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Series GSE21349 Query DataSets for GSE21349
Status Public on Oct 18, 2010
Title A compendium of myeloma associated chromosomal copy number abnormalities and their prognostic value
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Expression profiling by array
Summary To obtain a comprehensive genomic profile of presenting multiple myeloma cases we performed high resolution single nucleotide polymorphism (SNP) mapping array analysis in 114 samples alongside 258 samples analysed by U133 Plus 2.0 expression array (Affymetrix). We examined DNA copy number alterations and loss of heterozygosity (LOH) in order to define the spectrum of minimally deleted regions in which relevant genes of interest can be found. The most frequent deletions are located at 1p (30%), 6q (33%), 8q (25%), 12 (22%), 13q (59%), 14q (39%), 16q (35%), 17p (7%), 20 (12%) and 22 (18%). In addition, copy number-neutral LOH, or uniparental disomy, was also prevalent on 1q (8%), 16q (9%), and X (20%), and was associated with regions of gain and loss. Based on fluorescent in situ hybridisation (FISH) and expression quartile analysis, genes of prognostic importance were found to be located at 1p (FAF1, CDKN2C), 1q (ANP32E), and 17p (TP53). In addition, we identified common homozygously deleted genes which have functions relevant to myeloma biology. Taken together, the dysregulated genes from the myeloma genome indicate that the crucial pathways in myeloma pathogenesis include the NF-?B pathway, apoptosis, cell-cycle regulation and Wnt signalling.
 
Overall design SNP data: 114 tumour samples (MM) analyzed by Affymetrix 500K array set (Nsp+Sty), of which 80 samples have matched peripheral blood (PB) (non-tumour) DNA performed on the same array types. Matched tumour and non-tumour samples have the same ID number, e.g. MM400 and PB400

Expression data: 258 expression samples from CD138+ cell selection
 
Contributor(s) Walker BA, Morgan GJ
Citation(s) 20944071, 20616218, 22573403, 30602759, 30854481, 30213928, 27363682
Submission date Apr 15, 2010
Last update date Jul 18, 2019
Contact name Brian A Walker
E-mail(s) brian.walker@icr.ac.uk
Organization name The Institute of Cancer Research
Department Haemato-Oncology Research Unit
Lab Molecular Haematology Team
Street address 15 Cotswold Road
City Sutton
ZIP/Postal code SM2 5NG
Country United Kingdom
 
Platforms (3)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (491)
GSM392759 CD138_selected_plasma_cells_presentation_MM001
GSM392760 CD138_selected_plasma_cells_presentation_MM002
GSM392761 CD138_selected_plasma_cells_presentation_MM003
Relations
BioProject PRJNA126129

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
GSE21349_RAW.tar 8.6 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
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