Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers : a new approach for the molecular analysis of paraffin-embedded cancer tissue.
We have developed a protocol for degenerate oligonucleotide-primed-polymerase chain reaction-based array comparative genomic hybridization (array CGH) that, when combined with a laser microdissection technique, allows the analysis of cancer cell populations isolated from routine, formalin-fixed, paraffin-embedded tissue samples. Comparison of copy number changes detected by degenerate oligonucleotide-primed-polymerase chain reaction-based array CGH to those detected by conventional array CGH or fluorescence in situ hybridization, demonstrated that amplifications can be reliably detected. Using a genomic microarray containing 57 oncogenes, we screened a total of 28 breast cancer samples and obtained a detailed amplicon profile that is the most comprehensive to date in human breast cancer. The array CGH method described here will allow the genetic analysis of paraffin-embedded human cancer materials for example in the context of clinical trials.
Daigo
Y
Y
Department of Oncology, the Cambridge Institute for Medical Research/Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, Cambridge, United Kingdom.
Chin
S F
SF
Gorringe
K L
KL
Bobrow
L G
LG
Ponder
B A
BA
Pharoah
P D
PD
Caldas
C
C
D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D002871:Chromosome Banding; D002874:Chromosome Mapping; D005784:Gene Amplification; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D014407:Tumor Cells, Cultured