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

BMC Genomics

Research Article

Xiang-Dong Fu¹  Hai-Ri Li¹  Maggie L Chow²  Cynthia C Barnes²  Eric Courchesne²  Anthony Wynshaw-Boris³  Craig April⁴  Jian-Bing Fan⁴  Nicholas J Schork⁵  Mary E Winn⁶ 

[1] Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive # 0651, 92093, La Jolla, CA, USA;Department of Neuroscience, NIH-UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, 8110 La Jolla Shores Dr Ste 201, 92093, La Jolla, CA, USA;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, 94143- 0794, San Francisco, CA, USA;Illumina, Inc., 9885 Towne Centre Drive, 92121, San Diego, CA, USA;Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), The Scripps Research Institute, Room 306, 3344 North Torrey Pines Court, 92037, La Jolla, CA, USA;Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), The Scripps Research Institute, Room 306, 3344 North Torrey Pines Court, 92037, La Jolla, CA, USA;Graduate Program in Biomedical Sciences, Department of Medicine, University of California at San Diego, 92093, La Jolla, CA, USA;

关键词: Brain;    Gene Expression;    DASL;    IVT;   

DOI  :  10.1186/1471-2164-12-449

 received in 2011-03-19, accepted in 2011-09-10,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundGene 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.ResultsThe 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.ConclusionsOur 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.

【 授权许可】

Unknown   
© Chow et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.