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| Status |
Public on Jul 11, 2013 |
| Title |
cGvHD vs. non-cGvHD gene expression profiling in peripheral blood |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
We performed peripheral blood gene expression profiling to identify an array of transcriptional biomarkers that discriminate presence of active cGvHD requiring immunosuppression following allogeneic HCT. Peripheral blood mononuclear cells were prepared by Ficoll gradient and cryopreserved from 63 patients (median age 50 yrs; range 19-64) following allogeneic HCT (median 475 days post-HCT) on an IRB approved protocol. Samples were randomly selected into a training set (23 cGvHD and 19 without cGvHD) and test set (12 cGvHD and 9 without cGvHD) and processed on the Aligent whole human genome 44k microarray platform. Bioinformatics programs including AILUN, GeneSpring, SAM, and PAM were used to select a minimum gene-set (FDR <5%) to predict cGvHD in the training set. Patient characteristics in the two groups were collected for confounder/interaction analysis across the following parameters: age, gender, disease histology, disease status at HCT, graft source, conditioning regimen, white blood count (WBC) at sample, and follow-up status including relapse and survival. Type, grade, and activity of acute cGvHD and cGvHD at time of sample and at most recent follow-up were determined by two independent investigators by standard clinical criteria.
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| Overall design |
Three-condition experiment, 35 cGvHD vs. 28 non-cGvHD samples vs. 7 controls (cGvHDnoIS; no immunosuppression drug).
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| Contributor(s) |
Kohrt H, Li L, Heish S, Alizadeh A, Strober S, Sarwal M, Lowsky R |
| Citation(s) |
23685278 |
| Submission date |
Sep 01, 2010 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Li Li |
| E-mail(s) |
li.li@mssm.edu
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| Phone |
6507243765
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| Organization name |
Stanford University
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| Department |
Pediatric
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| Lab |
Sarwal Lab
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| Street address |
300 pastuer dr.,
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL6480 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
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| Samples (70)
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| Relations |
| BioProject |
PRJNA130511 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23924_RAW.tar |
1.0 Gb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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