Formalin-fixed, paraffin-embedded hybridization

DeVries S, Nyante S, Korkola J, et al. Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. J. Mol. Diagn. 2005 7 65-71. 

The preparations most often affixed to silane- (9) or poly-L-lysine-coated slides are Carnoy-fixed suspensions of metaphase cells for chromosome studies (see Chapter 47) cytospins of cultured cells followed by methanol fixation sections of formalin-fixed, paraffin-embedded tissues and frozen sections fixed with acetone or ethanol/acetic acid after cutting. Each of these approaches imparts different intracellular effects that may modify cytological detail and/or hybridization. (See Chapters 8 and 9 for a discussion of fixatives and frozen-section preparations.)... 

McMahon, M. J., and McQuaid, S. 1996. The use of microwave irradiation as a pretreatment to in situ hybridization for the detection of measles virus and chicken anaemia virus in formalin-fixed, paraffin-embedded tissue. Histochem. J. 28 157-164. 

Smith, K. L., Robbins, P. D., and Dawkins, H. J., 1994. c-erbB-2 amplification in breast cancer Detection in formalin-fixed, paraffin-embedded tissue by in situ hybridization. Hum. Pathol. 25 413-18. 

Recent times have seen the advent of high throughput assays such as array comparative genomic hybridization and cDNA microarray, which have lead to the rapid discovery of thousands of potential biomarkers. However, these need to be validated in tissue-based studies in large datasets to prove their potential utility. As these datasets are typically present in the form of formalin fixed paraffin-embedded tissue blocks, immunohistochemical (IHC) methods are ideal for validation. However, performing whole-section IHC on hundreds to thousands of blocks requires lot of resources in terms of reagents and time. In addition, an average block will yield less than 300 slides of 5 pm each. The tissue microarray (TMA) technique circumvents some of these problems. 

ISH is often possible on routinely processed formalin-fixed paraffin-embedded tissues. Retrospective studies of routinely processed human material are therefore feasible. Protease treatments prior to the hybridization may be necessary since the duration of fixation in autopsy material is often unknown. Sections of the same block have then to be examined to establish the optimum degree of protease digestion. 

Qian X, Jin L, Shearer BM, et al. Molecular diagnosis of Ewing s sarcoma/primitive neuroectodermal tumor in formalin-fixed paraffin-embedded tissues by RT-PCR and fluorescence in situ hybridization. Diagn Mol Pathol. 2005 14 23-28. 

Fig. i. Localizalion of nuclear RAR and RXR mRNAs in formalin-fixed and paraffin-embedded surgical. specimens by in situ hybridization. Sections of normal epithelium adjacent to human-bladder carcinoma were hybridized with RARa anti.sense (A) or sense (B) RAR(3 antisense (C) or sense (D) RARy antisense (E) or sense (F) RXRa antisense (G) or sense (H). 

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