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Series GSE15695 Query DataSets for GSE15695
Status Public on Mar 22, 2010
Title Comprehensive Homozygous Deletion Mapping of Myeloma Defines a Poor Prognosis Cell Death Gene Expression Signature
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Myeloma is a clonal malignancy of plasma cells. Poor prognosis risk is currently identified by clinical and cytogenetic features. However, these indicators do not capture all prognostic information. Gene expression analysis can be used to identify poor prognosis patients and this can be improved by combination with information about DNA level changes. Using SNP-based gene mapping in combination with global gene expression analysis we have identified homozygous deletions in genes and networks that are relevant to myeloma. From these, we have generated an expression-based signature associated with shorter survival in 247 patients and confirmed this signature in data from 2 independent groups totalling 800 patients. We identified 170 genes with homozygous deletions and corresponding loss of expression. Deletion within the “Cell Death” network was over-represented and cases with these deletions have impaired overall survival. We defined a gene expression signature of 97 cell death genes that reflects prognosis confirmed this in two independent data sets. We developed a simple 6-gene expression signature from the 97-gene signature that can be used to identify poor prognosis myeloma in the clinical environment. The signature can form the basis of future trials aimed at improving the outcome of poor prognosis myeloma.
 
Overall design 247 expression samples from CD138+ cell selection, 168 SNP-based gene mapping data from CD138+ cell selection and peripheral white blood cell
 
Contributor(s) Dickens NJ, Walker BA, Morgan GJ
Citation(s) 20215539, 21994415, 21856767, 30602759, 30854481, 30213928, 27363682, 26056083
Submission date Apr 16, 2009
Last update date Oct 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 (583)
GSM392759 CD138_selected_plasma_cells_presentation_MM001
GSM392760 CD138_selected_plasma_cells_presentation_MM002
GSM392761 CD138_selected_plasma_cells_presentation_MM003
Relations
BioProject PRJNA116645

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
GSE15695_RAW.tar 11.8 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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