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Peripheral blood gene expression profiles in COPD subjects

Bhattacharya, S and Tyagi, S and Srisuma, S and DeMeo, DL and Shapiro, SD and Bueno, R and Silverman, EK and Reilly, JJ and Mariani, TJ (2011) Peripheral blood gene expression profiles in COPD subjects. Journal of Clinical Bioinformatics, 1 (1).

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Abstract

To identify non-invasive gene expression markers for chronic obstructive pulmonary disease (COPD), we performed genome-wide expression profiling of peripheral blood samples from 12 subjects with significant airflow obstruction and an equal number of non-obstructed controls. RNA was isolated from Peripheral Blood Mononuclear Cells (PBMCs) and gene expression was assessed using Affymetrix U133 Plus 2.0 arrays.Tests for gene expression changes that discriminate between COPD cases (FEV < 70% predicted, FEV /FVC < 0.7) and controls (FEV > 80% predicted, FEV /FVC > 0.7) were performed using Significance Analysis of Microarrays (SAM) and Bayesian Analysis of Differential Gene Expression (BADGE). Using either test at high stringency (SAM median FDR = 0 or BADGE p < 0.01) we identified differential expression for 45 known genes. Correlation of gene expression with lung function measurements (FEV & FEV /FVC), using both Pearson and Spearman correlation coefficients (p < 0.05), identified a set of 86 genes. A total of 16 markers showed evidence of significant correlation (p < 0.05) with quantitative traits and differential expression between cases and controls. We further compared our peripheral gene expression markers with those we previously identified from lung tissue of the same cohort. Two genes, RP9and NAPE-PLD, were identified as decreased in COPD cases compared to controls in both lung tissue and blood. These results contribute to our understanding of gene expression changes in the peripheral blood of patients with COPD and may provide insight into potential mechanisms involved in the disease. © 2011 Bhattacharya et al; licensee BioMed Central Ltd. 1 1 1 1 1 1


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Bhattacharya, S
Tyagi, S
Srisuma, S
DeMeo, DL
Shapiro, SD
Bueno, R
Silverman, EK
Reilly, JJ
Mariani, TJ
Date: 24 April 2011
Date Type: Publication
Journal or Publication Title: Journal of Clinical Bioinformatics
Volume: 1
Number: 1
DOI or Unique Handle: 10.1186/2043-9113-1-12
Schools and Programs: School of Medicine > Medicine
Refereed: Yes
Date Deposited: 31 Oct 2016 16:29
Last Modified: 30 Mar 2021 15:55
URI: http://d-scholarship.pitt.edu/id/eprint/30073

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