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Series GSE8067 Query DataSets for GSE8067
Status Public on Oct 15, 2008
Title Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by genome tiling array
Summary Chromosomal instability (CIN) is the hallmark of colorectal adenoma to carcinoma progression in 85% of cases, with 20q gain as the most prominent aberration. Yet, the oncogenes at this chromosomal gain are still largely unknown. Here, we aimed to identify oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on gene expression in this amplicon. Segmentation of DNA copy number changes on 20q was performed by array CGH in 67 colorectal adenomas and carcinomas. Additionally, robust analysis of mRNA expression in these segments was performed in 68 adenomas and carcinomas. This approach revealed seven genes to be important in CIN related adenoma to carcinoma progression. These genes may both serve as highly specific biomarkers for presence of high-risk precursor lesions as well as potential targets for pharmaceutical intervention.
Keywords: Integration of array CGH and expression microarrays in colorectal cancer progression
 
Overall design We performed array CGH on a panel of 41 progressed adenomas, from which the adenoma and carcinoma components were separately analysed (total, 82 samples). The DNA obtained from these samples was extracted from formalin-fixed, paraffin-embedded material. Additionally we analysed a series of independent frozen adenomas and carcinomas by array CGH (34 adenomas and 33 carcinomas) and expression microarrays (37 adenomas and 31 carcinomas).
For array-CGH we used as reference DNA for all samples, a pool of 10 normal individuals. For expression microarrays we used as reference a commercial available RNA (pool of different cancer cell lines), from Strategene. No replicates nor dye swaps were done.
 
Contributor(s) Carvalho B, Postma C, Mongera S, Hopmans E, Diskin S, van de Wiel MA, van Criekinge W, Thas O, Matthäi A, Cuesta MA, Terhaar J, Craanen M, Schröck E, Ylstra B, Meijer GA
Citation(s) 18829976, 20089989, 22278361, 19672269, 20358421, 26148070
Submission date Jun 08, 2007
Last update date Apr 07, 2020
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 (5)
GPL2843 VUMC MACF human 6K BAC v45
GPL3055 VUMC MACF human 30K oligo v30
GPL3441 VUMC MACF human 5K BAC v12
Samples (217)
GSM197322 Adenoma component of a progressed adenoma (P25A_s23_b17)
GSM197326 Carcinoma component of a progressed adenoma (P25C_s22_b17)
GSM197636 Adenoma component of a progressed adenoma (P26A1_s24_b17)
Relations
BioProject PRJNA100903

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Supplementary data files not provided
Processed data included within Sample table

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