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.

Základní údaje

Originální název

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

Autoři

KNECHT, H. (276 Německo), Tomáš REIGL (203 Česká republika, domácí), M. KOTROVA (276 Německo), F. APPELT (276 Německo), P. STEWART (372 Irsko), Vojtěch BYSTRÝ (203 Česká republika, domácí), Adam KREJČÍ (203 Česká republika, domácí), A. GRIONI (380 Itálie), Karol PÁL (703 Slovensko, domácí), Kamila STRÁNSKÁ (203 Česká republika, domácí), Karla PLEVOVÁ (203 Česká republika, domácí), J. RIJNTJES (528 Nizozemské království), S. SONGIA (380 Itálie), M. SVATON (203 Česká republika), E. FRONKOVA (826 Velká Británie a Severní Irsko), J. BARTRAM (528 Nizozemské království), B. SCHEIJEN (276 Německo), D. HERRMANN (276 Německo), R. GARCIA-SANZ (724 Španělsko), J. HANCOCK (826 Velká Británie a Severní Irsko), J. MOPPETT (826 Velká Británie a Severní Irsko), J.J.M. VAN DONGEN (528 Nizozemské království), G. CAZZANIGA (380 Itálie), F. DAVI (250 Francie), P.J.T.A. GROENEN (528 Nizozemské království), M. HUMMEL (276 Německo), E.A. MACINTYRE (250 Francie), K. STAMATOPOULOS (300 Řecko), J. TRKA (203 Česká republika), A.W. LANGERAK (528 Nizozemské království), D. GONZALEZ (372 Irsko), C. POTT (276 Německo), M. BRUGGEMANN (276 Německo) a Nikos DARZENTAS (300 Řecko, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30204 Oncology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 8.665

Kód RIV

RIV/00216224:14740/19:00108523

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000484399300010

Klíčová slova anglicky

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

Štítky

14110212, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 8. 3. 2020 19:44, Mgr. Pavla Foltynová, Ph.D.

Anotace

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.

Návaznosti

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

NV16-34272A, projekt VaV

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

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 a 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, roč. 33, č. 9, s. 2254-2265. ISSN 0887-6924. Dostupné z: 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 a 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, roč.~33, č.~9, s.~2254-2265. ISSN~0887-6924. Dostupné z: https://dx.doi.org/10.1038/s41375-019-0499-4.

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