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

J 2021

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

HYNŠT, Jakub, Veronika NAVRKALOVÁ, Karol PÁL and Šárka POSPÍŠILOVÁ

Basic information

Original name

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

Authors

HYNŠT, Jakub (203 Czech Republic, belonging to the institution), Veronika NAVRKALOVÁ (203 Czech Republic, belonging to the institution), Karol PÁL (703 Slovakia, belonging to the institution) and Šárka POSPÍŠILOVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

PeerJ, London, PEERJ INC, 2021, 2167-8359

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30101 Human genetics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.061

RIV identification code

RIV/00216224:14740/21:00120097

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.7717/peerj.10897

UT WoS

000635103900002

Keywords in English

Bioinformatic analysis; SNV/indel; CNV; Clinical application; Molecular markers; NGS; Targeted panels

Abstract

V originále

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.

Links

EF16_026/0008448, research and development project

Name: Analýza českých genomů pro teranostiku

MUNI/A/1395/2019, interní kód MU

Name: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit VII (Acronym: VýDiTeHeMa VII)

Investor: Masaryk University, Category A

NV19-03-00091, research and development project

Name: Komplexní prognostický a prediktivní panel pro pacienty s chronickou lymfocytární leukémií: nástroj sekvenování nové generace vhodný pro klinickou praxi i studium genetického pozadí průběhu choroby

Investor: Ministry of Health of the CR

90091, large research infrastructures

Name: NCMG

Citovat

HYNŠT, Jakub, Veronika NAVRKALOVÁ, Karol PÁL and Šárka POSPÍŠILOVÁ. Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application. PeerJ. London: PEERJ INC, 2021, vol. 9, MAR 2021, p. 1-29. ISSN 2167-8359. Available from: https://dx.doi.org/10.7717/peerj.10897.

@article{1768001,
   author = {Hynšt, Jakub and Navrkalová, Veronika and Pál, Karol and Pospíšilová, Šárka},
   article_location = {London},
   article_number = {MAR 2021},
   doi = {http://dx.doi.org/10.7717/peerj.10897},
   keywords = {Bioinformatic analysis; SNV/indel; CNV; Clinical application; Molecular markers; NGS; Targeted panels},
   language = {eng},
   issn = {2167-8359},
   journal = {PeerJ},
   title = {Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application},
   url = {https://peerj.com/articles/10897/},
   volume = {9},
   year = {2021}
}

TY  - JOUR
ID  - 1768001
AU  - Hynšt, Jakub - Navrkalová, Veronika - Pál, Karol - Pospíšilová, Šárka
PY  - 2021
TI  - Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application
JF  - PeerJ
VL  - 9
IS  - MAR 2021
SP  - 1-29
EP  - 1-29
PB  - PEERJ INC
SN  - 21678359
KW  - Bioinformatic analysis
KW  - SNV/indel
KW  - CNV
KW  - Clinical application
KW  - Molecular markers
KW  - NGS
KW  - Targeted panels
UR  - https://peerj.com/articles/10897/
N2  - 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.
ER  -

HYNŠT, Jakub, Veronika NAVRKALOVÁ, Karol PÁL and Šárka POSPÍŠILOVÁ. Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application. \textit{PeerJ}. London: PEERJ INC, 2021, vol.~9, MAR 2021, p.~1-29. ISSN~2167-8359. Available from: https://dx.doi.org/10.7717/peerj.10897.

Detailed Information on Publication Record