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Open Access Research article

Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay

Mary E Winn12, Marian Shaw23, Craig April5, Brandy Klotzle5, Jian-Bing Fan5, Sarah S Murray234 and Nicholas J Schork234*

Author affiliations

1 Graduate Program in Biomedical Sciences, Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA

2 Scripps Genomic Medicine and Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA

3 Scripps Health, La Jolla, CA 92037, USA

4 Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA

5 Illumina Inc., San Diego, CA 92121, USA

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Citation and License

BMC Genomics 2011, 12:412  doi:10.1186/1471-2164-12-412

Published: 15 August 2011

Abstract

Background

Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such an analysis are often plagued by decreased sensitivity and reliability due to the effects of relatively high levels of globin mRNA in whole blood. Globin reduction assays have been shown to overcome such effects, but they require large amounts of total RNA and may induce distinct gene expression profiles. The Illumina whole genome DASL assay can detect gene expression levels using partially degraded RNA samples and has the potential to detect rare transcripts present in highly heterogeneous whole blood samples without the need for globin reduction. We assessed the utility of the whole genome DASL assay in an analysis of peripheral whole blood gene expression profiles.

Results

We find that gene expression detection is significantly increased with the use of whole genome DASL compared to the standard IVT-based direct hybridization. Additionally, globin-probe negative whole genome DASL did not exhibit significant improvements over globin-probe positive whole genome DASL. Globin reduction further increases the detection sensitivity and reliability of both whole genome DASL and IVT-based direct hybridization with little effect on raw intensity correlations. Raw intensity correlations between total RNA and globin reduced RNA were 0.955 for IVT-based direct hybridization and 0.979 for whole genome DASL.

Conclusions

Overall, the detection sensitivity of the whole genome DASL assay is higher than the IVT-based direct hybridization assay, with or without globin reduction, and should be considered in conjunction with globin reduction methods for future blood-based gene expression studies.