Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F21%3A00074381" target="_blank" >RIV/65269705:_____/21:00074381 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14740/21:00120097

Result on the web

<a href="https://peerj.com/articles/10897/" target="_blank" >https://peerj.com/articles/10897/</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.7717/peerj.10897" target="_blank" >10.7717/peerj.10897</a>

Result language

angličtina

Original language name

Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application

Original language description

Molecular profiling of tumor samples has acquired importance in cancer research, but currently also plays an important role in the clinical management of cancer patients. Rapid identification of genomic aberrations improves diagnosis, prognosis and effective therapy selection. This can be attributed mainly to the development of next-generation sequencing (NGS) methods, especially targeted DNA panels. Such panels enable a relatively inexpensive and rapid analysis of various aberrations with clinical impact specific to particular diagnoses. In this review, we discuss the experimental approaches and bioinformatic strategies available for the development of an NGS panel for a reliable analysis of selected biomarkers. Compliance with defined analytical steps is crucial to ensure accurate and reproducible results. In addition, a careful validation procedure has to be performed before the application of NGS targeted assays in routine clinical practice. With more focus on bioinformatics, we emphasize the need for thorough pipeline validation and management in relation to the particular experimental setting as an integral part of the NGS method establishment. A robust and reproducible bioinformatic analysis running on powerful machines is essential for proper detection of genomic variants in clinical settings since distinguishing between experimental noise and real biological variants is fundamental. This review summarizes state-of-the-art bioinformatic solutions for careful detection of the SNV/Indels and CNVs for targeted sequencing resulting in translation of sequencing data into clinically relevant information. Finally, we share our experience with the development of a custom targeted NGS panel for an integrated analysis of biomarkers in lymphoproliferative disorders.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

30204 - Oncology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2021

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

PEERJ

ISSN

2167-8359

e-ISSN

—

Volume of the periodical

9

Issue of the periodical within the volume

MAR

Country of publishing house

GB - UNITED KINGDOM

Number of pages

29

Pages from-to

"e10897"

UT code for WoS article

000635103900002

EID of the result in the Scopus database

2-s2.0-85103439696