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Series GSE21034 Query DataSets for GSE21034
Status Public on Jun 24, 2010
Title Whole-transcript and exon-level expression data for human primary and metastatic prostate cancer samples and control normal adjacent benign prostate
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Current knowledge of prostate cancer genomes is largely based on relatively small patient cohorts using single modality analysis platforms. Here we report concordant assessment of DNA copy number, mRNA and microRNA expression and focused exon resequencing in prostate tumors from 218 patients with primary or metastatic prostate cancer with a median of 5 years clinical follow-up, now made available as a public resource. Mutations in known, commonly mutated oncogenes and tumor suppressor genes such as PIK3CA, KRAS, BRAF and TP53 are present but generally rare. However, integrative analysis of mutations with copy number alterations (CNAs) and expression changes reveal alterations in the PI3K, RAS/RAF and androgen receptor (AR) pathways in nearly all metastatic samples and in a higher frequency of primary samples than previously suspected based on single-gene studies. Other new findings include evidence that the nuclear receptor coactivator NCOA2 functions as a driver oncogene in ~20 percent of primaries. Tumors with the androgen-driven TMPRSS2-ERG fusion were significantly associated with a small, previously unrecognized, prostate-specific 3p14 deletion that, through mRNA expression and resequencing analysis, implicates FOXP1, RYBP and SHQ1 as candidate cooperative tumor suppressors. Comparison of transcriptome and DNA copy number data from primary tumors for prognostic impact revealed that CNAs robustly define clusters of low- and high-risk disease beyond that achieved by Gleason score. In sum, this integrative genomic analysis of a substantial cohort of tumors clarifies the role of several known cancer pathways in prostate cancer, implicates several new ones, reveals a previously unappreciated role for CNAs in prognosis and provides a blueprint for clinical development of pathway inhibitors.
Overall design Human prostate samples were profiled on Affymetrix Human Exon 1.0 ST arrays per manufacturer's instructions.
Contributor(s) Taylor BS, Schultz N, Hieronymus H, Sawyers CL
Citation(s) 20579941
Submission date Mar 23, 2010
Last update date Jul 10, 2014
Contact name Barry Stephen Taylor
Organization name Memorial Sloan-Kettering Cancer Center
Street address 1275 York Avenue, Box #460
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (2)
GPL5188 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]
GPL10264 Affymetrix Human Exon 1.0 ST Array [CDF: HuEx_1_0_st_v2_main_A20071112_EP.cdf]
Samples (370)
GSM526134 Prostate tumor PCA0001 exon
GSM526135 Prostate tumor PCA0002 exon
GSM526136 Prostate tumor PCA0003 exon
This SubSeries is part of SuperSeries:
GSE21032 Integrative genomic profiling of human prostate cancer
BioProject PRJNA129695

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21034_RAW.tar 9.0 Gb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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