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Series GSE26389 Query DataSets for GSE26389
Status Public on May 10, 2012
Title Losses of chromosome 5q and 14q mark a subset of gastric cancers with good clinical outcome
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Purpose: To improve clinical outcome of gastric cancer patients, most emphasis is on improving therapeutic regimens, including more extensive surgery as well as (neo)adjuvant chemotherapy. The present study set out to identify, based on DNA copy number profiling, subgroups of patients with different clinical outcomes who thus would qualify for different therapy intensities. Experimental Design: DNA of 206 gastric cancer patients was isolated and analyzed by genome wide array comparative genomic hybridization. DNA copy number profiles were evaluated and correlated to lymph node status and survival. In addition, HSP90 protein expression was analyzed and correlated to survival in 290 gastric cancer patients. Results: Frequent (>20%) DNA copy number gains were observed on chromosomes 1p, 6p, 7p, 7q, 8q, 11q, 12q, 13q, 16p, 16q, 17q, 19p, 19q, 20p, 20q, 21q and 22q, and losses on chromosomes 4p, 4q, 6p, 6q, 9p, 13q and 21q. Lymph node negative gastric cancers showed significantly more losses on chromosomes 5q11.2-q35.1, 10q11.23-21.3 and 14q32.11-q32.33. In addition, losses on 5q11.2-q31.3 and 14q32.11-q32.33 were highly correlated to good clinical outcome, in both lymph node negative and positive gastric cancer patients. Loss of expression of HSP90, located on chromosome 14q32.2, correlated to good survival time. Conclusion: Genome wide DNA copy number profiling allows to identify a subgroup of gastric cancers, marked by losses on chromosomes 5q11.2-q31.3 and 14q32.11-q32.33 that have an excellent clinical outcome after surgery alone, and patients with these tumors are unlikely to benefit from additional intensified therapies. Possible biological mechanisms could involve loss of heat shock proteins, of which the coding genes are located at these chromosomal regions.
 
Overall design 183 gastric adenocarcinomas
 
Contributor(s) Buffart TE, Carvalho B, van Grieken NC, van Wieringen WN, Tijssen M, Klein Kranenbarg E, Grabsch HI, Ylstra B, van de Velde CJ, Meijer GA
Citation(s) 22531355
Submission date Jan 02, 2011
Last update date May 11, 2012
Contact name Daoud Sie
E-mail(s) [email protected]
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platforms (4)
GPL2842 VUMC MACF human 5K BAC v22
GPL10743 VUMC MACF human 5K BAC v37
GPL11274 VUMC MACF human 5K BAC v47
Samples (183)
GSM647662 Gastric cancer tissue samples (FFPE)_1
GSM647663 Gastric cancer tissue samples (FFPE)_2
GSM647664 Gastric cancer tissue samples (FFPE)_3
Relations
BioProject PRJNA136835

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
GSE26389_RAW.tar 281.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file
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