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Volume 12
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10.3390/genes12101472
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Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions

by
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 and
Leonardo Resta
1add Show full author list remove Hide full author list
1
Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy
2
Section of Ginecology and Obstetrics, Department of Biomedical Science and Oncology (DIMO), University of Bari “Aldo Moro”, 70124 Bari, Italy
3
Section of Legal Medicine, Interdisciplinary Department of Medicine, Bari Policlinico Hospital, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy
4
UOC di Anatomia Patologica, Fondazione IRCCS Casa Sollievo Della Sofferenza, 71013 San Giovanni Rotondo, Italy
5
Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy
6
Section of Reumathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy
*
Authors to whom correspondence should be addressed.
Academic Editor: Yutaka Suzuki
Genes 2021, 12(10), 1472; https://doi.org/10.3390/genes12101472
Received: 2 September 2021 / Revised: 17 September 2021 / Accepted: 21 September 2021 / Published: 23 September 2021
(This article belongs to the Section Technologies and Resources for Genetics)
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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. View Full-Text
Keywords: NGS; FFPE; PCR; DNA; RNA NGS; FFPE; PCR; DNA; RNA
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MDPI and ACS Style

Cazzato, G.; Caporusso, C.; Arezzo, F.; Cimmino, A.; Colagrande, A.; Loizzi, V.; Cormio, G.; Lettini, T.; Maiorano, E.; Scarcella, V.S.; Tarantino, P.; Marrone, M.; Stellacci, A.; Parente, P.; Romita, P.; De Marco, A.; Venerito, V.; Foti, C.; Ingravallo, G.; Rossi, R.; Resta, L. Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions. Genes 2021, 12, 1472. https://doi.org/10.3390/genes12101472

AMA Style

Cazzato G, Caporusso C, Arezzo F, Cimmino A, Colagrande A, Loizzi V, Cormio G, Lettini T, Maiorano E, Scarcella VS, Tarantino P, Marrone M, Stellacci A, Parente P, Romita P, De Marco A, Venerito V, Foti C, Ingravallo G, Rossi R, Resta L. Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions. Genes. 2021; 12(10):1472. https://doi.org/10.3390/genes12101472

Chicago/Turabian Style

Cazzato, Gerardo, Concetta Caporusso, Francesca Arezzo, Antonietta Cimmino, Anna Colagrande, Vera Loizzi, Gennaro Cormio, Teresa Lettini, Eugenio Maiorano, Vincenza S. Scarcella, Paola Tarantino, Maricla Marrone, Alessandra Stellacci, Paola Parente, Paolo Romita, Aurora De Marco, Vincenzo Venerito, Caterina Foti, Giuseppe Ingravallo, Roberta Rossi, and Leonardo Resta. 2021. "Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions" Genes 12, no. 10: 1472. https://doi.org/10.3390/genes12101472

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