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High resolution oligonucleotide CGH using DNA from archived prostate tissue
Author(s) -
Paris Pamela L.,
Sridharan Shivaranjani,
Scheffer Alicia,
Tsalenko Anya,
Bruhn Laurakay,
Collins Colin
Publication year - 2007
Publication title -
the prostate
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.295
H-Index - 123
eISSN - 1097-0045
pISSN - 0270-4137
DOI - 10.1002/pros.20632
Subject(s) - oligonucleotide , comparative genomic hybridization , biomarker discovery , computational biology , genomic dna , prostate , prostate cancer , biology , biomarker , oligomer restriction , dna , high resolution , cancer , genetics , genome , gene , proteomics , remote sensing , geology
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. Prostate 67: 1447–1455, 2007. © 2007 Wiley‐Liss, Inc.