**Nucleic Acids Extraction from Formalin-Fixed and Paraffin-Embedded Tissues**

Gisele R. Gouveia, Suzete C. Ferreira, Sheila A. C. Siqueira and Juliana Pereira

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/61581

#### **Abstract**

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Formalin-fixed paraffin-embedded (FFPE) tissues are an important sample source for ret‐ rospective studies. Despite its ability to preserve proteins and cell morphology, formalin hinders molecular biology tests since it fragments and chemically modifies nucleic acids, especially RNA. Although several studies describe techniques that allow extracting nu‐ cleic acids from FFPE tissues, so far there is no consensus in the literature about the best protocol to be used in this type of material. Thus, the current chapter aims to describe the factors affecting the FFPE tissue nucleic acid extracting process, compare the available protocols and to describe the modifications developed by our group in some protocols. Such modifications enable nucleic acids obtainment in satisfactory quantity and quality for molecular biology studies.

**Keywords:** DNA, RNA, FFPE, extraction

#### **1. Introduction**

Formalin-fixed paraffin-embedded (FFPE) tissues are of great importance to retrospective studies. Their main advantage lies on the possibility of correlating genetic and molecular bi‐ ology analyses with data from patients' medical records and clinical outcomes [1].

Formalin fixation is the most widely used method for tissue fragment preservation. It is a low-cost and easy-to-handle method, which preserves good morphological cell quality. The method is compatible with the antibodies used in the immunohistochemistry technique [2]. However, although formalin fixation and routine histological processing techniques pre‐ serve tissue cellular morphology and protein integrity, they also impair the obtainment of

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nucleic acids with the same quality, especially RNA, since they degrade and chemically modify such acids [3, 4].

Formalin replacement by other tissue fixatives such as Bouin, Carnoy, alcohol or HOPE (glu‐ tamic acid buffer Hepes-mediated organic solvent effect protection) may be an alternative to reverse the problem [4, 5]. However, since formalin is the fixative of choice in most patholo‐ gy departments, several research groups have sought to reverse the chemical changes caused by this fixative type.

Although several papers describe techniques that allow FFPE tissue nucleic acid extracting process [6–8, 3, 1, 4], so far there is no consensus in the literature about the best protocol to be used in this type of material.

The studies based on such approach not often detail the used methodology. Besides, not all the published techniques were reproduced by our group. It took us approximately 8 months to standardize the DNA and RNA extraction process in our FFPE tissues research.

The current chapter aims to describe the factors affecting the process of nucleic acid extrac‐ tion from FFPE tissue, compare the available protocols and to describe the modifications de‐ veloped by our group in some protocols that enable nucleic acids obtainment in satisfactory quantity and quality for molecular biology studies.
