title: Comparability of microarray data between amplified and non amplified RNA in colorectal carcinoma.
abstract: 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.
authors.affiliation: Department of Surgery, Friedrich-Alexander University, Erlangen-Nuremberg, Krankenhausstrasse 12, 91054 Erlangen, Germany. roland.croner@uk-erlangen.de
authors.forename: Roland S
authors.initials: RS
authors.lastname: Croner
authors.forename: Berthold
authors.initials: B
authors.lastname: Lausen
authors.forename: Vera
authors.initials: V
authors.lastname: Schellerer
authors.forename: Isabel
authors.initials: I
authors.lastname: Zeittraeger
authors.forename: Axel
authors.initials: A
authors.lastname: Wein
authors.forename: Claus
authors.initials: C
authors.lastname: Schildberg
authors.forename: Thomas
authors.initials: T
authors.lastname: Papadopoulos
authors.forename: Arno
authors.initials: A
authors.lastname: Dimmler
authors.forename: Eckhart G
authors.initials: EG
authors.lastname: Hahn
authors.forename: Werner
authors.initials: W
authors.lastname: Hohenberger
authors.forename: Wolfgang M
authors.initials: WM
authors.lastname: Brueckl
mesh_terms: D002277:Carcinoma / Q000235:genetics / Q000378:metabolism*; D016000:Cluster Analysis; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D042282:Microdissection; D009367:Neoplasm Staging; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012334:RNA, Neoplasm / Q000378:metabolism*; D015203:Reproducibility of Results
chemical_list: D012334:RNA, Neoplasm