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Comparability of Microarray Data between Amplified and Non Amplified RNA in Colorectal Carcinoma

Croner, RS and Lausen, B and Schellerer, V and Zeittraeger, I and Wein, A and Schildberg, C and Papadopoulos, T and Dimmler, A and Hahn, EG and Hohenberger, W and Brueckl, WM (2009) 'Comparability of Microarray Data between Amplified and Non Amplified RNA in Colorectal Carcinoma.' Journal of Biomedicine and Biotechnology, 2009 (837170). pp. 1-9. ISSN 1110-7243


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Microarray analysis reaches increasing popularity during the investigation of prognostic gene clusters in oncology. The standardisation of technical procedures will be essential to compare various datasets produced by different research groups. In several projects the amount of available tissue is limited. In such cases the preamplification of RNA might be necessary prior to microarray hybridisation. To evaluate the comparability of microarray results generated either by amplified or non amplified RNA we isolated RNA from colorectal cancer samples (stage UICC IV) following tumour tissue enrichment by macroscopic manual dissection (CMD). One part of the RNA was directly labelled and hybridised to GeneChips (HG-U133A, Affymetrix), the other part of the RNA was amplified according to the ?Eberwine? protocol and was then hybridised to the microarrays. During unsupervised hierarchical clustering the samples were divided in groups regarding the RNA pre-treatment and 5.726 differentially expressed genes were identified. Using independent microarray data of 31 amplified vs. 24 non amplified RNA samples from colon carcinomas (stage UICC III) in a set of 50 predictive genes we validated the amplification bias. In conclusion microarray data resulting from different pre-processing regarding RNA pre-amplification can not be compared within one analysis.

Item Type: Article
Uncontrolled Keywords: Humans; Carcinoma; Colorectal Neoplasms; RNA, Neoplasm; Neoplasm Staging; Microdissection; Oligonucleotide Array Sequence Analysis; Cluster Analysis; Reproducibility of Results; Gene Expression Profiling; Nucleic Acid Amplification Techniques; Nucleic Acid Hybridization
Subjects: Q Science > QA Mathematics
R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer)
Divisions: Faculty of Science and Health
Faculty of Science and Health > Mathematical Sciences, Department of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 12 Dec 2011 11:03
Last Modified: 06 Jan 2022 13:24

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