Baseline identification of clonal V(D)J sequences for DNA-based minimal residual disease detection in multiple myeloma

Tracking of clonal immunoglobulin V(D)J rearrangement sequences by next generation sequencing is highly sensitive for minimal residual disease in multiple myeloma. However, previous studies have found variable rates of V(D)J sequence identification at baseline, which could limit tracking. Here, we aimed to define the factors influencing the identification of clonal V(D)J sequences. Bone marrow mononuclear cells from 177 myeloma patients underwent V(D)J sequencing by the LymphoTrack assays (Invivoscribe). As a molecular control for tumor cell content, we sequenced the samples using our in-house myeloma panel myTYPE. V(D)J sequence clonality was identified in 81% of samples overall, as compared with 95% in samples where tumor-derived DNA was detectable by myTYPE. Clonality was detected more frequently in patients with lambda-restricted disease, mainly because of increased detection of kappa gene rearrangements. Finally, we describe how the tumor cell content of bone marrow aspirates decrease gradually in sequential pulls because of hemodilution: From the initial pull used for aspirate smear, to the final pull that is commonly used for research. In conclusion, baseline clonality detection rates of 95% or higher are feasible in multiple myeloma. Optimal performance depends on the use of good quality aspirates and/or subsequent tumor cell enrichment.

[1]  S. Steinberg,et al.  Treatment With Carfilzomib-Lenalidomide-Dexamethasone With Lenalidomide Extension in Patients With Smoldering or Newly Diagnosed Multiple Myeloma. , 2015, JAMA oncology.

[2]  G. Morgan,et al.  Immunoglobulin gene rearrangements and the pathogenesis of multiple myeloma. , 2007, Blood.

[3]  Donavan T. Cheng,et al.  Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. , 2015, The Journal of molecular diagnostics : JMD.

[4]  O. Landgren.  MRD Testing in Multiple Myeloma: From a Surrogate Marker of Clinical Outcomes to an Every-Day Clinical Tool. , 2018, Seminars in hematology.

[5]  N. Puig,et al.  Analytical and clinical validation of a novel in-house deep-sequencing method for minimal residual disease monitoring in a phase II trial for multiple myeloma , 2017, Leukemia.

[6]  T. Cedena,et al.  Prognostic value of deep sequencing method for minimal residual disease detection in multiple myeloma. , 2014, Blood.

[7]  Alex M. Fichtenholtz,et al.  Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing , 2013, Nature Biotechnology.

[8]  M. Moarii,et al.  Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups , 2017, Leukemia.

[9]  M. Arcila,et al.  Minimal residual disease detection of myeloma using sequencing of immunoglobulin heavy chain gene VDJ regions. , 2018, Seminars in hematology.

[10]  H. Goldschmidt,et al.  International Myeloma Working Group consensus criteria for response and minimal residual disease assessment in multiple myeloma. , 2016, The Lancet. Oncology.

[11]  Hans Erik Johnsen,et al.  International Myeloma Working Group updated criteria for the diagnosis of multiple myeloma. , 2014, The Lancet. Oncology.

[12]  A. Órfão,et al.  Depth of Response in Multiple Myeloma: A Pooled Analysis of Three PETHEMA/GEM Clinical Trials. , 2017, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[13]  A. Órfão,et al.  MRD detection in multiple myeloma: comparison between MSKCC 10-color single-tube and EuroFlow 8-color 2-tube methods. , 2017, Blood advances.

[14]  R. Pieters,et al.  Standardized MRD quantification in European ALL trials: Proceedings of the Second International Symposium on MRD assessment in Kiel, Germany, 18–20 September 2008 , 2010, Leukemia.

[15]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[16]  N. Munshi,et al.  Association of Minimal Residual Disease With Superior Survival Outcomes in Patients With Multiple Myeloma: A Meta-analysis , 2017, JAMA oncology.

[17]  T. Willis,et al.  Minimal residual disease negativity using deep sequencing is a major prognostic factor in multiple myeloma. , 2018, Blood.

[18]  Nicola D. Roberts,et al.  Genomic Classification and Prognosis in Acute Myeloid Leukemia. , 2016, The New England journal of medicine.

[19]  Marina Ruggeri,et al.  Report of the European Myeloma Network on multiparametric flow cytometry in multiple myeloma and related disorders , 2008, Haematologica.

[20]  M. Stetler-Stevenson,et al.  Minimal residual disease testing in multiple myeloma by flow cytometry: major heterogeneity. , 2013, Blood.

[21]  M Hummel,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 , 2003, Leukemia.

[22]  V. Carlton,et al.  Prognostic value of sequencing-based minimal residual disease detection in patients with multiple myeloma who underwent autologous stem-cell transplantation , 2017, Annals of oncology : official journal of the European Society for Medical Oncology.

[23]  M. van der Burg,et al.  Ordered recombination of immunoglobulin light chain genes occurs at the IGK locus but seems less strict at the IGL locus. , 2001, Blood.

[24]  W. Figg,et al.  Remission and Progression-Free Survival in Patients With Newly Diagnosed Multiple Myeloma Treated With Carfilzomib, Lenalidomide, and Dexamethasone: Five-Year Follow-up of a Phase 2 Clinical Trial , 2018, JAMA oncology.

[25]  A Orfao,et al.  Next Generation Flow for highly sensitive and standardized detection of minimal residual disease in multiple myeloma , 2017, Leukemia.

[26]  A. Stewart,et al.  Immunoglobulin gene analysis as a tool for investigating human immune responses , 2018, Immunological reviews.

[27]  N. Munshi,et al.  Minimal Residual Disease in Multiple Myeloma: Final Analysis of the IFM2009 Trial , 2017 .

[28]  Marcelo A. Navarrete,et al.  ARTISAN PCR: rapid identification of full‐length immunoglobulin rearrangements without primer binding bias , 2017, British journal of haematology.

[29]  F. Guillén-Grima,et al.  A simple flow-cytometry method to evaluate peripheral blood contamination of bone marrow aspirates. , 2017, Journal of immunological methods.

[30]  Ahmet Zehir,et al.  Next-Generation Assessment of Human Epidermal Growth Factor Receptor 2 (ERBB2) Amplification Status: Clinical Validation in the Context of a Hybrid Capture-Based, Comprehensive Solid Tumor Genomic Profiling Assay. , 2017, The Journal of molecular diagnostics : JMD.

[31]  J. Miguel,et al.  Incomplete DJH rearrangements as a novel tumor target for minimal residual disease quantitation in multiple myeloma using real-time PCR , 2003, Leukemia.

[32]  P. Campbell,et al.  A DNA target-enrichment approach to detect mutations, copy number changes and immunoglobulin translocations in multiple myeloma , 2016, Blood Cancer Journal.

[33]  M. Syed,et al.  Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms. , 2019, The Journal of molecular diagnostics : JMD.

[34]  M. Stetler-Stevenson,et al.  Myeloma minimal residual disease testing in the United States: Evidence of improved standardization , 2016, American journal of hematology.

[35]  M. Roshal.  Minimal Residual Disease Detection by Flow Cytometry in Multiple Myeloma: Why and How? , 2018, Seminars in hematology.

[36]  Ning Ma,et al.  IgBLAST: an immunoglobulin variable domain sequence analysis tool , 2013, Nucleic Acids Res..

[37]  Andre H Crepaldi,et al.  Daratumumab plus Bortezomib, Melphalan, and Prednisone for Untreated Myeloma , 2017, The New England journal of medicine.

[38]  A. Órfão,et al.  Molecular detection of minimal residual disease in multiple myeloma , 2018, British journal of haematology.

[39]  A. Palumbo,et al.  Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders , 2014, Leukemia.

[40]  A. Lesokhin,et al.  Minimal residual disease in multiple myeloma: bringing the bench to the bedside , 2015, Nature Reviews Clinical Oncology.

[41]  G. Merlini,et al.  Insights into the regulation of immunoglobulin light chain gene rearrangements via analysis of the κ light chain locus in λ myeloma , 2004 .

[42]  S. Devlin,et al.  Role of MRD status in relation to clinical outcomes in newly diagnosed multiple myeloma patients: a meta-analysis , 2016, Bone Marrow Transplantation.