Next-generation sequencing of immunoglobulin gene rearrangements for clonality assessment: a technical feasibility study by EuroClonality-NGS
Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
31197258
PubMed Central
PMC6756030
DOI
10.1038/s41375-019-0508-7
PII: 10.1038/s41375-019-0508-7
Knihovny.cz E-zdroje
- MeSH
- B-buněčný lymfom genetika MeSH
- genová přestavba genetika MeSH
- geny pro imunoglobuliny genetika MeSH
- imunoglobuliny - kappa-řetězce genetika MeSH
- lidé MeSH
- lymfoproliferativní nemoci genetika MeSH
- studie proveditelnosti MeSH
- těžké řetězce imunoglobulinů genetika MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- imunoglobuliny - kappa-řetězce MeSH
- těžké řetězce imunoglobulinů MeSH
One of the hallmarks of B lymphoid malignancies is a B cell clone characterized by a unique footprint of clonal immunoglobulin (IG) gene rearrangements that serves as a diagnostic marker for clonality assessment. The EuroClonality/BIOMED-2 assay is currently the gold standard for analyzing IG heavy chain (IGH) and κ light chain (IGK) gene rearrangements of suspected B cell lymphomas. Here, the EuroClonality-NGS Working Group presents a multicentre technical feasibility study of a novel approach involving next-generation sequencing (NGS) of IGH and IGK loci rearrangements that is highly suitable for detecting IG gene rearrangements in frozen and formalin-fixed paraffin-embedded tissue specimens. By employing gene-specific primers for IGH and IGK amplifying smaller amplicon sizes in combination with deep sequencing technology, this NGS-based IG clonality analysis showed robust performance, even in DNA samples of suboptimal DNA integrity, and a high clinical sensitivity for the detection of clonal rearrangements. Bioinformatics analyses of the high-throughput sequencing data with ARResT/Interrogate, a platform developed within the EuroClonality-NGS Working Group, allowed accurate identification of clonotypes in both polyclonal cell populations and monoclonal lymphoproliferative disorders. This multicentre feasibility study is an important step towards implementation of NGS-based clonality assessment in clinical practice, which will eventually improve lymphoma diagnostics.
Charité Universitätsmedizin Berlin Institute of Pathology D 10117 Berlin Germany
Department of Haematology Belfast City Hospital Belfast BT9 7AB UK
Department of Hematology University Hospital Schleswig Holstein 24105 Kiel Germany
Department of Pathology Radboud University Medical Center 6525 GA Nijmegen The Netherlands
Hematology Department Hospital Pitié Salpêtrière and Sorbonne University 75013 Paris France
Institute of Applied Biosciences GR 57001 Thermi Thessaloniki Greece
Zobrazit více v PubMed
Arnold A, Cossman J, Bakhshi A, Jaffe ES, Waldmann TA, Korsmeyer SJ. Immunoglobulin-gene rearrangements as unique clonal markers in human lymphoid neoplasms. N Engl J Med. 1983;309:1593–9. doi: 10.1056/NEJM198312293092601. PubMed DOI
van Dongen JJ, Wolvers-Tettero IL. Analysis of immunoglobulin and T cell receptor genes. Part II: Possibilities and limitations in the diagnosis and management of lymphoproliferative diseases and related disorders. Clin Chim Acta. 1991;198:93–174. doi: 10.1016/0009-8981(91)90247-A. PubMed DOI
Dudley DD, Chaudhuri J, Bassing CH, Alt FW. Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences. Adv Immunol. 2005;86:43–112. doi: 10.1016/S0065-2776(04)86002-4. PubMed DOI
Di Noia JM, Neuberger MS. Molecular mechanisms of antibody somatic hypermutation. Annu Rev Biochem. 2007;76:1–22. doi: 10.1146/annurev.biochem.76.061705.090740. PubMed DOI
Arber DA. Molecular diagnostic approach to non-Hodgkin’s lymphoma. J Mol Diagn. 2000;2:178–90. doi: 10.1016/S1525-1578(10)60636-8. PubMed DOI PMC
Gazzola A, Mannu C, Rossi M, Laginestra MA, Sapienza MR, Fuligni F, et al. The evolution of clonality testing in the diagnosis and monitoring of hematological malignancies. Ther Adv Hematol. 2014;5:35–47. doi: 10.1177/2040620713519729. PubMed DOI PMC
van Dongen JJ, Langerak AW, Bruggemann M, Evans PA, Hummel M, Lavender FL, et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia. 2003;17:2257–317. doi: 10.1038/sj.leu.2403202. PubMed DOI
Evans PA, Pott C, Groenen PJ, Salles G, Davi F, Berger F, et al. Significantly improved PCR-based clonality testing in B-cell malignancies by use of multiple immunoglobulin gene targets. Report of the BIOMED-2 Concerted Action BHM4-CT98-3936. Leukemia. 2007;21:207–14. doi: 10.1038/sj.leu.2404479. PubMed DOI
Langerak AW, Groenen PJ, Bruggemann M, Beldjord K, Bellan C, Bonello L, et al. EuroClonality/BIOMED-2 guidelines for interpretation and reporting of Ig/TCR clonality testing in suspected lymphoproliferations. Leukemia. 2012;26:2159–71. doi: 10.1038/leu.2012.246. PubMed DOI PMC
Halldorsdottir AM, Zehnbauer BA, Burack WR. Application of BIOMED-2 clonality assays to formalin-fixed paraffin embedded follicular lymphoma specimens: superior performance of the IGK assays compared to IGH for suboptimal specimens. Leuk Lymphoma. 2007;48:1338–43. doi: 10.1080/10428190701377022. PubMed DOI
Liu H, Bench AJ, Bacon CM, Payne K, Huang Y, Scott MA, et al. A practical strategy for the routine use of BIOMED-2 PCR assays for detection of B- and T-cell clonality in diagnostic haematopathology. Br J Haematol. 2007;138:31–43. doi: 10.1111/j.1365-2141.2007.06618.x. PubMed DOI
Morales AV, Arber DA, Seo K, Kohler S, Kim YH, Sundram UN. Evaluation of B-cell clonality using the BIOMED-2 PCR method effectively distinguishes cutaneous B-cell lymphoma from benign lymphoid infiltrates. Am J Derm. 2008;30:425–30. doi: 10.1097/DAD.0b013e31818118f7. PubMed DOI
Patel KP, Pan Q, Wang Y, Maitta RW, Du J, Xue X, et al. Comparison of BIOMED-2 versus laboratory-developed polymerase chain reaction assays for detecting T-cell receptor-gamma gene rearrangements. J Mol Diagn. 2010;12:226–37. doi: 10.2353/jmoldx.2010.090042. PubMed DOI PMC
Boyd SD, Gaeta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, et al. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. J Immunol. 2010;184:6986–92. doi: 10.4049/jimmunol.1000445. PubMed DOI PMC
Wu YC, Kipling D, Leong HS, Martin V, Ademokun AA, Dunn-Walters DK. High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations. Blood. 2010;116:1070–8. doi: 10.1182/blood-2010-03-275859. PubMed DOI PMC
Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009;19:1817–24. doi: 10.1101/gr.092924.109. PubMed DOI PMC
Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood. 2009;114:4099–107. doi: 10.1182/blood-2009-04-217604. PubMed DOI PMC
Benichou J, Ben-Hamo R, Louzoun Y, Efroni S. Rep-Seq: uncovering the immunological repertoire through next-generation sequencing. Immunology. 2012;135:183–91. doi: 10.1111/j.1365-2567.2011.03527.x. PubMed DOI PMC
Ghraichy Marie, Galson Jacob D., Kelly Dominic F., Trück Johannes. B-cell receptor repertoire sequencing in patients with primary immunodeficiency: a review. Immunology. 2017;153(2):145–160. doi: 10.1111/imm.12865. PubMed DOI PMC
Campbell PJ, Pleasance ED, Stephens PJ, Dicks E, Rance R, Goodhead I, et al. Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci USA. 2008;105:13081–6. doi: 10.1073/pnas.0801523105. PubMed DOI PMC
Jiang Y, Nie K, Redmond D, Melnick AM, Tam W, Elemento O. VDJ-Seq: deep sequencing analysis of rearranged immunoglobulin heavy chain gene to reveal clonal evolution patterns of B cell lymphoma. J Vis Exp. 2015;106:e53215. PubMed PMC
Roschewski M, Dunleavy K, Pittaluga S, Moorhead M, Pepin F, Kong K, et al. Circulating tumour DNA and CT monitoring in patients with untreated diffuse large B-cell lymphoma: a correlative biomarker study. Lancet Oncol. 2015;16:541–9. doi: 10.1016/S1470-2045(15)70106-3. PubMed DOI PMC
Sarkozy C, Huet S, Carlton VE, Fabiani B, Delmer A, Jardin F, et al. The prognostic value of clonal heterogeneity and quantitative assessment of plasma circulating clonal IG-VDJ sequences at diagnosis in patients with follicular lymphoma. Oncotarget. 2017;8:8765–74. doi: 10.18632/oncotarget.14448. PubMed DOI PMC
Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med. 2009;1:12ra23. doi: 10.1126/scitranslmed.3000540. PubMed DOI PMC
Ladetto M, Bruggemann M, Monitillo L, Ferrero S, Pepin F, Drandi D, et al. Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders. Leukemia. 2014;28:1299–307. doi: 10.1038/leu.2013.375. PubMed DOI
Pulsipher MA, Carlson C, Langholz B, Wall DA, Schultz KR, Bunin N, et al. IgH-V(D)J NGS-MRD measurement pre- and early post-allotransplant defines very low- and very high-risk ALL patients. Blood. 2015;125:3501–8. doi: 10.1182/blood-2014-12-615757. PubMed DOI PMC
Faham M, Zheng J, Moorhead M, Carlton VE, Stow P, Coustan-Smith E, et al. Deep-sequencing approach for minimal residual disease detection in acute lymphoblastic leukemia. Blood. 2012;120:5173–80. doi: 10.1182/blood-2012-07-444042. PubMed DOI PMC
Alamyar E, Duroux P, Lefranc MP, Giudicelli V. IMGT((R)) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol. 2012;882:569–604. doi: 10.1007/978-1-61779-842-9_32. PubMed DOI
Giraud M, Salson M, Duez M, Villenet C, Quief S, Caillault A, et al. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genom. 2014;15:409. doi: 10.1186/1471-2164-15-409. PubMed DOI PMC
Paciello G, Acquaviva A, Pighi C, Ferrarini A, Macii E, Zamo A, et al. VDJSeq-Solver: in silico V(D)J recombination detection tool. PLoS ONE. 2015;10:e0118192. doi: 10.1371/journal.pone.0118192. PubMed DOI PMC
Russ DE, Ho KY, Longo NS. HTJoinSolver: human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs. BMC Bioinforma. 2015;16:170. doi: 10.1186/s12859-015-0589-x. PubMed DOI PMC
Bystry V, Reigl T, Krejci A, Demko M, Hanakova B, Grioni A, et al. ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data. Bioinformatics. 2017;33:435–7. PubMed
Knecht H, Reigl T, Kotrova M, Appelt F, Stewart P, Bystry V, et al. Quality control and quantification in IG/TR next-generation sequencing maker identification: protocols and bioinformatic functionalities developed by EuoClonality-NGS. Leukemia. 2019; in press (this issue). PubMed PMC
Bruggemann M, Kotrova M, Knecht H, Bartram J, Boudjogrha M, Bystry V, et al. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukemia: a EuroClonality-NGS validation study. Leukemia. 2019; in press (this issue). PubMed PMC
Boer A, Tirumalae R, Bresch M, Falk TM. Pseudoclonality in cutaneous pseudolymphomas: a pitfall in interpretation of rearrangement studies. Br J Dermatol. 2008;159:394–402. doi: 10.1111/j.1365-2133.2008.08670.x. PubMed DOI