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Series GSE7946 Query DataSets for GSE7946
Status Public on May 30, 2007
Title SNP array analysis of chromosomal instability patterns discriminates rectal adenomas from carcinomas
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Total mesorectal excision (TME) is the standard treatment for rectal cancer, while transanal endoscopic microsurgery (TEM) is a recently introduced surgical approach for the treatment of rectal adenomas. Incorrect preoperative staging before TEM is a problem. To identify genetic changes that might correlate with tumour stage and could lead to optimized treatment selection we performed a genome-wide chromosomal instability search in a homogeneous, clinical cohort of rectal tumours. 78 rectal tumours during different clinical stages were analysed with 10K single nucleotide polymorphism (SNP) arrays. Logistic regression was performed to build a quantitative model of specific chromosomal aberrations. Overall, most cases (95%) had one or more chromosomal aberrations. We observed a clear correlation between the total number of aberrations and the different tumour stages. Specifically, the chromosomal events: gain of 8q22–24, 13q and 20q, and loss of 17p and 18q12–22, were far more abundant in carcinoma than in adenoma. In adenoma fractions from cases with a carcinoma (infiltrating at least in the submucosa), twice the amount of such ‘malignant aberrations’ was observed, compared to pure adenomas. Furthermore, combined aberrations such as gain of 13q and loss of 18q were only found in adenomatous fractions of carcinomas and not in benign lesions. Based on these five genomic events associated with carcinoma, a clear distinction between adenoma and carcinoma tissue could be made. These data should be validated further in order that they may be used in preoperative staging of rectal tumours.
Keywords: SNP array copy number and LOH study
 
Overall design 78 tumor samples and 19 reference normal samples
 
Contributor(s) Lips EH, de Graaf EJ, Tollenaar RA, van Eijk R, Szuhai K, Karsten T, Nanya Y, Ogawa S, van de Velde CJ, Eilers PH, van Wezel T, Morreau H
Citation(s) 17471469, 18959792
Submission date May 29, 2007
Last update date Mar 17, 2012
Contact name Esther Lips
E-mail(s) e.lips@nki.nl
Phone +31-20-5122039
Organization name NKI-AVL
Department Molecular Pathology
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
 
Platforms (2)
GPL1266 [Mapping10K_Xba131] Affymetrix Human Mapping 10K SNP Array
GPL2641 [Mapping10K_Xba142] Affymetrix Human Mapping 10K 2.0 Array
Samples (97)
GSM194951 Frozen rectal tumor sample (A137)
GSM194952 Frozen rectal tumor sample (A138)
GSM194953 Frozen rectal tumor sample (A140)
Relations
BioProject PRJNA100123

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
GSE7946_RAW.tar 184.7 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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