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Review Article
* Correspondence to:
F. Lewis, Histopathology, The
Leeds Teaching Hospitals NHS
Trust, Leeds, UK.
E-mail: fraserl@pathology.leeds.
ac.uk
Abstract
The histopathology archive represents a vast, well-characterized source of specimens covering
virtually every disease and is available for molecular biological investigation. The archive has in
recent years become widely used for molecular genetic analysis and DNA can be routinely
extracted from formalin-xed, parafn-embedded tissue. More recently, archival specimens have
become a source of material for extensive analysis of mRNA expression utilizing DNA
microarrays, real-time quantitative reverse transcriptase polymerase chain reaction (PCR), and
in situ hybridization and amplication techniques. These techniques will enable a greater
understanding of the changes that occur in gene function during every stage of the development of
disease and will lead to better diagnosis, better evaluation of prognosis, and better treatment
through targeted therapeutic regimes. Copyright # 2001 John Wiley & Sons, Ltd.
Keywords: archive; formalin-xed; parafn-embedded tissue; RNA extraction; reverse
transcriptase PCR; real-time quantitative PCR; in situ hybridisation; in situ amplication;
expression arrays
Introduction
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F. Lewis et al.
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Expression arrays
DNA expression arrays can be used to identify
qualitatively up- and down-regulation of genes at
certain stages of a disease. Most array technology
requires the use of large quantities of high quality
mRNA which has to be recovered from fresh clinical
specimens. Where prospective collection of specimens
is problematic due to the rarity of the disease, it has
been proposed that RNA extracted from archival
specimens could be utilized on custom expression
arrays. Despite the very low molecular weight of the
RNA typically isolated from parafn-embedded material, cDNA probes can be generated using sensitive
labelling strategies, without requiring any additional
nucleic acid amplication. High-quality data can be
obtained on hybridization to a microarray: preliminary
studies using tumour samples suggest that up to 80%
of genes can be quantitatively detected in a parafnembedded sample, compared with a fresh-frozen
sample from the same patient (Genentech, unpublished
data). Factors such as sample collection and the degree
of xation will probably affect the extent of applicability of microarray analysis to parafn-embedded
material, but the potential is exciting.
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F. Lewis et al.
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Figure 3. DNA contamination of total RNA extracts from archival specimens was identied by performing PCR directly on RNA
extracts without a reverse transcriptase step. No amplication of thymidylate synthase was observed in 45 total RNA extracts.
Three out of 45 of the same RNA samples showed amplication of GAPDH (circles) as a result of amplication of the GAPDH
pseudogene, indicating that 3/45 samples were contaminated with DNA. The squares show amplication from cDNA for TS and
GAPDH
Conclusion
The prospective collection of specimens can take a
considerable length of time, particularly for rarer
diseases. The archive can provide a valuable source of
material from which expressed genes can be investigated at virtually every stage of development of a
disease. As better techniques evolve for the extraction,
quantitation, and localization of RNA from formalinxed, parafn-embedded tissue, the value of the
archive will grow even stronger. The ultimate goal is
to develop a greater understanding of the changes that
occur in gene function during the progression of a
disease. The knowledge acquired will enable a better
diagnosis and a better evaluation of the prognosis
tailored to the disease occurring within an individual
Copyright # 2001 John Wiley & Sons, Ltd.
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