title: Gene expression analysis of whole blood, peripheral blood mononuclear cells, and lymphoblastoid cell lines from the Framingham Heart Study.
abstract: Despite a growing number of reports of gene expression analysis from blood-derived RNA sources, there have been few systematic comparisons of various RNA sources in transcriptomic analysis or for biomarker discovery in the context of cardiovascular disease (CVD). As a pilot study of the Systems Approach to Biomarker Research (SABRe) in CVD Initiative, this investigation used Affymetrix Exon arrays to characterize gene expression of three blood-derived RNA sources: lymphoblastoid cell lines (LCL), whole blood using PAXgene tubes (PAX), and peripheral blood mononuclear cells (PBMC). Their performance was compared in relation to identifying transcript associations with sex and CVD risk factors, such as age, high-density lipoprotein, and smoking status, and the differential blood cell count. We also identified a set of exons that vary substantially between participants, but consistently in each RNA source. Such exons are thus stable phenotypes of the participant and may potentially become useful fingerprinting biomarkers. In agreement with previous studies, we found that each of the RNA sources is distinct. Unlike PAX and PBMC, LCL gene expression showed little association with the differential blood count. LCL, however, was able to detect two genes related to smoking status. PAX and PBMC identified Y-chromosome probe sets similarly and slightly better than LCL.
authors: The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA.
authors: Roby
authors: R
authors: Joehanes
authors: Andrew D
authors: AD
authors: Johnson
authors: Jennifer J
authors: JJ
authors: Barb
authors: Nalini
authors: N
authors: Raghavachari
authors: Poching
authors: P
authors: Liu
authors: Kimberly A
authors: KA
authors: Woodhouse
authors: Christopher J
authors: CJ
authors: O'Donnell
authors: Peter J
authors: PJ
authors: Munson
authors: Daniel
authors: D
authors: Levy
mesh_terms: D000328:Adult; D015415:Biomarkers / Q000032:analysis / Q000097:blood / Q000378:metabolism; D001769:Blood / Q000378:metabolism*; D002318:Cardiovascular Diseases / Q000097:blood* / Q000175:diagnosis / Q000209:etiology / Q000235:genetics; D002460:Cell Line; D015331:Cohort Studies; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism*; D008214:Lymphocytes / Q000378:metabolism* / Q000473:pathology; D008297:Male; D008404:Massachusetts; D046228:Microarray Analysis; D008875:Middle Aged; D010865:Pilot Projects
chemical_list: D015415:Biomarkers