LYmphoid NeXt-Generation Sequencing (LYNX) Panel A
Comprehensive Capture-Based Sequencing Tool for the Analysis of
Prognostic and Predictive Markers in Lymphoid Malignancies

J 2021

LYmphoid NeXt-Generation Sequencing (LYNX) Panel A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies

NAVRKALOVÁ, Veronika, Karla PLEVOVÁ, Jakub HYNŠT, Karol PÁL, Andrea MAREČKOVÁ et. al.

Basic information

Original name

LYmphoid NeXt-Generation Sequencing (LYNX) Panel A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies

Authors

NAVRKALOVÁ, Veronika (203 Czech Republic, belonging to the institution), Karla PLEVOVÁ (203 Czech Republic, belonging to the institution), Jakub HYNŠT (203 Czech Republic, belonging to the institution), Karol PÁL (703 Slovakia, belonging to the institution), Andrea MAREČKOVÁ (203 Czech Republic, belonging to the institution), Tomáš REIGL (203 Czech Republic, belonging to the institution), Hana JELÍNKOVÁ (203 Czech Republic), Zuzana VRZALOVÁ (203 Czech Republic, belonging to the institution), Kamila STRÁNSKÁ (203 Czech Republic, belonging to the institution), Šárka PAVLOVÁ (203 Czech Republic, belonging to the institution), Anna PANOVSKÁ (203 Czech Republic, belonging to the institution), Andrea JANÍKOVÁ (203 Czech Republic, belonging to the institution), Michael DOUBEK (203 Czech Republic, belonging to the institution), Jana KOTAŠKOVÁ (203 Czech Republic, belonging to the institution) and Šárka POSPÍŠILOVÁ (203 Czech Republic, belonging to the institution)

Edition

The journal of molecular diagnostics. Bethesda, MD, American Society for Investigative Pathology/Association for Molecular Pathology, 2021, 1525-1578

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30109 Pathology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.341

RIV identification code

RIV/00216224:14740/21:00124277

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1016/j.jmoldx.2021.05.007

UT WoS

000678377900007

Keywords in English

LYNX; Lymphoid Malignancies; Prognostic and Predictive Markers

Abstract

V originále

B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (>6 Mb) and recurrent chromosomal aber-rations (>300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel repre-sents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.

Links

LM2018140, research and development project

Name: e-Infrastruktura CZ (Acronym: e-INFRA CZ)

Investor: Ministry of Education, Youth and Sports of the CR

90132, large research infrastructures

Name: NCMG II

Citovat

NAVRKALOVÁ, Veronika, Karla PLEVOVÁ, Jakub HYNŠT, Karol PÁL, Andrea MAREČKOVÁ, Tomáš REIGL, Hana JELÍNKOVÁ, Zuzana VRZALOVÁ, Kamila STRÁNSKÁ, Šárka PAVLOVÁ, Anna PANOVSKÁ, Andrea JANÍKOVÁ, Michael DOUBEK, Jana KOTAŠKOVÁ and Šárka POSPÍŠILOVÁ. LYmphoid NeXt-Generation Sequencing (LYNX) Panel A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. The journal of molecular diagnostics. Bethesda, MD: American Society for Investigative Pathology/Association for Molecular Pathology, 2021, vol. 23, No 8, p. 959-974. ISSN 1525-1578. Available from: https://dx.doi.org/10.1016/j.jmoldx.2021.05.007.

@article{1836805,
   author = {Navrkalová, Veronika and Plevová, Karla and Hynšt, Jakub and Pál, Karol and Marečková, Andrea and Reigl, Tomáš and Jelínková, Hana and Vrzalová, Zuzana and Stránská, Kamila and Pavlová, Šárka and Panovská, Anna and Janíková, Andrea and Doubek, Michael and Kotašková, Jana and Pospíšilová, Šárka},
   article_location = {Bethesda, MD},
   article_number = {8},
   doi = {http://dx.doi.org/10.1016/j.jmoldx.2021.05.007},
   keywords = {LYNX; Lymphoid Malignancies; Prognostic and Predictive Markers},
   language = {eng},
   issn = {1525-1578},
   journal = {The journal of molecular diagnostics.},
   title = {LYmphoid NeXt-Generation Sequencing (LYNX) Panel A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies},
   url = {https://www.sciencedirect.com/science/article/pii/S1525157821001343?via%3Dihub},
   volume = {23},
   year = {2021}
}

TY  - JOUR
ID  - 1836805
AU  - Navrkalová, Veronika - Plevová, Karla - Hynšt, Jakub - Pál, Karol - Marečková, Andrea - Reigl, Tomáš - Jelínková, Hana - Vrzalová, Zuzana - Stránská, Kamila - Pavlová, Šárka - Panovská, Anna - Janíková, Andrea - Doubek, Michael - Kotašková, Jana - Pospíšilová, Šárka
PY  - 2021
TI  - LYmphoid NeXt-Generation Sequencing (LYNX) Panel A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies
JF  - The journal of molecular diagnostics.
VL  - 23
IS  - 8
SP  - 959-974
EP  - 959-974
PB  - American Society for Investigative Pathology/Association for Molecular Pathology
SN  - 15251578
KW  - LYNX
KW  - Lymphoid Malignancies
KW  - Prognostic and Predictive Markers
UR  - https://www.sciencedirect.com/science/article/pii/S1525157821001343?via%3Dihub
N2  - B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (>6 Mb) and recurrent chromosomal aber-rations (>300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel repre-sents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
ER  -

NAVRKALOVÁ, Veronika, Karla PLEVOVÁ, Jakub HYNŠT, Karol PÁL, Andrea MAREČKOVÁ, Tomáš REIGL, Hana JELÍNKOVÁ, Zuzana VRZALOVÁ, Kamila STRÁNSKÁ, Šárka PAVLOVÁ, Anna PANOVSKÁ, Andrea JANÍKOVÁ, Michael DOUBEK, Jana KOTAŠKOVÁ and Šárka POSPÍŠILOVÁ. LYmphoid NeXt-Generation Sequencing (LYNX) Panel A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. \textit{The journal of molecular diagnostics.}. Bethesda, MD: American Society for Investigative Pathology/Association for Molecular Pathology, 2021, vol.~23, No~8, p.~959-974. ISSN~1525-1578. Available from: https://dx.doi.org/10.1016/j.jmoldx.2021.05.007.

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