Standardized next-generation sequencing of immunoglobulin and
T-cell receptor gene recombinations for MRD marker
identification in acute lymphoblastic leukaemia; a
EuroClonality-NGS validation study

J 2019

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

BRUGGEMANN, M., M. KOTROVA, H. KNECHT, J. BARTRAM, M. BOUDJOGRHA et. al.

Basic information

Original name

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Authors

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

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/00216224:14740/19:00108540

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/s41375-019-0496-7

UT WoS

000484399300009

Keywords in English

MINIMAL RESIDUAL DISEASE; TIME QUANTITATIVE PCR; CONCERTED ACTION; BONE-MARROW; REARRANGEMENTS; RELAPSE; HEAVY; QUANTIFICATION; CHILDREN; PRIMERS

Abstract

V originále

Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was spiked into each sample as a library-specific quality control and calibrator. NGS identified 259 (average 5.2/sample, range 0-14) clonal sequences vs. Sanger-sequencing 248 (average 5.0/sample, range 0-14). NGS primers covered possible IG/TR rearrangement types more completely compared with local multiplex PCR sets and enabled sequencing of bi-allelic rearrangements and weak PCR products. The cPT-QC showed high reproducibility across all laboratories. These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in 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

BRUGGEMANN, M., M. KOTROVA, H. KNECHT, J. BARTRAM, M. BOUDJOGRHA, Vojtěch BYSTRÝ, G. FAZIO, E. FRONKOVA, M. GIRAUD, A. GRIONI, J. HANCOCK, D. HERRMANN, C. JIMENEZ, Adam KREJČÍ, J. MOPPETT, Tomáš REIGL, M. SALSON, B. SCHEIJEN, M. SCHWARZ, S. SONGIA, M. SVATON, J.J.M. VAN DONGEN, P. VILLARESE, S. WAKEMAN, G. WRIGHT, G. CAZZANIGA, F. DAVI, R. GARCIA-SANZ, D. GONZALEZ, P.J.T.A. GROENEN, M. HUMMEL, E.A. MACINTYRE, K. STAMATOPOULOS, C. POTT, J. TRKA, Nikos DARZENTAS and A.W. LANGERAK. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study. Leukemia. London: Nature Publishing Group, 2019, vol. 33, No 9, p. 2241-2253. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-019-0496-7.

@article{1581687,
   author = {Bruggemann, M. and Kotrova, M. and Knecht, H. and Bartram, J. and Boudjogrha, M. and Bystrý, Vojtěch and Fazio, G. and Fronkova, E. and Giraud, M. and Grioni, A. and Hancock, J. and Herrmann, D. and Jimenez, C. and Krejčí, Adam and Moppett, J. and Reigl, Tomáš and Salson, M. and Scheijen, B. and Schwarz, M. and Songia, S. and Svaton, M. and van Dongen, J.J.M. and Villarese, P. and Wakeman, S. and Wright, G. and Cazzaniga, G. and Davi, F. and GarciaandSanz, R. and Gonzalez, D. and Groenen, P.J.T.A. and Hummel, M. and Macintyre, E.A. and Stamatopoulos, K. and Pott, C. and Trka, J. and Darzentas, Nikos and Langerak, A.W.},
   article_location = {London},
   article_number = {9},
   doi = {http://dx.doi.org/10.1038/s41375-019-0496-7},
   keywords = {MINIMAL RESIDUAL DISEASE; TIME QUANTITATIVE PCR; CONCERTED ACTION; BONE-MARROW; REARRANGEMENTS; RELAPSE; HEAVY; QUANTIFICATION; CHILDREN; PRIMERS},
   language = {eng},
   issn = {0887-6924},
   journal = {Leukemia},
   title = {Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study},
   url = {https://www.nature.com/articles/s41375-019-0496-7.pdf},
   volume = {33},
   year = {2019}
}

TY  - JOUR
ID  - 1581687
AU  - Bruggemann, M. - Kotrova, M. - Knecht, H. - Bartram, J. - Boudjogrha, M. - Bystrý, Vojtěch - Fazio, G. - Fronkova, E. - Giraud, M. - Grioni, A. - Hancock, J. - Herrmann, D. - Jimenez, C. - Krejčí, Adam - Moppett, J. - Reigl, Tomáš - Salson, M. - Scheijen, B. - Schwarz, M. - Songia, S. - Svaton, M. - van Dongen, J.J.M. - Villarese, P. - Wakeman, S. - Wright, G. - Cazzaniga, G. - Davi, F. - Garcia-Sanz, R. - Gonzalez, D. - Groenen, P.J.T.A. - Hummel, M. - Macintyre, E.A. - Stamatopoulos, K. - Pott, C. - Trka, J. - Darzentas, Nikos - Langerak, A.W.
PY  - 2019
TI  - Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study
JF  - Leukemia
VL  - 33
IS  - 9
SP  - 2241-2253
EP  - 2241-2253
PB  - Nature Publishing Group
SN  - 08876924
KW  - MINIMAL RESIDUAL DISEASE
KW  - TIME QUANTITATIVE PCR
KW  - CONCERTED ACTION
KW  - BONE-MARROW
KW  - REARRANGEMENTS
KW  - RELAPSE
KW  - HEAVY
KW  - QUANTIFICATION
KW  - CHILDREN
KW  - PRIMERS
UR  - https://www.nature.com/articles/s41375-019-0496-7.pdf
L2  - https://www.nature.com/articles/s41375-019-0496-7.pdf
N2  - Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was spiked into each sample as a library-specific quality control and calibrator. NGS identified 259 (average 5.2/sample, range 0-14) clonal sequences vs. Sanger-sequencing 248 (average 5.0/sample, range 0-14). NGS primers covered possible IG/TR rearrangement types more completely compared with local multiplex PCR sets and enabled sequencing of bi-allelic rearrangements and weak PCR products. The cPT-QC showed high reproducibility across all laboratories. These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in lymphoid malignancies.
ER  -

BRUGGEMANN, M., M. KOTROVA, H. KNECHT, J. BARTRAM, M. BOUDJOGRHA, Vojtěch BYSTRÝ, G. FAZIO, E. FRONKOVA, M. GIRAUD, A. GRIONI, J. HANCOCK, D. HERRMANN, C. JIMENEZ, Adam KREJČÍ, J. MOPPETT, Tomáš REIGL, M. SALSON, B. SCHEIJEN, M. SCHWARZ, S. SONGIA, M. SVATON, J.J.M. VAN DONGEN, P. VILLARESE, S. WAKEMAN, G. WRIGHT, G. CAZZANIGA, F. DAVI, R. GARCIA-SANZ, D. GONZALEZ, P.J.T.A. GROENEN, M. HUMMEL, E.A. MACINTYRE, K. STAMATOPOULOS, C. POTT, J. TRKA, Nikos DARZENTAS and A.W. LANGERAK. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study. \textit{Leukemia}. London: Nature Publishing Group, 2019, vol.~33, No~9, p.~2241-2253. ISSN~0887-6924. Available from: https://dx.doi.org/10.1038/s41375-019-0496-7.

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