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Series GSE23418 Query DataSets for GSE23418
Status Public on Jun 13, 2011
Title Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers
Organism Homo sapiens
Experiment type Genome variation profiling by array
Genome variation profiling by genome tiling array
Summary Purpose: Small bowel adenocarcinoma (SBA) is a rare cancer and consequently the number of clinical trials has been very limited due to the small numbers of patients. Chemotherapy regimens are currently rather arbitrarily chosen between either a colorectal (CRC) or a gastric cancer (GC) regimen. Chromosomal copy number aberrations are a hallmark of solid tumours and can be measured by array comparative genomic hybridization (aCGH). The aim of the present study is to investigate whether genome-wide copy number aberrations of SBA are more similar to CRC or GC in order to support treatment of SBA according to either regimen. Experimental Design: A total of 85 GCs, CRCs and SBAs were selected from existing in house aCGH datasets based on array quality and clinical parameters. Differences and similarities in gains and losses of the three tumor types were analyzed using supervised and unsupervised analysis. Results: Hierarchical clustering revealed substantial overlap of chromosomal copy number profiles between SBA and CRC and less overlap between SBA and GC. Chromosome 13q13.2-q31.3 is primarily gained in SBA and CRC and the strongest feature discriminating SBA from GC. Further strong discriminating copy number characteristics are aberrations at chromosomes 1p36.3-p34.3, 4p15.3-q35.2, 9p24.3-p11.1 and 17p13.3-p13.2. Conclusions: SBA is more similar to CRC than to GC, based on genome-wide copy number aberrations. These data provide molecular support for treatment of SBA according to a CRC regimen.
Overall design 29 gastric adenocarcinomas on 5K or 6K BAC arrays of which 2 samples are also done on 30K oligonucleotide arrays as control samples, 29 colorectal adenocarcinomas on 5K or 6K BAC arrays of which 2 samples are also done on 30K oligonucleotide arrays as control, 27 small bowel adenocarcinomas done on 30K oligonucleotide arrays of which 2 samples are also done on 5K BAC arrays as control.
Contributor(s) Haan JC, Buffart TE, Eijk PP, van de Wiel MA, Howdle P, Mulder CC, vandeVelde CJ, Quirke P, Nagtegaal ID, vanGrieken NC, Grabsch H, Meijer GA, Ylstra B
Citation(s) 21586687
Submission date Aug 04, 2010
Last update date Apr 24, 2013
Contact name Daoud Sie
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 (11)
GPL2826 VUMC MACF human 30K oligo v31
GPL2827 VUMC MACF human 30K oligo v44
GPL2842 VUMC MACF human 5K BAC v22
Samples (91)
GSM115212 Carcinoma VUMC_C012_b31_s72
GSM197326 Carcinoma component of a progressed adenoma (P25C_s22_b17)
GSM197642 Carcinoma component of a progressed adenoma (P24C_s21_b17)
BioProject PRJNA131089

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
GSE23418_RAW.tar 47.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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