Formalin-fixed, paraffin-embedded application

Johnson NA, Hamoudi RA, Ichimura K, et al. Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells. Lab. Invest. 2006 86 968-978. 

Ronci M, Bonanno E, Colantoni A, et al. Protein unlocking procedures of formalin-fixed paraffin-embedded tissues application to MALDI-TOF imaging MS investigations. Proteomics 2008 8 3702-3714. 

Stauber J, Lemaire R, Franck J, et al. MALDI imaging of formalin-fixed paraffin-embedded tissues application to model animals of Parkinson disease for biomarker hunting. J. Proteome Res. 2008 7 969-978. 

Polymerase chain reaction (PCR), on the other hand, has several advantages it can be used to analyze small numbers of tumor cells, DNA from formalin-fixed, paraffin-embedded tumor tissue can be used, and it can be automated and standardized. Quantitative PCR techniques are currently being assessed for their clinical application to HF.R-2 DNA testing (Vona et al., 1999). However, presently the PCR technology is not optimally suited for routine, clinical application (see next section for details of quantitative analysis of HER-2Ineu expression). 

Because of the superior morphology provided by formalin-fixed paraffin-embedded tissues, this has become the medium of choice for most clinical and research studies. The peroxidase-labeled antibody method, introduced in 1968, was the first practical application of antibodies to paraffin-embedded tissues and overcame some of the limitations of earlier fluorescence antibody methods (1). These pioneering studies using enzyme labels instead of fluorescent dyes opened the door to the development of modern methods of immuohistochemistry. 

Indeed, recent reports demonstrated the potential use of enzymatic digestion combined with LC-ESI-MS/MS directly on formalin-fixed paraffin-embedded tissues to identify tumor biomarkers (for a review see [68]). The ultimate hope would be to mobilize such powerful MS tools to routine clinical application for in vitro diagnosis assays. 

The type 1 TLS/CHOP chimeric transcript is a result of the above-mentioned t(12 16) and is a very sensitive and specific molecular alteration for the myxoid/round cell liposarcoma entityOikawa and colleagues have developed a monoclonal antibody to this fusion transcript, which they claim is highly specific and sensitive with formalin-fixed paraffin-embedded tissue. However, there is no literature on its use. As a diagnostic tool, this is a good example of a genomic application of me. 

Cartun, R. W., Coles, F. B., and Pastusrak, W. T. (1987) Utilization of monoclonal antibody L26 in the identification, and confirmation of B-cell lymphomas a sensitive and specific marker applicable to formalin- and B5-fixed, paraffin-embedded tissues. Am. J. Pathol. 129,415 21. 

APPLICATION OF SHOTGUN PROTEOMICS TO FORMALIN-FIXED AND PARAFFIN-EMBEDDED TISSUES... 

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