Abstract

Next-generation sequencing (NGS) has become a cornerstone of precision oncology, requiring standardized workflows in molecular pathology laboratories. The analytical phase, which includes all procedures from nucleic acid quantification to variant interpretation, plays a central role in ensuring the accuracy and clinical utility of molecular results. This document aims at supporting pathology teams—comprising pathologists, technicians, and molecular biologists—during the implementation and execution of the analytical phase of NGS testing. Key topics include clinical indications, platform and gene panel selection, bioinformatics pipelines, quality assurance strategies, and organizational considerations. The goal is to promote standardized, high-quality molecular diagnostics to advance precision pathology.

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Authors

Elena Guerini-Rocco - IEO

Konstantinos Venetis - IEO https://orcid.org/0000-0002-0163-879X

Silvia Bessi - , Azienda USL Toscana Centro https://orcid.org/0000-0001-6444-1620

Simonetta Buglioni - IFO https://orcid.org/0000-0002-5066-1523

Caterina Chiappetta - Umberto I University Hospital, Rome https://orcid.org/0000-0001-8527-7559

Dario de Biase - University of Bologna

Giovanna De Maglio - Santa Maria della Misericordia Hospital, Udine https://orcid.org/0000-0002-8884-3306

Paolo Graziano - Sapienza https://orcid.org/0000-0001-7066-7896

Elisabetta Macerola - University Hospital of Pisa https://orcid.org/0000-0002-0235-799X

Caterina Marchiò - Candiolo

Elisa Melucci - IFO https://orcid.org/0000-0003-4908-5271

Mariantonia Nacchio - Federico II

Federica Natoni - Hospital of Santa Rosa, Viterbo

Andrea Vingiani - Fondazione IRCCS Istituto Nazionale dei Tumori https://orcid.org/0000-0002-9827-3976

Nicola Fusco - European Institute of Oncology

Umberto Malapelle - Federico II https://orcid.org/0000-0002-6429-0620

Giancarlo Pruneri - Fondazione IRCCS Istituto Nazionale dei Tumori

Fabio Pagni - University of Milano Bicocca

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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Copyright

Copyright (c) 2025 Società Italiana di Anatomia Patologica e Citopatologia Diagnostica, Divisione Italiana della International Academy of Pathology

How to Cite
Guerini-Rocco, E., Venetis, K., Bessi, S., Buglioni, S., Chiappetta, C., de Biase, D., De Maglio, G., Graziano, P., Macerola, E., Marchiò, C., Melucci, E., Nacchio, M., Natoni, F., Vingiani, A., Fusco, N., Malapelle, U., Pruneri, G., & Pagni, F. (2025). Part II – Analytical phase. Pathologica - Journal of the Italian Society of Anatomic Pathology and Diagnostic Cytopathology, 117(2 (Suppl. 1). Retrieved from https://www.pathologica.it/article/view/1216
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