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| Status |
Public on Jul 26, 2011 |
| Title |
Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range ρ = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P<1*10-16) with higher variability (P<1*10-16) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (ρ =0.83; ρ =0.79) between the expression levels of detected probes were much lower compared to the two B-cell isolation methods (ρ =0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs. Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes before application in large clinical studies.
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| Overall design |
In the present study, we investigated variability and consistency in gene expression profiles between five of the most common post venipuncture methods of cell and RNA isolation: whole blood (PAXgene (PAX)), PBMCs, Epstein-Barr virus (EBV) transformed LCLs, CD19-specific B-cells subsets (B-cell CD19), CD20-specific B-cells subsets (B-cell CD20). Using samples from six individuals collected during two visits, we evaluated the differences and concordances of global gene expression profiles, the biological and technical variability seen in these approaches, cell-type specific gene expression signatures and their relevance to large-scale biobanking initiatives.
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| Contributor(s) |
Min JL, Barrett A, Watts T, Pettersson FH, Lockstone HE, Lindgren CM, Taylor JM, Allen M, Zondervan KT, McCarthy MI |
| Citation(s) |
20141636 |
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| Submission date |
Jul 25, 2011 |
| Last update date |
Mar 23, 2012 |
| Contact name |
Josine Min |
| E-mail(s) |
jlmin@well.ox.ac.uk
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| Organization name |
The Wellcome Trust Centre for Human Genetics
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| Street address |
Roosevelt Drive
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| City |
Oxford |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL7350 |
Aalborg University Illumina human-6 v2.0 expression beadchip |
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| Samples (56)
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| Relations |
| BioProject |
PRJNA146313 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE30916_non-normalized.txt.gz |
10.8 Mb |
(ftp)(http) |
TXT |
| GSE30916_normalized.txt.gz |
13.6 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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