Skip to main content
PMC home page
Medline Book to support NIHPA logoLink to Medline Book to support NIHPA
. 2022;2453:43–59. doi: 10.1007/978-1-0716-2115-8_3

One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia.

Patrick Villarese, Chrystelle Abdo, Matthieu Bertrand, Florian Thonier, Mathieu Giraud, Mikaël Salson, Elizabeth Macintyre
PMCID: PMC9761905  PMID: 35622319

Abstract

Within the EuroClonality-NGS group, immune repertoire analysis for target identification in lymphoid malignancies was initially developed using two-stage amplicon approaches, essentially as a progressive modification of preceding methods developed for Sanger sequencing. This approach has, however, limitations with respect to sample handling, adaptation to automation, and risk of contamination by amplicon products. We therefore developed one-step PCR amplicon methods with individual barcoding for batched analysis for IGH, IGK, TRD, TRG, and TRB rearrangements, followed by Vidjil-based data analysis.

Full text of this article can be found in Bookshelf.

References

  1. Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302(5909):575–581 doi: 10.1038/302575a0. [DOI] [PubMed]
  2. Evans PAS, Pott C, Groenen PJTA, Salles G, Davi F, Berger F et al (2007) 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 21(2):207–214 doi: 10.1038/sj.leu.2404479. [DOI] [PubMed]
  3. Langerak AW, Groenen PJTA, Brüggemann M, Beldjord K, Bellan C, Bonello L et al (2012) EuroClonality/BIOMED-2 guidelines for interpretation and reporting of Ig/TCR clonality testing in suspected lymphoproliferations. Leukemia 26(10):2159–2171 doi: 10.1038/leu.2012.246. [DOI] [PMC free article] [PubMed]
  4. van Dongen JJM, Langerak AW, Brüggemann M, Evans PA, Hummel M, Lavender FL et al (2003) 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 17(12):2257–2317 doi: 10.1038/sj.leu.2403202. [DOI] [PubMed]
  5. Langerak AW, Brüggemann M, Davi F, Darzentas N, van Dongen JJM, Gonzalez D et al (2017) High-throughput Immunogenetics for clinical and research applications in immunohematology: potential and challenges. J Immunol 198(10):3765–3774 doi: 10.4049/jimmunol.1602050. [DOI] [PubMed]
  6. Scheijen B, Meijers RWJ, Rijntjes J, van der Klift MY, Möbs M, Steinhilber J et al (2019) Next-generation sequencing of immunoglobulin gene rearrangements for clonality assessment: a technical feasibility study by EuroClonality-NGS. Leukemia 33(9):2227–2240 doi: 10.1038/s41375-019-0508-7. [DOI] [PMC free article] [PubMed]
  7. Kotrova M, Trka J, Kneba M, Brüggemann M (2017) Is next-generation sequencing the way to go for residual disease monitoring in acute lymphoblastic leukemia? Mol Diagn Ther 21(5):481–492 doi: 10.1007/s40291-017-0277-9. [DOI] [PubMed]
  8. Logan AC, Gao H, Wang C, Sahaf B, Jones CD, Marshall EL et al (2011) High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proc Natl Acad Sci U S A 108(52):21194–21199 doi: 10.1073/pnas.1118357109. [DOI] [PMC free article] [PubMed]
  9. Wu D, Sherwood A, Fromm JR, Winter SS, Dunsmore KP, Loh ML et al (2012) High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci Transl Med 4(134):134ra63 doi: 10.1126/scitranslmed.3003656. [DOI] [PubMed]
  10. Brüggemann M, Kotrová M, Knecht H, Bartram J, Boudjogrha M, Bystry V et al (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. Leukemia 33(9):2241–2253 doi: 10.1038/s41375-019-0496-7. [DOI] [PMC free article] [PubMed]
  11. Giraud M, Salson M, Duez M, Villenet C, Quief S, Caillault A et al (2014) Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics 15:409 doi: 10.1186/1471-2164-15-409. [DOI] [PMC free article] [PubMed]
  12. Alamyar E, Duroux P, Lefranc M-P, Giudicelli V (2012) IMGT(®) 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 882:569–604 doi: 10.1007/978-1-61779-842-9_32. [DOI] [PubMed]
  13. Aouinti S, Giudicelli V, Duroux P, Malouche D, Kossida S, Lefranc MP (2016) IMGT/StatClonotype for pairwise evaluation and visualization of NGS IG and TR IMGT clonotype (AA) diversity or expression from IMGT/HighV-QUEST. Front Immunol 7:339 doi: 10.3389/fimmu.2016.00339. [DOI] [PMC free article] [PubMed]
  14. Lefranc M-P (2014) Immunoglobulin and T cell receptor genes: IMGT® and the birth and rise of Immunoinformatics. Front Immunol 5:22 doi: 10.3389/fimmu.2014.00022. [DOI] [PMC free article] [PubMed]
  15. Lefranc M-P, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S et al (2015) IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res 43(Database issue):D413–D422 doi: 10.1093/nar/gku1056. [DOI] [PMC free article] [PubMed]

RESOURCES