Comment[ArrayExpressAccession]	E-GEOD-57317
MAGE-TAB Version	1.1				
Public Release Date	2015-01-20
Investigation Title	Gene expression profiles of patients with multiple myeloma who have been treated previously				
Comment[Submitted Name]	Gene expression profiles of patients with multiple myeloma who have been treated previously
Experiment Description	This Series represents the gene expression profiles of patients with multiple myeloma who have been treated previously. In brief, Total Therapy 6 (TT6) is an open label phase 2 protocol for patients with symptomatic multiple myeloma, who had been treated with more than one cycle of prior therapy excluding autologous hematopoietic stem cell transplant. This protocol was approved by the institutional review board on March 25, 2009 (IRB#108053). The TT6 treatment regimen consists of induction therapy  with Melphalan/Bortezomib/Thalidomide/Dexamethasone/Cisplatin/Doxorubicin/Cyclophosphamide/Etoposide (M-VTD-PACE) followed by a  high dose M-VTD-PACE based tandem transplant. Maintenance therapy consists of Bortezomib/Lenalidomide/Dexamethasone alternating with Borteomib/Melphalan/Dexamethasone every months for 3 years. We analyzed CD138+ selected cells of previously treated MM patients by microarray.				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Heuck	Heuck			
Person First Name	Christoph	Christoph			
Person Mid Initials	J				
Person Email	cjheuck@uams.edu				
Person Affiliation	University of Arkansas for Medical Sciences				
Person Address	Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, 4301 W Markham, Little Rock, AR, USA				
Person Roles	submitter				
Protocol Name	P-GSE57317-1	P-GSE57317-3	P-GSE57317-4	P-GSE57317-2	P-GSE57317-5
Protocol Description	Data are processed using the 'affy' Bioconductor library packages for R. ID_REF =  VALUE = Data shown are normalized using the MAS5 algorithm.	Samples were labels using the Affymetrix 3' IVT Express kit, according to the manufacturer's instructions.	Samples were hybridized, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain kit (P/N 900720) according to the manufacturer's recommendations.	Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA).	Chips were scanned using the HG-U133 Plus 2.0 v2.2 on an Affymetrix Autoloader 3000DX scanner.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	molecular subgroup	os censored	gep70 score	OS time	
Experimental Factor Type	molecular subgroup	os censored	gep70 score	OS time	
Publication Title	Five gene probes carry most of the discriminatory power of the 70-gene risk model in multiple myeloma.				
Publication Author List	Heuck CJ, Qu P, van Rhee F, Waheed S, Usmani SZ, Epstein J, Zhang Q, Edmondson R, Hoering A, Crowley J, Barlogie B				
PubMed ID	25079174				
Publication DOI	10.1038/leu.2014.232				
Comment[SecondaryAccession]	GSE57317				
Comment[GEOReleaseDate]	2015-01-20				
Comment[ArrayExpressSubmissionDate]	2014-05-05				
Comment[GEOLastUpdateDate]	2015-01-20				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-57317.sdrf.txt