title: Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples.
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.
authors: 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.
authors: Maggie L
authors: ML
authors: Chow
authors: Hai-Ri
authors: HR
authors: Li
authors: Mary E
authors: ME
authors: Winn
authors: Craig
authors: C
authors: April
authors: Cynthia C
authors: CC
authors: Barnes
authors: Anthony
authors: A
authors: Wynshaw-Boris
authors: Jian-Bing
authors: JB
authors: Fan
authors: Xiang-Dong
authors: XD
authors: Fu
authors: Eric
authors: E
authors: Courchesne
authors: Nicholas J
authors: NJ
authors: Schork
mesh_terms: D001321:Autistic Disorder / Q000235:genetics; D001921:Brain / Q000378:metabolism*; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D005615:Freezing; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000235:genetics; D020871:RNA Stability; D015203:Reproducibility of Results
chemical_list: D005404:Fixatives; D005557:Formaldehyde; D012313:RNA