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Series GSE14655 Query DataSets for GSE14655
Status Public on May 25, 2010
Title Indices of Tolerance (IOT): Cross-platform biomarkers that identify kidney transplant tolerance
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Being able to identify patients in whom immunological tolerance has been established or is developing would allow an individually tailored approach to post-transplant management of kidney allograft recipients. Ex vivo immunological monitoring was performed on samples from five groups of European renal transplant recipients (“IOT samples”): ten drug-free tolerant recipients who were functionally stable despite remaining immunosuppression-free for more than one year (Tol-DF); also functionally stable patients on minimal immunosuppression (<10 mg/day prednisone, s-LP); stable patients maintained with calcineurin inhibitors (s-CNI); stable patients maintained on CNI-free immunosuppression regimen (s-nCNI); patients showing signs of chronic rejection (CR) and healthy controls (HC). Among the investigation of other biomarkers and bioassays, gene expression profiles were generated on custom Agilent 8x15K 60mer oligonucleotide microarrays (“RISET 2.0”) on the IOT cohort (training set) and on an independent cohort of patients from the ITN (USA) that contained similar groups of patients and included 23 tolerant recipients (“ITN samples”, test set). Set of genes were identified, whose expression on whole blood allowed the identification of 100% of the tolerant recipients in the training set and 84% in the test set.

Keywords: classification of clinical samples, tolerance prediction
 
Overall design IOT samples: 13 samples from 10 Tol-DF patients, 16 samples from 11 s-LP patients, 8 samples from 8 s-nCNI patients, 40 samples from 28 s-CNI patients, 10 samples from 9 CR patients, and 8 samples from 8 HC donors were analysed on a custom Agilent 8x15K 60mer oligonucleotide microarray encomprising 5069 probes in triplicates. The microarray is dedicated to transplantation research and was designed based on current literature and published and unpublished data provided by the RISET consortium. For the probe selection procedure we specially focused on the detection of multiple transcript variants of a gene, on optimized hybridization properties of the probes, and on the avoidance of crosshybridization. The sampling dates of replicate samples from the same patient range from one day to 1.5 years. ITN samples: 31 samples from 23 Tol-DF patients, 14 samples from 11 s-LP patients, 52 samples from 34 s-CNI patients, 25 samples from 18 CR patients, and 20 samples from 20 HC donors were analysed on the same microarray platform and served as test set. The samples of the two cohorts differ in the protocol of RNA preparation.
 
Contributor(s) Tomiuk S, Janssen U, Hernandez-Fuentes MP, Sawitzki B, Sagoo P, Perucha E, Stephens DA, Miqueu P, Chapman S, Craciun L, Sergeant R, Brouard S, Rovis F, Jimenez E, Ballow A, Giral M, Le Moine A, Braudeau C, Hilton R, Peters B, Bourcier K, Sharif A, Krajewska M, Lord G, Roberts I, Goldman M, Wood KJ, Newel K, Seyfert-Margolis V, Turka L, Warrens AN, Volk H, Soulillou J, Lechler RI
Citation(s) 20501943
Submission date Jan 30, 2009
Last update date Aug 08, 2013
Contact name Stefan Tomiuk
E-mail(s) stefant@miltenyibiotec.de
Organization name Miltenyi Biotec GmbH
Department Bioinformatics
Street address Friedrich-Ebert-Str. 68
City Bergisch-Gladbach
ZIP/Postal code 51429
Country Germany
 
Platforms (1)
GPL8136 Agilent RISET 2.0 8x15K 60mer oligonucleotide microarray
Samples (237)
GSM365615 sample of patient EU3.002
GSM365616 sample of patient EU3.003
GSM365617 sample of patient EU3.004
Relations
BioProject PRJNA112341

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
GSE14655_RAW.tar 667.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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