NDLI: Comparison of snap freezing versus ethanol fixation for gene expression profiling of tissue specimens.

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Year: 2004 Volume: 6 Issue: 3

Year: 2004 Volume: 6 Issue: 2

Year: 2004 Volume: 6 Issue: 1

Comparison of snap freezing versus ethanol fixation for gene expression profiling of tissue specimens.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Perlmutter, Mark A. Best, Carolyn J. M. Gillespie, John W. Gathright, Yvonne González, Sergio Velasco, Alfredo Linehan, W. Marston Emmert-Buck, Michael R. Chuaqui, Rodrigo F.
Description	Country affiliation: United States Author Affiliation: Perlmutter MA ( Pathogenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.)
Abstract	Frozen tissue specimens are the gold standard for molecular analysis. However, snap freezing presents several challenges regarding collection and storage of tissue, and preservation of histological detail. We evaluate an alternative preservation method, ethanol fixation followed by paraffin embedding, by analyzing expression profiles of microdissected cells on Affymetrix oligonucleotide arrays of three matched benign prostatic hyperplasia (BPH) and tumor samples processed with each preservation method. Frozen samples generated an average present call of 26% of the probe sets, compared to 4.5% in ethanol-paraffin samples. Eighty-eight percent of the probe sets called present in the ethanol-paraffin samples were also present in the frozen specimens. Comparing ethanol-paraffin BPH to tumor, 52 probe sets showed a twofold differential expression or higher in at least two cases, 23 of which were also differentially expressed in at least one frozen case. Despite a significant drop in the number of transcripts detectable, the data suggests that the obtainable information in ethanol-fixed samples may be useful for molecular profiling where frozen tissue is not available. However, ethanol fixation and paraffin embedding of tissue specimens is not optimal for high-throughput mRNA expression analysis. Improved methods for transcript profiling of archival samples, and/or tissue processing are still required.
File Format	HTM / HTML
ISSN	15251578
e-ISSN	19437811
Journal	The Journal of Molecular Diagnostics
Issue Number	4
Volume Number	6
Language	English
Publisher	Elsevier
Publisher Date	2004-11-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Molecular Biology Ethanol Pharmacology Gene Expression Regulation Prostate Pathology Prostatic Hyperplasia Specimen Handling Tissue Fixation Fixatives Freezing Gene Expression Profiling Genome, Human Lasers Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Paraffin Chemistry Paraffin Embedding Metabolism Rna, Messenger Rna, Neoplasm
Content Type	Text
Resource Type	Article
Subject	Molecular Medicine Pathology and Forensic Medicine

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