Quality control and quantification in IG/TR next-generation
sequencing marker identification: protocols and bioinformatic
functionalities by EuroClonality-NGS

J 2019

Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

KNECHT, H., Tomáš REIGL, M. KOTROVA, F. APPELT, P. STEWART et. al.

Basic information

Original name

Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

Authors

KNECHT, H. (276 Germany), Tomáš REIGL (203 Czech Republic, belonging to the institution), M. KOTROVA (276 Germany), F. APPELT (276 Germany), P. STEWART (372 Ireland), Vojtěch BYSTRÝ (203 Czech Republic, belonging to the institution), Adam KREJČÍ (203 Czech Republic, belonging to the institution), A. GRIONI (380 Italy), Karol PÁL (703 Slovakia, belonging to the institution), Kamila STRÁNSKÁ (203 Czech Republic, belonging to the institution), Karla PLEVOVÁ (203 Czech Republic, belonging to the institution), J. RIJNTJES (528 Netherlands), S. SONGIA (380 Italy), M. SVATON (203 Czech Republic), E. FRONKOVA (826 United Kingdom of Great Britain and Northern Ireland), J. BARTRAM (528 Netherlands), B. SCHEIJEN (276 Germany), D. HERRMANN (276 Germany), R. GARCIA-SANZ (724 Spain), J. HANCOCK (826 United Kingdom of Great Britain and Northern Ireland), J. MOPPETT (826 United Kingdom of Great Britain and Northern Ireland), J.J.M. VAN DONGEN (528 Netherlands), G. CAZZANIGA (380 Italy), F. DAVI (250 France), P.J.T.A. GROENEN (528 Netherlands), M. HUMMEL (276 Germany), E.A. MACINTYRE (250 France), K. STAMATOPOULOS (300 Greece), J. TRKA (203 Czech Republic), A.W. LANGERAK (528 Netherlands), D. GONZALEZ (372 Ireland), C. POTT (276 Germany), M. BRUGGEMANN (276 Germany) and Nikos DARZENTAS (300 Greece, guarantor, belonging to the institution)

Edition

Leukemia, London, Nature Publishing Group, 2019, 0887-6924

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30204 Oncology

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: 8.665

RIV identification code

RIV/00216224:14740/19:00108523

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/s41375-019-0499-4

UT WoS

000484399300010

Keywords in English

MINIMAL RESIDUAL DISEASE; ACUTE LYMPHOBLASTIC-LEUKEMIA; CELL LYMPHOMA; IMMUNOGLOBULIN; PCR; STANDARDIZATION; PRIMERS; RELAPSE; RISK

Abstract

V originále

Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.

Links

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

NV16-34272A, research and development project

Name: Encyklopedie CLL podskupin: unikátní znalostní databáze vybavená bioinformatickými nástroji použitelná v personalizované biomedicíně a klinické praxi

90091, large research infrastructures

Name: NCMG

Citovat

KNECHT, H., Tomáš REIGL, M. KOTROVA, F. APPELT, P. STEWART, Vojtěch BYSTRÝ, Adam KREJČÍ, A. GRIONI, Karol PÁL, Kamila STRÁNSKÁ, Karla PLEVOVÁ, J. RIJNTJES, S. SONGIA, M. SVATON, E. FRONKOVA, J. BARTRAM, B. SCHEIJEN, D. HERRMANN, R. GARCIA-SANZ, J. HANCOCK, J. MOPPETT, J.J.M. VAN DONGEN, G. CAZZANIGA, F. DAVI, P.J.T.A. GROENEN, M. HUMMEL, E.A. MACINTYRE, K. STAMATOPOULOS, J. TRKA, A.W. LANGERAK, D. GONZALEZ, C. POTT, M. BRUGGEMANN and Nikos DARZENTAS. Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS. Leukemia. London: Nature Publishing Group, 2019, vol. 33, No 9, p. 2254-2265. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-019-0499-4.

@article{1569017,
   author = {Knecht, H. and Reigl, Tomáš and Kotrova, M. and Appelt, F. and Stewart, P. and Bystrý, Vojtěch and Krejčí, Adam and Grioni, A. and Pál, Karol and Stránská, Kamila and Plevová, Karla and Rijntjes, J. and Songia, S. and Svaton, M. and Fronkova, E. and Bartram, J. and Scheijen, B. and Herrmann, D. and GarciaandSanz, R. and Hancock, J. and Moppett, J. and van Dongen, J.J.M. and Cazzaniga, G. and Davi, F. and Groenen, P.J.T.A. and Hummel, M. and Macintyre, E.A. and Stamatopoulos, K. and Trka, J. and Langerak, A.W. and Gonzalez, D. and Pott, C. and Bruggemann, M. and Darzentas, Nikos},
   article_location = {London},
   article_number = {9},
   doi = {http://dx.doi.org/10.1038/s41375-019-0499-4},
   keywords = {MINIMAL RESIDUAL DISEASE; ACUTE LYMPHOBLASTIC-LEUKEMIA; CELL LYMPHOMA; IMMUNOGLOBULIN; PCR; STANDARDIZATION; PRIMERS; RELAPSE; RISK},
   language = {eng},
   issn = {0887-6924},
   journal = {Leukemia},
   title = {Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS},
   url = {https://www.nature.com/articles/s41375-019-0499-4.pdf},
   volume = {33},
   year = {2019}
}

TY  - JOUR
ID  - 1569017
AU  - Knecht, H. - Reigl, Tomáš - Kotrova, M. - Appelt, F. - Stewart, P. - Bystrý, Vojtěch - Krejčí, Adam - Grioni, A. - Pál, Karol - Stránská, Kamila - Plevová, Karla - Rijntjes, J. - Songia, S. - Svaton, M. - Fronkova, E. - Bartram, J. - Scheijen, B. - Herrmann, D. - Garcia-Sanz, R. - Hancock, J. - Moppett, J. - van Dongen, J.J.M. - Cazzaniga, G. - Davi, F. - Groenen, P.J.T.A. - Hummel, M. - Macintyre, E.A. - Stamatopoulos, K. - Trka, J. - Langerak, A.W. - Gonzalez, D. - Pott, C. - Bruggemann, M. - Darzentas, Nikos
PY  - 2019
TI  - Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS
JF  - Leukemia
VL  - 33
IS  - 9
SP  - 2254-2265
EP  - 2254-2265
PB  - Nature Publishing Group
SN  - 08876924
KW  - MINIMAL RESIDUAL DISEASE
KW  - ACUTE LYMPHOBLASTIC-LEUKEMIA
KW  - CELL LYMPHOMA
KW  - IMMUNOGLOBULIN
KW  - PCR
KW  - STANDARDIZATION
KW  - PRIMERS
KW  - RELAPSE
KW  - RISK
UR  - https://www.nature.com/articles/s41375-019-0499-4.pdf
L2  - https://www.nature.com/articles/s41375-019-0499-4.pdf
N2  - Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.
ER  -

KNECHT, H., Tomáš REIGL, M. KOTROVA, F. APPELT, P. STEWART, Vojtěch BYSTRÝ, Adam KREJČÍ, A. GRIONI, Karol PÁL, Kamila STRÁNSKÁ, Karla PLEVOVÁ, J. RIJNTJES, S. SONGIA, M. SVATON, E. FRONKOVA, J. BARTRAM, B. SCHEIJEN, D. HERRMANN, R. GARCIA-SANZ, J. HANCOCK, J. MOPPETT, J.J.M. VAN DONGEN, G. CAZZANIGA, F. DAVI, P.J.T.A. GROENEN, M. HUMMEL, E.A. MACINTYRE, K. STAMATOPOULOS, J. TRKA, A.W. LANGERAK, D. GONZALEZ, C. POTT, M. BRUGGEMANN and Nikos DARZENTAS. Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS. \textit{Leukemia}. London: Nature Publishing Group, 2019, vol.~33, No~9, p.~2254-2265. ISSN~0887-6924. Available from: https://dx.doi.org/10.1038/s41375-019-0499-4.

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