Comment[ArrayExpressAccession] E-GEOD-46449 MAGE-TAB Version 1.1 Public Release Date 2013-06-25 Investigation Title Expression data from Patients with Bipolar (BP) Disorder and Matched Control Subjects Comment[Submitted Name] Expression data from Patients with Bipolar (BP) Disorder and Matched Control Subjects Experiment Description There are currently no biological tests that differentiate patients with bipolar disorder (BPD) from healthy controls. While there is evidence that peripheral gene expression differences between patients and controls can be utilized as biomarkers for psychiatric illness, it is unclear whether current use or residual effects of antipsychotic and mood stabilizer medication drives much of the differential transcription. We therefore tested whether expression changes in first-episode, never-medicated bipolar patients, can contribute to a biological classifier that is less influenced by medication and could potentially form a practicable biomarker assay for BPD. We employed microarray technology to measure global leukocyte gene expression in first-episode (n=3) and currently medicated BPD patients (n=26), and matched healthy controls (n=25). Following an initial feature selection of the microarray data, we developed a cross-validated 10-gene model that was able to correctly predict the diagnostic group of the training sample (26 medicated patients and 12 controls), with 89% sensitivity and 75% specificity (p<0.001). The 10-gene predictor was further explored via testing on an independent test cohort consisting of three pairs of monozygotic twins discordant for BPD, plus the original enrichment sample cohort (the three never-medicated BPD patients and 13 matched control subjects), and a sample of experimental replicates (n=34). 83% of the independent test sample was correctly predicted, with a sensitivity of 67% and specificity of 100% (although this result did not reach statistical significance). Additionally, 88% of sample diagnostic classes were classified correctly for both the enrichment (p=0.015) and the replicate samples (p<0.001). Peripheral blood leukocytes (PBLs) from whole blood were collected from 26 patients with bipolar disorder who had previously received medication, three patients with bipolar disorder who were experiencing their first hospitalization and had not previously received medication, and 25 matched control subjects, for RNA extraction and hybridization on Affymetrix microarrays. Immediately after blood collection, blood samples were split into two (when a sufficient volume had been collected); an "1" and replicate "2" sample (thus two separate RNA extractions, cDNA and cRNA syntheses and array hybridizations were performed). 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 Clelland Clelland Clelland Person First Name Catherine Catherine James Person Mid Initials L D Person Email cc2786@columbia.edu Person Affiliation Columbia University Medical Center Person Address Columbia University Medical Center, 630 West 168th Street, P&S 12-461A, New York, NY, USA Person Roles submitter Protocol Name P-GSE46449-1 P-GSE46449-3 P-GSE46449-4 P-GSE46449-2 P-GSE46449-5 Protocol Description The data were analyzed using BRB-Array Tools versions: 3.8.1 (as described in the manuscript) and 4.2.1 (the processed matrix GEO data). Cell files were imported into the BRBArray Tools package, and converted to normalized intensity values using the Almost RMA (aRMA) algorithm. A total of 199 cel files were imported into the project, including expression data obtained from patients with other psychiatric disorders. Normalized intensity values reflect the a-RMA parameters employed across the entire sample dataset. Analyses were performed on the sub-set of samples relevent to the study hypothesis. Cel files and processed matrix data for those samples are uploaded here. ID_REF = VALUE = log2 a-RMA signal from BRB-Array Tools version: 4.2.1 Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 ug of cRNA was hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, using standard procedures. Total RNA was extracted from leukocytes using the QIAamp RNA Blood Mini Kit (Qiagen), with an off-collumn Dnase (Qiagen) treatment followed by purification using an RNeasy MinElute column (Qiagen). All procedures were performed according to the manufacturer's instructions (Qiagen). GeneChips were scanned using the GeneChip Scanner 3000 with Autoloader Protocol Type normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name GENOTYPE AGE Experimental Factor Type genotype age Comment[SecondaryAccession] GSE46449 Comment[GEOReleaseDate] 2013-06-25 Comment[ArrayExpressSubmissionDate] 2013-04-29 Comment[GEOLastUpdateDate] 2013-06-25 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-46449.sdrf.txt