forename: Kees J
authors.initials: KJ
authors.lastname: Vissers
authors.forename: Vivienne J E
authors.initials: VJ
authors.lastname: Watson
authors.forename: Mark F
authors.initials: MF
authors.lastname: Wildhagen
authors.forename: Colin
authors.initials: C
authors.lastname: Collins
authors.forename: Herman
authors.initials: H
authors.lastname: Van Dekken
mesh_terms: D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D005557:Formaldehyde; D006652:Histological Techniques; D006801:Humans; D008297:Male; D009362:Neoplasm Metastasis; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010232:Paraffin; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology*; D012680:Sensitivity and Specificity; D016896:Treatment Outcome
chemical_list: D005557:Formaldehyde; D010232:Paraffin