High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.
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.
Paris
Pamela L
PL
Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94115, USA.
Albertson
Donna G
DG
Alers
Janneke C
JC
Andaya
Armann
A
Carroll
Peter
P
Fridlyand
Jane
J
Jain
Ajay N
AN
Kamkar
Sherwin
S
Kowbel
David
D
Krijtenburg
Pieter-Jaap
PJ
Pinkel
Daniel
D
Schröder
Fritz H
FH
Vissers
Kees J
KJ
Watson
Vivienne J E
VJ
Wildhagen
Mark F
MF
Collins
Colin
C
Van Dekken
Herman
H
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
D005557:Formaldehyde; D010232:Paraffin