title: High-resolution global profiling of genomic alterations with long oligonucleotide microarray.
abstract: Cancer represents the phenotypic end point of multiple genetic lesions that endow cells with a full range of biological properties required for tumorigenesis. Among the hallmark features of the cancer genome are recurrent regional gains and losses that, upon detailed characterization, have provided highly productive discovery paths for new oncogenes and tumor suppressor genes. In this study, we describe the use of an oligonucleotide-based microarray platform and development of requisite assay conditions and bioinformatic mining tools that permits high-resolution genome-wide array-comparative genome hybridization profiling of human and mouse tumors. Using a commercially available 60-mer oligonucleotide microarray, we demonstrate that this platform provides sufficient sensitivity to detect single-copy difference in gene dosage of full complexity genomic DNA while offering high resolution. The commercial availability of the microarrays and associated reagents, along with the technical protocols and analytical tools described in this report, should provide investigators with the immediate capacity to perform DNA analysis of normal and diseased genomes in a global and detailed manner.
authors.affiliation: Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA.
authors.forename: Cameron
authors.initials: C
authors.lastname: Brennan
authors.forename: Yunyu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Christopher
authors.initials: C
authors.lastname: Leo
authors.forename: Bin
authors.initials: B
authors.lastname: Feng
authors.forename: Craig
authors.initials: C
authors.lastname: Cauwels
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Aguirre
authors.forename: Minjung
authors.initials: M
authors.lastname: Kim
authors.forename: Alexei
authors.initials: A
authors.lastname: Protopopov
authors.forename: Lynda
authors.initials: L
authors.lastname: Chin
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D019295:Computational Biology / Q000379:methods*; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D018628:Gene Dosage; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008297:Male; D051379:Mice; D009369:Neoplasms / Q000235:genetics*; D009374:Neoplasms, Experimental / Q000235:genetics; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods
chemical_list: D004273:DNA, Neoplasm