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Series GSE3281 Query DataSets for GSE3281
Status Public on Sep 10, 2005
Title Breast Cancer aCGH
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by array
Summary Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH) analysis of DNA copy number variation in a series of primary human breast tumors. We have profiled DNA copy number alteration across 6,691 mapped human genes, in 44 predominantly advanced, primary breast tumors and 10 breast cancer cell lines. While the overall patterns of DNA amplification and deletion corroborate previous cytogenetic studies, the high-resolution (gene-by-gene) mapping of amplicon boundaries and the quantitative analysis of amplicon shape provide significant improvement in the localization of candidate oncogenes. Parallel microarray measurements of mRNA levels reveal the remarkable degree to which variation in gene copy number contributes to variation in gene expression in tumor cells. Specifically, we find that 62% of highly amplified genes show moderately or highly elevated expression, that DNA copy number influences gene expression across a wide range of DNA copy number alterations (deletion, low-, mid- and high-level amplification), that on average, a 2-fold change in DNA copy number is associated with a corresponding 1.5-fold change in mRNA levels, and that overall, at least 12% of all the variation in gene expression among the breast tumors is directly attributable to underlying variation in gene copy number. These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set, arrayCGH
 
Overall design Using regression correlation
Web link http://genome-www.stanford.edu/aCGH_breast/
 
Contributor(s) Perou C, Pollack J
Citation(s) 12297621
Submission date Sep 09, 2005
Last update date Mar 16, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (2)
GPL180 SVC
GPL2830 SVI
Samples (100)
GSM1844 BC402B-BE
GSM1845 BC709B-BE
GSM1846 BC107B-BE
Relations
BioProject PRJNA92939

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Supplementary data files not provided

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