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Review
. 2021 Sep 23;12(10):1472.
doi: 10.3390/genes12101472.

Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions

Gerardo Cazzato  1 , Concetta Caporusso  1 , Francesca Arezzo  2 , Antonietta Cimmino  1 , Anna Colagrande  1 , Vera Loizzi  2 , Gennaro Cormio  2 , Teresa Lettini  1 , Eugenio Maiorano  1 , Vincenza Sara Scarcella  1 , Paola Tarantino  1 , Maricla Marrone  3 , Alessandra Stellacci  3 , Paola Parente  4 , Paolo Romita  5 , Aurora De Marco  5 , Vincenzo Venerito  6 , Caterina Foti  5 , Giuseppe Ingravallo  1 , Roberta Rossi  1 , Leonardo Resta  1
Affiliations
Review

Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions

Gerardo Cazzato et al. Genes (Basel). .

Abstract

Over the years, increasing information has been asked of the pathologist: we have moved from a purely morphological diagnosis to biomolecular and genetic studies, which have made it possible to implement the use of molecular targeted therapies, such as anti-epidermal growth factor receptor (EGFR) molecules in EGFR-mutated lung cancer, for example. Today, next generation sequencing (NGS) has changed the approach to neoplasms, to the extent that, in a short time, it has gained a place of absolute importance and diagnostic, prognostic and therapeutic utility. In this scenario, formaldehyde-fixed and paraffin-embedded (FFPE) biological tissue samples are a source of clinical and molecular information. However, problems can arise in the genetic material (DNA and RNA) for use in NGS due to fixation, and work is being devoted to possible strategies to reduce its effects. In this paper, we discuss the applications of FFPE tissue samples in the execution of NGS, we focus on the problems arising with the use of this type of material for nucleic acid extraction and, finally, we consider the most useful strategies to prevent and reduce single nucleotide polymorphisms (SNV) and other fixation artifacts.

Keywords: DNA; FFPE; NGS; PCR; RNA.

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Conflict of interest statement

The authors declare no conflict of interest.

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