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Open Access Highly Accessed Research article

Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples

Maggie L Chow1, Hai-Ri Li2, Mary E Winn34, Craig April5, Cynthia C Barnes1, Anthony Wynshaw-Boris6, Jian-Bing Fan5, Xiang-Dong Fu2*, Eric Courchesne1* and Nicholas J Schork3*

Author affiliations

1 Department of Neuroscience, NIH-UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, 8110 La Jolla Shores Dr Ste 201, La Jolla, CA 92093, USA

2 Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive # 0651, La Jolla, CA 92093, USA

3 Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), The Scripps Research Institute, 3344 North Torrey Pines Court, Room 306, La Jolla, CA 92037, USA

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

5 Illumina, Inc. 9885 Towne Centre Drive, San Diego, CA 92121, USA

6 Division of Medical Genetics, Department of Pediatrics and Institute of Human Genetics, University of California San Francisco, School of Medicine, Box 0794, Core Campus, HSE 901F, San Francisco, CA 94143- 0794, USA

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Citation and License

BMC Genomics 2011, 12:449  doi:10.1186/1471-2164-12-449

Published: 10 September 2011

Abstract

Background

Gene expression assays have been shown to yield high quality genome-wide data from partially degraded RNA samples. However, these methods have not yet been applied to postmortem human brain tissue, despite their potential to overcome poor RNA quality and other technical limitations inherent in many assays. We compared cDNA-mediated annealing, selection, and ligation (DASL)- and in vitro transcription (IVT)-based genome-wide expression profiling assays on RNA samples from artificially degraded reference pools, frozen brain tissue, and formalin-fixed brain tissue.

Results

The DASL-based platform produced expression results of greater reliability than the IVT-based platform in artificially degraded reference brain RNA and RNA from frozen tissue-based samples. Although data associated with a small sample of formalin-fixed RNA samples were poor when obtained from both assays, the DASL-based platform exhibited greater reliability in a subset of probes and samples.

Conclusions

Our results suggest that the DASL-based gene expression-profiling platform may confer some advantages on mRNA assays of the brain over traditional IVT-based methods. We ultimately consider the implications of these results on investigations of neuropsychiatric disorders.

Keywords:
Brain; Gene Expression; DASL; IVT