Tissue handling for genome-wide expression analysis: A review of the issues, evidence, and opportunities

Fabiola Medeiros, C. Ted Rigl, Glenda G. Anderson, Shawn H. Becker, Kevin C. Halling

Research output: Contribution to journalReview articlepeer-review

75 Scopus citations


Context. - Molecular diagnostic applications that use microarrays to analyze large numbers of genes simultaneously require high-quality mRNA. As these genome-wide expression assays become more commonly used in medical practice, pathologists and oncologists will benefit from understanding the importance of obtaining high-quality RNA in order to generate reliable diagnostic and prognostic information, especially as these relate to cancer. Objective. - To review the effects that different tissue preservation techniques have on RNA quality and to provide practical advice on changes in tissue acquisition and handling that may soon be needed for certain clinical situations. Data Sources. - A review of recent literature on RNA quality, tissue fixation, cancer diagnosis, and gene expression analysis. Conclusions. - Studies have consistently shown that frozen tissue yields more intact RNA than formalin-fixed, paraffin-embedded tissue. The chemical modification, cross-linking, and fragmentation caused by formalin fixation often render RNA unsuitable for microarray analysis. Thus, when expression analysis involving hundreds or more than 1000 gene markers is contemplated, pathologists should consider freezing a specimen within half an hour (preferably within minutes) of surgical resection and storing it at -80°C or below. In coming years, pathologists will need to work closely with oncologists and other clinicians to determine when saving frozen tissue for microarray expression analysis is both practical and necessary. In select cases, the benefit of implementing a few extra tissue-handling steps may improve diagnostic and prognostic capability.

Original languageEnglish (US)
Pages (from-to)1805-1816
Number of pages12
JournalArchives of Pathology and Laboratory Medicine
Issue number12
StatePublished - Dec 2007

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Medical Laboratory Technology


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