Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders

James Peter Stewart; Jana Gazdova; Nikos Darzentas; Dorte Wren; Paula Proszek; Grazia Fazio; Simona Songia; Miguel Alcoceba; Maria Eugenia Sarasquete; Patrick Villarese; Michele Y. Van Der Klift; Kim C. Heezen; Neil McCafferty; Karol Pal; Mark Catherwood; Chang Sik Kim; Shambhavi Srivastava; Leonie I. Kroeze; Elizabeth Hodges; Kostas Stamatopoulos; Wolfram Klapper; Elisa Genuardi; Simone Ferrero; Michiel Van Den Brand; Giovanni Cazzaniga; Frederic Davi; Lesley Ann Sutton; Ramon Garcia-Sanz; Patricia J.T.A. Groenen; Elizabeth A. Macintyre; Monika Bruggemann; Christiane Pott; Anton W. Langerak; David Gonzalez

doi:10.1182/bloodadvances.2020004056

Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders

James Peter Stewart, Jana Gazdova, Nikos Darzentas, Dorte Wren, Paula Proszek, Grazia Fazio, Simona Songia, Miguel Alcoceba, Maria Eugenia Sarasquete, Patrick Villarese, Michele Y. Van Der Klift, Kim C. Heezen, Neil McCafferty, Karol Pal, Mark Catherwood, Chang Sik Kim, Shambhavi Srivastava, Leonie I. Kroeze, Elizabeth Hodges, Kostas StamatopoulosWolfram Klapper, Elisa Genuardi, Simone Ferrero, Michiel Van Den Brand, Giovanni Cazzaniga, Frederic Davi, Lesley Ann Sutton, Ramon Garcia-Sanz, Patricia J.T.A. Groenen, Elizabeth A. Macintyre, Monika Bruggemann, Christiane Pott, Anton W. Langerak, David Gonzalez^*

^*Corresponding author for this work

Immunology

Research output: Contribution to journal › Article › Academic › peer-review

21 Citations (Scopus)

Abstract

Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B-and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-To-end workflow for simultaneous detection of B-and T-cell clonality, translocations, CNAs, and sequence variants.

Original language	English
Pages (from-to)	3188-3198
Number of pages	11
Journal	Blood advances
Volume	5
Issue number	16
DOIs	https://doi.org/10.1182/bloodadvances.2020004056
Publication status	Published - 24 Aug 2021

Bibliographical note

Funding Information:
The Northern Ireland High Performance Computing Service provided computing resources, funded by the Engineering and Physical Sciences Research Council (EP/T022175).

Funding Information:
Conflict-of-interest disclosure: M.A. has received honoraria from Janssen and nonfinancial support (event attendance) from Janssen, AbbVie, and Roche. W.K. has received research grants from Roche, Regeneron, Amgen, and Takeda. L.-A.S. has received honoraria from Janssen. R.G.-S. has received honoraria, consultancy, and/or research funding from Amgen, Bristol-Myers Squibb, Gilead, Incyte, Janssen, Novartis, Pharmacyclics, and Takeda. E.M. provides consultancy services to Servier for minimal residual disease measurement in ALL. A.W.L. has received contract research support from Roche-Genentech, Gilead, and Janssen. D.G. has received honoraria, consultancy, and/or research funding from Roche, AstraZeneca, Novar-tis, Incyte, Eli Lilly, and Illumina and is cofounder of Univ8 Genomics. The remaining authors declare no competing financial interests.

Publisher Copyright:
© 2021 American Society of Hematology. All rights reserved.

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10.1182/bloodadvances.2020004056

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Stewart, J. P., Gazdova, J., Darzentas, N., Wren, D., Proszek, P., Fazio, G., Songia, S., Alcoceba, M., Sarasquete, M. E., Villarese, P., Van Der Klift, M. Y., Heezen, K. C., McCafferty, N., Pal, K., Catherwood, M., Kim, C. S., Srivastava, S., Kroeze, L. I., Hodges, E., ... Gonzalez, D. (2021). Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood advances, 5(16), 3188-3198. https://doi.org/10.1182/bloodadvances.2020004056

@article{c681c73552b94f4d87e65c5961ac7c79,

title = "Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders",

abstract = "Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B-and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-To-end workflow for simultaneous detection of B-and T-cell clonality, translocations, CNAs, and sequence variants.",

author = "Stewart, {James Peter} and Jana Gazdova and Nikos Darzentas and Dorte Wren and Paula Proszek and Grazia Fazio and Simona Songia and Miguel Alcoceba and Sarasquete, {Maria Eugenia} and Patrick Villarese and {Van Der Klift}, {Michele Y.} and Heezen, {Kim C.} and Neil McCafferty and Karol Pal and Mark Catherwood and Kim, {Chang Sik} and Shambhavi Srivastava and Kroeze, {Leonie I.} and Elizabeth Hodges and Kostas Stamatopoulos and Wolfram Klapper and Elisa Genuardi and Simone Ferrero and {Van Den Brand}, Michiel and Giovanni Cazzaniga and Frederic Davi and Sutton, {Lesley Ann} and Ramon Garcia-Sanz and Groenen, {Patricia J.T.A.} and Macintyre, {Elizabeth A.} and Monika Bruggemann and Christiane Pott and Langerak, {Anton W.} and David Gonzalez",

note = "Funding Information: The Northern Ireland High Performance Computing Service provided computing resources, funded by the Engineering and Physical Sciences Research Council (EP/T022175). Funding Information: Conflict-of-interest disclosure: M.A. has received honoraria from Janssen and nonfinancial support (event attendance) from Janssen, AbbVie, and Roche. W.K. has received research grants from Roche, Regeneron, Amgen, and Takeda. L.-A.S. has received honoraria from Janssen. R.G.-S. has received honoraria, consultancy, and/or research funding from Amgen, Bristol-Myers Squibb, Gilead, Incyte, Janssen, Novartis, Pharmacyclics, and Takeda. E.M. provides consultancy services to Servier for minimal residual disease measurement in ALL. A.W.L. has received contract research support from Roche-Genentech, Gilead, and Janssen. D.G. has received honoraria, consultancy, and/or research funding from Roche, AstraZeneca, Novar-tis, Incyte, Eli Lilly, and Illumina and is cofounder of Univ8 Genomics. The remaining authors declare no competing financial interests. Publisher Copyright: {\textcopyright} 2021 American Society of Hematology. All rights reserved.",

year = "2021",

month = aug,

day = "24",

doi = "10.1182/bloodadvances.2020004056",

language = "English",

volume = "5",

pages = "3188--3198",

journal = "Blood advances",

issn = "2473-9529",

publisher = "American Society of Hematology",

number = "16",

}

Stewart, JP, Gazdova, J, Darzentas, N, Wren, D, Proszek, P, Fazio, G, Songia, S, Alcoceba, M, Sarasquete, ME, Villarese, P, Van Der Klift, MY , Heezen, KC, McCafferty, N, Pal, K, Catherwood, M, Kim, CS, Srivastava, S, Kroeze, LI, Hodges, E, Stamatopoulos, K, Klapper, W, Genuardi, E, Ferrero, S, Van Den Brand, M, Cazzaniga, G, Davi, F, Sutton, LA, Garcia-Sanz, R, Groenen, PJTA, Macintyre, EA, Bruggemann, M, Pott, C, Langerak, AW & Gonzalez, D 2021, 'Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders', Blood advances, vol. 5, no. 16, pp. 3188-3198. https://doi.org/10.1182/bloodadvances.2020004056

TY - JOUR

T1 - Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders

AU - Stewart, James Peter

AU - Gazdova, Jana

AU - Darzentas, Nikos

AU - Wren, Dorte

AU - Proszek, Paula

AU - Fazio, Grazia

AU - Songia, Simona

AU - Alcoceba, Miguel

AU - Sarasquete, Maria Eugenia

AU - Villarese, Patrick

AU - Van Der Klift, Michele Y.

AU - Heezen, Kim C.

AU - McCafferty, Neil

AU - Pal, Karol

AU - Catherwood, Mark

AU - Kim, Chang Sik

AU - Srivastava, Shambhavi

AU - Kroeze, Leonie I.

AU - Hodges, Elizabeth

AU - Stamatopoulos, Kostas

AU - Klapper, Wolfram

AU - Genuardi, Elisa

AU - Ferrero, Simone

AU - Van Den Brand, Michiel

AU - Cazzaniga, Giovanni

AU - Davi, Frederic

AU - Sutton, Lesley Ann

AU - Garcia-Sanz, Ramon

AU - Groenen, Patricia J.T.A.

AU - Macintyre, Elizabeth A.

AU - Bruggemann, Monika

AU - Pott, Christiane

AU - Langerak, Anton W.

AU - Gonzalez, David

N1 - Funding Information: The Northern Ireland High Performance Computing Service provided computing resources, funded by the Engineering and Physical Sciences Research Council (EP/T022175). Funding Information: Conflict-of-interest disclosure: M.A. has received honoraria from Janssen and nonfinancial support (event attendance) from Janssen, AbbVie, and Roche. W.K. has received research grants from Roche, Regeneron, Amgen, and Takeda. L.-A.S. has received honoraria from Janssen. R.G.-S. has received honoraria, consultancy, and/or research funding from Amgen, Bristol-Myers Squibb, Gilead, Incyte, Janssen, Novartis, Pharmacyclics, and Takeda. E.M. provides consultancy services to Servier for minimal residual disease measurement in ALL. A.W.L. has received contract research support from Roche-Genentech, Gilead, and Janssen. D.G. has received honoraria, consultancy, and/or research funding from Roche, AstraZeneca, Novar-tis, Incyte, Eli Lilly, and Illumina and is cofounder of Univ8 Genomics. The remaining authors declare no competing financial interests. Publisher Copyright: © 2021 American Society of Hematology. All rights reserved.

PY - 2021/8/24

Y1 - 2021/8/24

N2 - Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B-and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-To-end workflow for simultaneous detection of B-and T-cell clonality, translocations, CNAs, and sequence variants.

AB - Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B-and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-To-end workflow for simultaneous detection of B-and T-cell clonality, translocations, CNAs, and sequence variants.

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U2 - 10.1182/bloodadvances.2020004056

DO - 10.1182/bloodadvances.2020004056

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SP - 3188

EP - 3198

JO - Blood advances

JF - Blood advances

IS - 16

ER -

Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders

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