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Antigen Receptors Gene Analysis for Minimal Residual Disease Detection in Acute Lymphoblastic Leukemia: The Role of High Throughput Sequencing. HEMATO 2023. [DOI: 10.3390/hemato4010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The prognosis of adult acute lymphoblastic leukemia (ALL) is variable but more often dismal. Indeed, its clinical management is challenging, current therapies inducing complete remission in 65–90% of cases, but only 30–40% of patients being cured. The major determinant of treatment failure is relapse; consequently, measurement of residual leukemic blast (minimal residual disease, MRD) has become a powerful independent prognostic indicator in adults. Numerous evidences have also supported the clinical relevance of MRD assessment for risk class assignment and treatment selection. MRD can be virtually evaluated in all ALL patients using different technologies, such as polymerase chain reaction amplification of fusion transcripts and clonal rearrangements of antigen receptor genes, flow cytometric study of leukemic immunophenotypes and, the most recent, high throughput sequencing (HTS). In this review, the authors focused on the latest developments on MRD monitoring with emphasis on the use of HTS, as well as on the clinical impact of MRD monitoring.
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2
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Genuardi E, Romano G, Beccuti M, Alessandria B, Mannina D, Califano C, Rota Scalabrini D, Cortelazzo S, Ladetto M, Ferrero S, Calogero RA, Cordero F. Application of the Euro Clonality next-generation sequencing-based marker screening approach to detect immunoglobulin heavy chain rearrangements in mantle cell lymphoma patients: first data from the Fondazione Italiana Linfomi MCL0208 trial. Br J Haematol 2021; 194:378-381. [PMID: 34002365 PMCID: PMC8515379 DOI: 10.1111/bjh.17519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/06/2021] [Indexed: 01/09/2023]
Abstract
Minimal residual disease (MRD) determined by classic polymerase chain reaction (PCR) methods is a powerful outcome predictor in mantle cell lymphoma (MCL). Nevertheless, some technical pitfalls can reduce the rate of of molecular markers. Therefore, we applied the EuroClonality‐NGS IGH (next‐generation sequencing immunoglobulin heavy chain) method (previously published in acute lymphoblastic leukaemia) to 20 MCL patients enrolled in an Italian phase III trial sponsored by Fondazione Italiana Linfomi. Results from this preliminary investigation show that EuroClonality‐NGS IGH method is feasible in the MCL context, detecting a molecular IGH target in 19/20 investigated cases, allowing MRD monitoring also in those patients lacking a molecular marker for classical screening approaches.
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Affiliation(s)
- Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences - Hematology Division, University of Torino, Torino, Italy
| | - Greta Romano
- Department of Computer Sciences, University of Torino, Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo (Torino), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Marco Beccuti
- Department of Computer Sciences, University of Torino, Torino, Italy
| | - Beatrice Alessandria
- Department of Molecular Biotechnologies and Health Sciences - Hematology Division, University of Torino, Torino, Italy
| | - Donato Mannina
- Azienda Ospedaliera Papardo- UOC di Ematologia, Messina, Italy
| | | | | | | | - Marco Ladetto
- Division of Hematology, Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Simone Ferrero
- Department of Molecular Biotechnologies and Health Sciences - Hematology Division, University of Torino, Torino, Italy.,Hematology Division, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Francesca Cordero
- Department of Computer Sciences, University of Torino, Torino, Italy
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3
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Kumar A, Bantilan KS, Jacob AP, Park A, Schoninger SF, Sauter C, Ulaner GA, Casulo C, Faham M, Kong KA, Grewal RK, Gerecitano J, Hamilton A, Hamlin P, Matasar M, Moskowitz CH, Noy A, Palomba ML, Portlock CS, Younes A, Willis T, Zelenetz AD. Noninvasive Monitoring of Mantle Cell Lymphoma by Immunoglobulin Gene Next-Generation Sequencing in a Phase 2 Study of Sequential Chemoradioimmunotherapy Followed by Autologous Stem-Cell Rescue. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2021; 21:230-237.e12. [PMID: 33558202 PMCID: PMC9476895 DOI: 10.1016/j.clml.2020.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/20/2020] [Indexed: 11/28/2022]
Abstract
Limited information exists in mantle cell lymphoma (MCL) on the performance of next-generation sequencing–based assay of immunoglobulin gene rearrangements for minimal residual disease (MRD) assessment. Posttreatment peripheral blood samples were collected from 16 MCL patients and analyzed with the Adaptive Biotechnologies MRD assay, which identified early molecular relapse. We observed more sensitivity in the cellular versus acellular compartment.
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MESH Headings
- Aged
- Chemoradiotherapy
- DNA, Neoplasm/blood
- Female
- Gene Rearrangement
- High-Throughput Nucleotide Sequencing
- Humans
- Immunoglobulins/genetics
- Immunotherapy
- Induction Chemotherapy
- Lymphoma, Mantle-Cell/blood
- Lymphoma, Mantle-Cell/diagnosis
- Lymphoma, Mantle-Cell/genetics
- Lymphoma, Mantle-Cell/therapy
- Male
- Middle Aged
- Neoplasm Recurrence, Local/blood
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm, Residual
- Neoplastic Cells, Circulating
- Prospective Studies
- Remission Induction
- Stem Cell Transplantation
- Transplantation, Autologous
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Affiliation(s)
- Anita Kumar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - K S Bantilan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A P Jacob
- Adaptive Biotechnologies, Seattle, WA
| | - A Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - S F Schoninger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - C Sauter
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - G A Ulaner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - C Casulo
- Department of Medicine, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY
| | - M Faham
- Adaptive Biotechnologies, Seattle, WA
| | - K A Kong
- Adaptive Biotechnologies, Seattle, WA
| | - R K Grewal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - J Gerecitano
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A Hamilton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - P Hamlin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - M Matasar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - C H Moskowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A Noy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - M L Palomba
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - C S Portlock
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A Younes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - T Willis
- Adaptive Biotechnologies, Seattle, WA
| | - A D Zelenetz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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4
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Jung D, Jain P, Yao Y, Wang M. Advances in the assessment of minimal residual disease in mantle cell lymphoma. J Hematol Oncol 2020; 13:127. [PMID: 32972438 PMCID: PMC7513535 DOI: 10.1186/s13045-020-00961-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
The clinical impact of minimal residual disease detection at early time points or during follow-ups has been shown to accurately predict relapses among patients with lymphomas, mainly in follicular and diffuse large B cell lymphoma. The field of minimal residual disease testing in mantle cell lymphoma is still evolving but has great impact in determining the prognosis. Flow cytometry and polymerase chain reaction-based testing are most commonly used methods in practice; however, these methods are not sensitive enough to detect the dynamic changes that underline lymphoma progression. Newer methods using next-generation sequencing, such as ClonoSeq, are being incorporated in clinical trials. Other techniques under evolution include CAPP-seq and anchored multiplex polymerase chain reaction-based methods. This review article aims to provide a comprehensive update on the status of minimal residual disease detection and its prognostic effect in mantle cell patients. The role of circulating tumor DNA-based minimal residual disease detection in lymphomas is also discussed.
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Affiliation(s)
- Dayoung Jung
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Preetesh Jain
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.,Department of Hemapathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Yixin Yao
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Michael Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
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Cortelazzo S, Ponzoni M, Ferreri AJM, Dreyling M. Mantle cell lymphoma. Crit Rev Oncol Hematol 2020; 153:103038. [PMID: 32739830 DOI: 10.1016/j.critrevonc.2020.103038] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 06/29/2019] [Accepted: 06/23/2020] [Indexed: 12/11/2022] Open
Abstract
MCL is a well-characterized generally aggressive lymphoma with a poor prognosis. However, patients with a more indolent disease have been reported in whom the initiation of therapy can be delayed without any consequence for the survival. In 2017 the World Health Organization updated the classification of MCL describing two main subtypes with specific molecular characteristics and clinical features, classical and indolent leukaemic nonnodal MCL. Recent research results suggested an improving outcome of this neoplasm. The addition of rituximab to conventional chemotherapy has increased overall response rates, but it did not improve overall survival compared to chemotherapy alone. The use of intensive frontline therapies including rituximab and consolidation with autologous stem cell transplantation ameliorated response rate and prolonged progression-free survival in young fit patients, but any impact on survival remains to be proven. Furthermore, the optimal timing, cytoreductive regimen and conditioning regimen, and the clinical implications of achieving a disease remission even at molecular level remain to be elucidated. The development of targeted therapies as the consequence of better understanding of pathogenetic pathways in MCL might improve the outcome of conventional chemotherapy and spare the toxicity of intense therapy in most patients. Cases not eligible for intensive regimens, may be considered for less demanding therapies, such as the combination of rituximab either with CHOP or with purine analogues, or bendamustine. Allogeneic SCT can be an effective option for relapsed disease in patients who are fit enough and have a compatible donor. Maintenance rituximab may be considered after response to immunochemotherapy as the first-line strategy in a wide range of patients. Finally, since the optimal approach to the management of MCL is still evolving, it is critical that these patients are enrolled in clinical trials to identify the better treatment options.
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Affiliation(s)
| | - Maurilio Ponzoni
- Pathology Unit, San Raffaele Scientific Institute, Milan, Italy; Unit of Lymphoid Malignancies, San Raffaele Scientific Institute, Milan, Italy
| | - Andrés J M Ferreri
- Unit of Lymphoid Malignancies, San Raffaele Scientific Institute, Milan, Italy; Medical Oncology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Martin Dreyling
- Medizinische Klinik III der Universität München-Grosshadern, München, Germany
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Wang Y, Wen FQ. [Latest advances in minimal residual disease evaluation in B-cell lymphoproliferative disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:667-671. [PMID: 32571470 PMCID: PMC7390215 DOI: 10.7499/j.issn.1008-8830.1912034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
The clearance of cancer cells is closely associated with the prognosis of various hematologic malignancies. Clinical studies have shown that minimal residual disease (MRD) can directly reflect the clearance of cancer cells, but the tools for MRD detection need to be improved. This article reviews the latest advances in the MRD detection by digital polymerase chain reaction and next-generation sequencing in B-cell lymphoproliferative disease.
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Affiliation(s)
- Yan Wang
- Department of Pediatric Hematology and Oncology, Shenzhen Children's Hospital, China Medical University, Shenzhen, Guangdong 518031, China.
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Galimberti S, Genuardi E, Mazziotta F, Iovino L, Morabito F, Grassi S, Ciabatti E, Guerrini F, Petrini M. The Minimal Residual Disease in Non-Hodgkin's Lymphomas: From the Laboratory to the Clinical Practice. Front Oncol 2019; 9:528. [PMID: 31293969 PMCID: PMC6606710 DOI: 10.3389/fonc.2019.00528] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/31/2019] [Indexed: 01/05/2023] Open
Abstract
Minimal residual disease (MRD) in non-Hodgkin's lymphomas (NHLs) still represents matter of interest and debate: indeed, the new available treatments offer higher rates of complete responses and MRD negativity than in the past, with a positive impact on the long-term survival. Furthermore, the introduction of more sensitive and accurate molecular techniques, such as digital PCR (ddPCR) and the next generation sequencing techniques (NGS), increased the possibility of identifying molecular targets to be followed after therapy (such as rearrangement of immunoglobulins, fusion genes, or mutations). This review focused on how molecular biology can help to detect MRD in different types of NHLs and how MRD can change the clinical practice in 2019. In follicular lymphoma (FL), contamination of the grafts and molecular disease persistence after transplantation represent a negative prognostic factors. The combination of Rituximab or Obinutuzumab with Bendamustine seems to be the most effective way to clear MRD in FL patients receiving chemo-immunotherapy (further studies are in progress), and also 90Yttrium-Ibritumomab-Tiuxetan offers a deep clearance of molecular disease. Finally, molecular MRD can further stratify PET-negative cases, with subjects both PET- and MRD-negative presenting the best outcome. In aggressive lymphomas, MRD has a relevant prognostic power and can represent the platform for immunotherapy (such as CAR-T). In diffuse large B-cell lymphoma (DLBCL), the assessment of MRD in the plasma (where cell-free DNA and exosomes circulate) seems to be more predictive than the bone marrow analysis or peripheral blood mononuclear cells. Finally, NGS technologies could be more useful than the classical "patient allele-specific PCR" because they can identify any possible clone emerging during the treatment or follow-up, even if different from that identified at diagnosis, thus predicting relapse. After all, the present available molecular approaches can move MRD from the bench side to the clinical practice.
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Affiliation(s)
- Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Turin, Italy
| | - Francesco Mazziotta
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Lorenzo Iovino
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Clinical and Translational Sciences School of Doctorate, University of Pisa, Pisa, Italy
| | - Fortunato Morabito
- Hematology Oncology Department, Augusta Victoria Hospital, East Jerusalem, Israel.,Biotechnology Research Unit, Cosenza, Italy
| | - Susanna Grassi
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Elena Ciabatti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Guerrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Petrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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8
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Kulkarni N, Alessandrì L, Panero R, Arigoni M, Olivero M, Ferrero G, Cordero F, Beccuti M, Calogero RA. Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. BMC Bioinformatics 2018; 19:349. [PMID: 30367595 PMCID: PMC6191970 DOI: 10.1186/s12859-018-2296-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Reproducibility of a research is a key element in the modern science and it is mandatory for any industrial application. It represents the ability of replicating an experiment independently by the location and the operator. Therefore, a study can be considered reproducible only if all used data are available and the exploited computational analysis workflow is clearly described. However, today for reproducing a complex bioinformatics analysis, the raw data and the list of tools used in the workflow could be not enough to guarantee the reproducibility of the results obtained. Indeed, different releases of the same tools and/or of the system libraries (exploited by such tools) might lead to sneaky reproducibility issues. Results To address this challenge, we established the Reproducible Bioinformatics Project (RBP), which is a non-profit and open-source project, whose aim is to provide a schema and an infrastructure, based on docker images and R package, to provide reproducible results in Bioinformatics. One or more Docker images are then defined for a workflow (typically one for each task), while the workflow implementation is handled via R-functions embedded in a package available at github repository. Thus, a bioinformatician participating to the project has firstly to integrate her/his workflow modules into Docker image(s) exploiting an Ubuntu docker image developed ad hoc by RPB to make easier this task. Secondly, the workflow implementation must be realized in R according to an R-skeleton function made available by RPB to guarantee homogeneity and reusability among different RPB functions. Moreover she/he has to provide the R vignette explaining the package functionality together with an example dataset which can be used to improve the user confidence in the workflow utilization. Conclusions Reproducible Bioinformatics Project provides a general schema and an infrastructure to distribute robust and reproducible workflows. Thus, it guarantees to final users the ability to repeat consistently any analysis independently by the used UNIX-like architecture.
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Affiliation(s)
- Neha Kulkarni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Luca Alessandrì
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Riccardo Panero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Martina Olivero
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Giulio Ferrero
- Department of Computer Sciences, University of Torino, Torino, Italy
| | - Francesca Cordero
- Department of Computer Sciences, University of Torino, Torino, Italy.
| | - Marco Beccuti
- Department of Computer Sciences, University of Torino, Torino, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.
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New Molecular Technologies for Minimal Residual Disease Evaluation in B-Cell Lymphoid Malignancies. J Clin Med 2018; 7:jcm7090288. [PMID: 30231510 PMCID: PMC6162632 DOI: 10.3390/jcm7090288] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022] Open
Abstract
The clearance of malignant clonal cells significantly correlates with clinical outcomes in many hematologic malignancies. Accurate and high throughput tools for minimal residual disease (MRD) detection are needed to overcome some drawbacks of standard molecular techniques; such novel tools have allowed for higher sensitivity analyses and more precise stratification of patients, based on molecular response to therapy. In this review, we depict the recently introduced digital PCR and next-generation sequencing technologies, describing their current application for MRD monitoring in lymphoproliferative disorders. Moreover, we illustrate the feasibility of these new technologies to test less invasive and more patient-friendly tissues sources, such as "liquid biopsy".
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