Cargando…
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
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 appli...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756028/ https://www.ncbi.nlm.nih.gov/pubmed/31243313 http://dx.doi.org/10.1038/s41375-019-0496-7 |
_version_ | 1783453336413929472 |
---|---|
author | Brüggemann, Monika Kotrová, Michaela Knecht, Henrik Bartram, Jack Boudjogrha, Myriam Bystry, Vojtech Fazio, Grazia Froňková, Eva Giraud, Mathieu Grioni, Andrea Hancock, Jeremy Herrmann, Dietrich Jiménez, Cristina Krejci, Adam Moppett, John Reigl, Tomas Salson, Mikael Scheijen, Blanca Schwarz, Martin Songia, Simona Svaton, Michael van Dongen, Jacques J. M. Villarese, Patrick Wakeman, Stephanie Wright, Gary Cazzaniga, Giovanni Davi, Frédéric García-Sanz, Ramón Gonzalez, David Groenen, Patricia J. T. A. Hummel, Michael Macintyre, Elizabeth A. Stamatopoulos, Kostas Pott, Christiane Trka, Jan Darzentas, Nikos Langerak, Anton W. |
author_facet | Brüggemann, Monika Kotrová, Michaela Knecht, Henrik Bartram, Jack Boudjogrha, Myriam Bystry, Vojtech Fazio, Grazia Froňková, Eva Giraud, Mathieu Grioni, Andrea Hancock, Jeremy Herrmann, Dietrich Jiménez, Cristina Krejci, Adam Moppett, John Reigl, Tomas Salson, Mikael Scheijen, Blanca Schwarz, Martin Songia, Simona Svaton, Michael van Dongen, Jacques J. M. Villarese, Patrick Wakeman, Stephanie Wright, Gary Cazzaniga, Giovanni Davi, Frédéric García-Sanz, Ramón Gonzalez, David Groenen, Patricia J. T. A. Hummel, Michael Macintyre, Elizabeth A. Stamatopoulos, Kostas Pott, Christiane Trka, Jan Darzentas, Nikos Langerak, Anton W. |
author_sort | Brüggemann, Monika |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6756028 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-67560282019-09-24 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 Brüggemann, Monika Kotrová, Michaela Knecht, Henrik Bartram, Jack Boudjogrha, Myriam Bystry, Vojtech Fazio, Grazia Froňková, Eva Giraud, Mathieu Grioni, Andrea Hancock, Jeremy Herrmann, Dietrich Jiménez, Cristina Krejci, Adam Moppett, John Reigl, Tomas Salson, Mikael Scheijen, Blanca Schwarz, Martin Songia, Simona Svaton, Michael van Dongen, Jacques J. M. Villarese, Patrick Wakeman, Stephanie Wright, Gary Cazzaniga, Giovanni Davi, Frédéric García-Sanz, Ramón Gonzalez, David Groenen, Patricia J. T. A. Hummel, Michael Macintyre, Elizabeth A. Stamatopoulos, Kostas Pott, Christiane Trka, Jan Darzentas, Nikos Langerak, Anton W. Leukemia Article 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. Nature Publishing Group UK 2019-06-26 2019 /pmc/articles/PMC6756028/ /pubmed/31243313 http://dx.doi.org/10.1038/s41375-019-0496-7 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Brüggemann, Monika Kotrová, Michaela Knecht, Henrik Bartram, Jack Boudjogrha, Myriam Bystry, Vojtech Fazio, Grazia Froňková, Eva Giraud, Mathieu Grioni, Andrea Hancock, Jeremy Herrmann, Dietrich Jiménez, Cristina Krejci, Adam Moppett, John Reigl, Tomas Salson, Mikael Scheijen, Blanca Schwarz, Martin Songia, Simona Svaton, Michael van Dongen, Jacques J. M. Villarese, Patrick Wakeman, Stephanie Wright, Gary Cazzaniga, Giovanni Davi, Frédéric García-Sanz, Ramón Gonzalez, David Groenen, Patricia J. T. A. Hummel, Michael Macintyre, Elizabeth A. Stamatopoulos, Kostas Pott, Christiane Trka, Jan Darzentas, Nikos Langerak, Anton W. 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 |
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 |
title_full | 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 |
title_fullStr | 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 |
title_full_unstemmed | 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 |
title_short | 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 |
title_sort | 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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756028/ https://www.ncbi.nlm.nih.gov/pubmed/31243313 http://dx.doi.org/10.1038/s41375-019-0496-7 |
work_keys_str_mv | AT bruggemannmonika standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT kotrovamichaela standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT knechthenrik standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT bartramjack standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT boudjogrhamyriam standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT bystryvojtech standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT faziograzia standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT fronkovaeva standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT giraudmathieu standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT grioniandrea standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT hancockjeremy standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT herrmanndietrich standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT jimenezcristina standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT krejciadam standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT moppettjohn standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT reigltomas standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT salsonmikael standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT scheijenblanca standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT schwarzmartin standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT songiasimona standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT svatonmichael standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT vandongenjacquesjm standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT villaresepatrick standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT wakemanstephanie standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT wrightgary standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT cazzanigagiovanni standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT davifrederic standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT garciasanzramon standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT gonzalezdavid standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT groenenpatriciajta standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT hummelmichael standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT macintyreelizabetha standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT stamatopouloskostas standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT pottchristiane standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT trkajan standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT darzentasnikos standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT langerakantonw standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy AT standardizednextgenerationsequencingofimmunoglobulinandtcellreceptorgenerecombinationsformrdmarkeridentificationinacutelymphoblasticleukaemiaaeuroclonalityngsvalidationstudy |