Gene expression profiling of blood is a valuable tool for diagnostics in a wide range of diseases, particularly those involving the immune system and cancer. Before peripheral blood or cell lines can be used in large cohorts to characterise differences between a patient group and healthy controls, it is important to understand the underlying biological and technical factors that contribute to the gene expression measurements. Our results give insight into the variability and characterisation of biological differences between post venipuncture methods including LCLs, purified B-cells (CD19 and CD20), PBMCs and whole blood samples for global gene expression profiling. The number of expressed genes as well the gene expression measurements differ significantly between different isolation techniques. Although the PAXgene system is suitable for large-scale gene expression profiling, particularly in large epidemiological and biobank studies where immediate sample processing is not always practical, the PAX samples showed a decrease in the number of expressed genes and lower gene expression values with higher variability compared to the PBMCs. Although whole blood samples contain more cell populations with different relative proportions than PBMCs, expression
