alexa Optimization of the Isolation and Amplification of RNA From Formalin-fixed, Paraffin-embedded Tissue: The Armed Forces Institute of Pathology Experience and Literature Review.
Pathology

Pathology

Journal of Forensic Pathology

Author(s): Krafft AE, Duncan BW, Bijwaard KE, Taubenberger JK, Lichy JH

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Abstract Background: RNA is extensively degraded by routine formalin fixation to fragments averaging 200 nucleotides (nt). Several methods for the recovery of amplifiable RNA from formalin-fixed, paraffin-embedded tissue have been described; however, a universally accepted approach in a clinical molecular diagnostic laboratory has not yet emerged. Methods and Results: Amplifiable RNA can be recovered with high efficiency from all types of formalin-fixed, paraffin-embedded tissue using proteinase K digestion, either a phenol-chloroform or an acidic guanidinium thiocyanate-phenol chloroform extraction step, and isopropanol precipitation in the presence of glycogen. Designing primers to detect a small target was critical for consistent RNA amplification in the following assays, with the target size indicated: hepatitis C virus, 169nt; morbillivirus, 78 nt; influenza virus, 113 nt; the npm-alk fusion product resulting from t(2;5) translocation, 175 nt; and the bcr-abl fusion product resulting from t(9;22) translocation, 93 or 168 nt. Conclusions: With use of beta-2-microglobulin as the control messenger RNA target for assessing the recovery of amplifiable RNA from human tissue, amplifiable RNA was recovered from 216 of 225 blocks (96\%). In a series of veterinary specimens, which were largely postmortem and moderately to severely autolyzed, 158 of 199 blocks (79\%) yielded amplifiable RNA using a beta-actin target. Amplifiable influenza RNA has been recovered from archival paraffin blocks as old as 79 years. This article was published in Mol Diagn and referenced in Journal of Forensic Pathology

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