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Series GSE7376 Query DataSets for GSE7376
Status Public on Oct 23, 2007
Title Detection of novel amplification units in prostate cancer
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Genome-wide screening for regions of genetic gains and losses on nine prostate cancer cell lines (PC3, DU145, LNCaP, CWR22, and derived sublines) was carried out using comparative genomic hybridization on a 35 K longmer oligonucleotide microarray (arrayCGH). Compared to conventional chromosomal CGH more deletions and small regions of gains, particularly in pericentromeric regions and regions next to the telomers, were detected. As a proof for the high-resolution of arrayCGH we further analyzed a small amplification unit of 1.7 MB at 9p13.3, which was found in CWR22 and CWR22-Rv1. Increased copy number was confirmed by fluorescence in situ hybridization using the BAC clone RP11-165H19 from the amplified region comprising the two genes interleukin 11 receptor alpha (IL11-RA) and dynactin 3 (DCTN3). Using quantitative real time PCR (qPCR) we could demonstrate that IL11-RA is the gene with the highest copy number gain in the cell lines compared to DCTN3 suggesting IL11-RA to be the amplification target. Screening of 20 primary prostate carcinomas by qPCR revealed a high frequency of IL11-RA copy number gain in 75% of the tumors analyzed. Gain of DCTN3 was only found in two cases together with a gain of IL11-RA. Thus, IL11-RA is a frequently amplified gene in prostate cancer with amplification being supposed to be one mechanism of IL11-RA overexpression in this tumor type.
Keywords: comparative genomic hybridization
 
Overall design whole genome array comparative genomic hybridization
 
Contributor(s) Kamradt J, Jung V, Wahrheit K, Tolosi L, Rahnenfuhrer J, Rubie C, Walker R, Davis S, Stoeckle M, Meltzer P, Wullich B
Citation(s) 17712417
Submission date Mar 27, 2007
Last update date Mar 17, 2012
Contact name Sean Davis
E-mail(s) sdavis2@mail.nih.gov
Phone 301-435-2652
Organization name National Cancer Institute
Lab Genetics Branch
Street address 37 Convent Drive, Room 6138
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL5046 nhgri_qiagenv3_cgh
Samples (11)
GSM177474 HV3-20-53CGH
GSM177475 HV3-20-58CGH
GSM177476 HV3-20-59CGH
Relations
BioProject PRJNA100409

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
GSE7376_RAW.tar 30.1 Mb (http)(custom) TAR (of TXT)

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