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Series GSE5051 Query DataSets for GSE5051
Status Public on Aug 29, 2006
Title Cross-Platform Array Comparative Genomic Hybridization (array CGH) Meta-Analysis
Organism Homo sapiens
Experiment type Genome variation profiling by array
Genome variation profiling by genome tiling array
Summary A series of studies have been published that evaluate the chromosomal copy number changes of different tumor classes using array Comparative Genomic Hybridization (array CGH), however the chromosomal aberrations that distinguish the different tumor classes have not been fully characterized. Therefore, we performed a meta-analysis of different array CGH data sets in an attempt to classify samples tested across different platforms. As opposed to RNA expression a common reference is used in dual channel CGH arrays: normal human DNA, theoretically facilitating cross-platform analysis. To this aim, cell line and primary cancer data sets from three
different dual channel array CGH platforms obtained by four different institutes were integrated. The cell line data were used to develop preprocessing methods which performed noise reduction
and transformed samples into a common format. The transformed array CGH profiles allowed perfect clustering by cell line, but importantly not by platform or institute. The same preprocessing
procedures used for the cell line data were applied to data from 373 primary tumors profiled by array CGH, including controls. Results indicated that there is no apparent feature related to the
institute or platform and that array CGH allows for unambiguous cross-platform meta-analysis. Major clusters with common tissue origin were identified. Interestingly, tumors of hematopoietic
and mesenchymal origins cluster separately from tumors of epithelial origin. Therefore it can be concluded that chromosomal aberrations of tumors from hematopoietic and mesenchymal origin versus tumors of epithelial origin are distinct, and these differences can be picked up by metaanalysis of array CGH data. This suggests the possibility of prospectively using combined analysis of diverse copy number datasets for cancer subtype classification.
Keywords: comparative genomic hybridization, meta-analysis, cancer
Overall design 20 cell lines and 140 tumor samples.
Contributor(s) Jong K, Marchiori E, van der Vaart A, Suet-Feung C, Carvalho B, Tijssen M, Eijk P, van den IJssel P, Grabsch H, Quirke P, Oudejans JJ, Meijer GA, Caldas C, Ylstra B
Citation(s) 16936777
Submission date Jun 12, 2006
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 (8)
GPL28 HumArray 1.14
GPL2819 VUMC MACF human 30K oligo v42
GPL2826 VUMC MACF human 30K oligo v31
Samples (167)
GSM73557 BT474 (ATCC nr. HTB-20) Breast tumor cell line BT474_b42_s56
GSM75169 MDA-MB-468 (ATCC nr. HTB-137) Breast tumor cell line MDA468_b41_s07
GSM75170 SUM159 epithelial Breast tumor cell line SUM159_b36_s50
BioProject PRJNA96691

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