TY - JOUR
T1 - Tissue handling for genome-wide expression analysis
T2 - A review of the issues, evidence, and opportunities
AU - Medeiros, Fabiola
AU - Rigl, C. Ted
AU - Anderson, Glenda G.
AU - Becker, Shawn H.
AU - Halling, Kevin C.
PY - 2007/12
Y1 - 2007/12
N2 - 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.
AB - 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.
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M3 - Review article
C2 - 18081440
AN - SCOPUS:37349059336
SN - 0003-9985
VL - 131
SP - 1805
EP - 1816
JO - Archives of Pathology and Laboratory Medicine
JF - Archives of Pathology and Laboratory Medicine
IS - 12
ER -