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Series GSE17047 Query DataSets for GSE17047
Status Public on Apr 19, 2010
Title Candidate driver genes in focal chromosomal aberrations of stage II colon cancer
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Expression profiling by array
Summary Chromosomal instable colorectal cancer is marked by specific large chromosomal copy number aberrations. Recently, focal aberrations of 3Mb or smaller have been identified as a common phenomenon in cancer. Inherent to their limited size, these aberrations harbour one or few genes. The aim of this study is to identify recurrent focal chromosomal aberrations and their candidate driver genes in a well defined series of stage II colon cancers and assess their potential clinical relevance. High resolution DNA copy number profiles were obtained from 38 formalin fixed paraffin embedded colon cancer samples with matched normal mucosa as a reference using array comparative genomic hybridization. In total, 81 focal chromosomal aberrations were identified that harboured 177 genes. Statistical validation of focal aberrations and identification of candidate driver genes was performed by enrichment analysis and mapping copy number and mutation data of colorectal-, breast-, pancreatic cancer and glioblastomas to loci of focal aberrations in stage II colon cancer. This analysis demonstrated a significant overlap with previously identified focal amplifications in colorectal cancer, but not with cancers from other sites. In contrast, focal deletions seem less tumour type specific since they also show significant overlap with focal deletions of other sites. Focal deletions detected are significantly enriched for cancer genes and genes frequently mutated in colorectal cancer. The mRNA expression of these genes is significantly correlated with DNA copy number status, supporting the relevance of focal aberrations. Loss of 5q34 and gain of 13q22.1 were identified as independent prognostic factors of survival in this series of patients. In conclusion, focal chromosomal copy number aberrations in stage II colon cancer are enriched in cancer genes which contribute to and drive the process of colorectal cancer development. DNA copy number status of these genes correlate with mRNA expression and some are associated with clinical outcome.
 
Overall design 38 Stage II colorectal cancer (CRC) tissue samples (FFPE) of which 19 were done on expression arrays.
One sample (Stage II colorectal cancer tissue samples (FFPE) 26) was also done on the 135K NimbleGen array.
Fresh frozen and FFPE of the same CRC stage I sample was done on 105K agilent. The fresh frozen was across array in silico set out against a pool of blood of 18 healthy females.
 
Contributor(s) Brosens RP, Haan JC, Carvalho B, Rustenburg F, Grabsch H, Quirke P, Engel AF, Cuesta MA, Maughan N, Flens M, Meijer GA, Ylstra B
Citation(s) 20593488
Submission date Jul 10, 2009
Last update date Sep 01, 2015
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
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)
GPL6848 Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Probe Name version)
GPL8693 Agilent-019015 HD CGH Microarray (2X105K) Oxford design AMADID#019015 (Feature number version)
GPL8841 Agilent-014950 Human Genome CGH Microarray 4x44K (Probe Name version)
Samples (61)
GSM426557 Stage II colorectal cancer tissue samples (FFPE) 1
GSM426558 Stage II colorectal cancer tissue samples (FFPE) 2
GSM426559 Stage II colorectal cancer tissue samples (FFPE) 4
Relations
BioProject PRJNA117771

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
GSE17047_RAW.tar 861.6 Mb (http)(custom) TAR (of PAIR, TXT)
Processed data included within Sample table
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