Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 101
Release date: Jan 1 2008
Last update date: Aug 10 2018
Access: Public
Dataset link Diagnosis of Acute Lung Rejection by Gene Expression Profiling of Bronchoalveolar Lavage Cells

Experimental Protocol


Lung transplant recipients surviving at least 30 days after transplantation at the University of Minnesota were eligible for enrollment in the study. The study was approved by the University’s Institutional Review Board, and all patients provided written informed consent. Subjects underwent scheduled surveillance (n = 22) and clinically indicated (decreased pulmonary function tests or new radiographic abnormalities) bronchoscopies (n = 10), in which 100-200 cc of sterile saline was instilled into a single anatomic location (right middle lobe or lingula), and recovered using gentle suction. 4-6 transbronchial biopsies (TBB) were obtained from the same subsegmental location as the BAL, and 4-6 additional TBB were obtained from the lower lobe of the same lung. After sending samples for clinical tests, approximately 50 ml of the recovered BAL effluent was immediately placed on ice. BAL cell counts and differentials were determined with a hemocytometer. Specimens from subjects with active bronchopulmonary infections (as determined by history, exam, chest radiograph, and the results of routine laboratory tests and cultures) were excluded from analysis. All biopsy specimens were graded according to standard International Society for Heart and Lung Transplantation criteria8. Vascular and airway cellular infiltrate were scored separately on A (vascular) and B (airway) scales, each score ranging from 0 to 48;23;24. For the purposes of this analysis, acute rejection was defined as a combined A+B score greater than or equal to 2; and no-rejection was defined as a combined A+B score less than 2. The BAL samples used in this study were selected according to strict criteria that were designed to maximize potential differences in gene expression between acute rejection and non-acute rejection BAL samples; and to minimize bias from confounding factors. Each subject (n=32) was represented by one BAL sample in this study. Control subjects and samples (n=14) were selected according to the following criteria: 1) A+B score was 0 or 1 for all biopsies collected from each subject during his/her post-transplant course; 2) at least three biopsies had been graded from each subject; 3) the subject had survived at least one year post-transplant; 4) the selected BAL sample was culture negative for pathogenic bacteria, fungi, and viruses; and 5) the selected sample was from a patient that had not developed BOS or was collected at least 6 months prior to the development of BOS. Rejection subjects and samples (n=18) were selected according to the following criteria: 1) the BAL sample was culture negative for pathogenic bacteria, fungi, and viruses; 2) for subjects with more than one acute rejection sample, we used the first acute rejection sample (A+B score > 1); 3) BOS grade was 0 at the time of BAL sampling (although some subjects subsequently developed BOS).

Repositories


GEO

GSE6095

ArrayExpress

E-GEOD-6095

BioProject

PRJNA97655

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Contact


Jeff Lande