High resolution oligonucleotide CGH using DNA from archived prostate tissue.
BACKGROUND
The current focus on biomarker discovery is a result of an improved understanding of the biological basis for carcinogenesis and advances in technology. Biomarkers can aid in diagnosis, prognosis, treatment selection, and drug development. There is an urgent need for high-resolution tools that perform well using archived tissue for biomarker discovery and tools that can translate into the clinic.


METHODS
Oligonucleotide array comparative genomic hybridization (oCGH) was compared to BAC-based aCGH using unamplified total genomic DNA from formalin fixed paraffin-embedded (FFPE) prostate tissue.


RESULTS
The copy number aberrations detected with the BAC and oligonucleotide arrays were highly correlated in cases where the arrays contained probes in similar genomic locations. The oligonucleotide array platform provided more precise mapping due to the higher density of oligonucleotide probes.


CONCLUSIONS
These results demonstrate the utility of high-resolution oligonucleotide arrays designed to use genomic DNA for CGH measurements using archived tissue samples for discovery and clinic based assays.
Paris
Pamela L
PL
Department of Urology, Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94143, USA.
Sridharan
Shivaranjani
S
Scheffer
Alicia
A
Tsalenko
Anya
A
Bruhn
Laurakay
L
Collins
Colin
C
D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D004273:DNA, Neoplasm / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D008297:Male; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011471:Prostatic Neoplasms / Q000235:genetics*
D004273:DNA, Neoplasm