1
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Alcoceba M, Stewart JP, García-Álvarez M, Díaz LG, Jiménez C, Medina A, Chillón MC, Gazdova J, Blanco O, Díaz FJ, Peñarrubia MJ, Fernández S, Montes C, Cabero A, Caballero MD, García-Sanz R, González M, González D, Tamayo P, Gutiérrez NC, García-Sancho AM, Sarasquete ME. Liquid biopsy for molecular characterization of diffuse large B-cell lymphoma and early assessment of minimal residual disease. Br J Haematol 2024; 205:109-121. [PMID: 38811363 DOI: 10.1111/bjh.19458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/01/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024]
Abstract
Circulating tumour DNA (ctDNA) allows genotyping and minimal residual disease (MRD) detection in lymphomas. Using a next-generation sequencing (NGS) approach (EuroClonality-NDC), we evaluated the clinical and prognostic value of ctDNA in a series of R-CHOP-treated diffuse large B-cell lymphoma (DLBCL) patients at baseline (n = 68) and after two cycles (n = 59), monitored by metabolic imaging (positron emission tomography combined with computed tomography [PET/CT]). A molecular marker was identified in 61/68 (90%) ctDNA samples at diagnosis. Pretreatment high ctDNA levels significantly correlated with elevated lactate dehydrogenase, advanced stage, high-risk International Prognostic Index and a trend to shorter 2-year progression-free survival (PFS). Valuable NGS data after two cycles of treatment were obtained in 44 cases, and 38 achieved major molecular response (MMR; 2.5-log drop in ctDNA). PFS curves displayed statistically significant differences among those achieving MMR versus those not achieving MMR (2-year PFS of 76% vs. 0%, p < 0.001). Similarly, more than 66% reduction in ΔSUVmax by PET/CT identified two subgroups with different prognosis (2-year PFS of 83% vs. 38%; p < 0.001). Combining both approaches MMR and ΔSUVmax reduction, a better stratification was observed (2-year PFS of 84% vs. 17% vs. 0%, p < 0.001). EuroClonality-NDC panel allows the detection of a molecular marker in the ctDNA in 90% of DLBCL. ctDNA reduction at two cycles and its combination with interim PET results improve patient prognosis stratification.
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MESH Headings
- Humans
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/blood
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/pathology
- Neoplasm, Residual/diagnosis
- Female
- Male
- Middle Aged
- Aged
- Adult
- Circulating Tumor DNA/blood
- Circulating Tumor DNA/genetics
- Liquid Biopsy/methods
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Aged, 80 and over
- Positron Emission Tomography Computed Tomography
- Rituximab/therapeutic use
- Rituximab/administration & dosage
- Cyclophosphamide/therapeutic use
- Cyclophosphamide/administration & dosage
- Biomarkers, Tumor/blood
- Vincristine/therapeutic use
- Vincristine/administration & dosage
- Prognosis
- Doxorubicin/therapeutic use
- Doxorubicin/administration & dosage
- High-Throughput Nucleotide Sequencing
- Prednisone/therapeutic use
- Prednisone/administration & dosage
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Affiliation(s)
- Miguel Alcoceba
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
- Grupo de trabajo cooperativo de linfomas y procesos linfoproliferativos de la SCLHH, Castilla y León, Spain
| | - James P Stewart
- Patrick G Johnston Centre for Cancer Research, Queens University Belfast, Belfast, UK
| | - María García-Álvarez
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Luis G Díaz
- Servicio de Medicina Nuclear, Hospital Universitario de Salamanca (HUS/IBSAL), Salamanca, Spain
| | - Cristina Jiménez
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Alejandro Medina
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
| | - M Carmen Chillón
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Jana Gazdova
- Patrick G Johnston Centre for Cancer Research, Queens University Belfast, Belfast, UK
| | - Oscar Blanco
- Servicio de Anatomía Patológica, Hospital Universitario de Salamanca (HUS/IBSAL), Salamanca, Spain
| | - Francisco J Díaz
- Servicio de Hematologia, Complejo Asistencial de Burgos, Burgos, Spain
| | - María J Peñarrubia
- Servicio de Hematologia, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Silvia Fernández
- Servicio de Hematologia, Complejo Asistencial Universitario de León, León, Spain
| | - Carlos Montes
- Servicio de Radiofísica y Protección Radiológica, Hospital Universitario de Salamanca (HUS/IBSAL), Salamanca, Spain
| | - Almudena Cabero
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
- Grupo de trabajo cooperativo de linfomas y procesos linfoproliferativos de la SCLHH, Castilla y León, Spain
| | - María D Caballero
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
- Grupo de trabajo cooperativo de linfomas y procesos linfoproliferativos de la SCLHH, Castilla y León, Spain
| | - Ramón García-Sanz
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
- Grupo de trabajo cooperativo de linfomas y procesos linfoproliferativos de la SCLHH, Castilla y León, Spain
| | - Marcos González
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
- Grupo de trabajo cooperativo de linfomas y procesos linfoproliferativos de la SCLHH, Castilla y León, Spain
| | - David González
- Patrick G Johnston Centre for Cancer Research, Queens University Belfast, Belfast, UK
| | - Pilar Tamayo
- Servicio de Medicina Nuclear, Hospital Universitario de Salamanca (HUS/IBSAL), Salamanca, Spain
| | - Norma C Gutiérrez
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Alejandro Martín García-Sancho
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
- Grupo de trabajo cooperativo de linfomas y procesos linfoproliferativos de la SCLHH, Castilla y León, Spain
| | - M Eugenia Sarasquete
- Servicio de Hematologia, Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC, y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Spain
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2
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Hess JF, Kotrová M, Fricke B, Songia S, Rigamonti S, Cavagna R, Tosi M, Paust N, Langerak AW, Spinelli O, Cazzaniga G, Brüggemann M, Hutzenlaub T. Clinical pilot study on microfluidic automation of IGH-VJ library preparation for next generation sequencing. Clin Chem Lab Med 2024; 62:e164-e167. [PMID: 38153095 DOI: 10.1515/cclm-2023-1346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Affiliation(s)
- Jacob F Hess
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Michaela Kotrová
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Birgit Fricke
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Simona Songia
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Silvia Rigamonti
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Roberta Cavagna
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Manuela Tosi
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Nils Paust
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Orietta Spinelli
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Giovanni Cazzaniga
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Tobias Hutzenlaub
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
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3
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Ahn WK, Yu K, Kim H, Lee ST, Choi JR, Han JW, Lyu CJ, Hahn S, Shin S. Monitoring measurable residual disease in paediatric acute lymphoblastic leukaemia using immunoglobulin gene clonality based on next-generation sequencing. Cancer Cell Int 2024; 24:218. [PMID: 38918782 PMCID: PMC11201849 DOI: 10.1186/s12935-024-03404-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Assessment of measurable residual disease (MRD) is an essential prognostic tool for B-lymphoblastic leukaemia (B-ALL). In this study, we evaluated the utility of next-generation sequencing (NGS)-based MRD assessment in real-world clinical practice. METHOD The study included 93 paediatric patients with B-ALL treated at our institution between January 2017 and June 2022. Clonality for IGH or IGK rearrangements was identified in most bone marrow samples (91/93, 97.8%) obtained at diagnosis. RESULTS In 421 monitoring samples, concordance was 74.8% between NGS and multiparameter flow cytometry and 70.7% between NGS and reverse transcription-PCR. Elevated quantities of clones of IGH alone (P < 0.001; hazard ratio [HR], 22.2; 95% confidence interval [CI], 7.1-69.1), IGK alone (P = 0.011; HR, 5.8; 95% CI, 1.5-22.5), and IGH or IGK (P < 0.001; HR, 7.2; 95% CI, 2.6-20.0) were associated with an increased risk of relapse. Detection of new clone(s) in NGS was also associated with inferior relapse-free survival (P < 0.001; HR, 18.1; 95% CI, 3.0-108.6). Multivariable analysis confirmed age at diagnosis, BCR::ABL1-like mutation, TCF3::PBX1 mutation, and increased quantity of IGH or IGK clones during monitoring as unfavourable factors. CONCLUSION In conclusion, this study highlights the usefulness of NGS-based MRD as a routine assessment tool for prognostication of paediatric patients with B-ALL.
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Affiliation(s)
- Won Kee Ahn
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Kyunghee Yu
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hongkyung Kim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Dxome Co. Ltd, Seongnam-si, , Gyeonggi-do, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Dxome Co. Ltd, Seongnam-si, , Gyeonggi-do, Korea
| | - Jung Woo Han
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Chuhl Joo Lyu
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Seungmin Hahn
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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4
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Liu Y, Ho C, Yu W, Huang Y, Miller J, Gao Q, Syed M, Ma Y, Wang M, Maciag L, Petrova-Drus K, Zhu M, Yao J, Vanderbilt C, Durham B, Benhamida J, Ewalt MD, Dogan A, Roshal M, Nafa K, Arcila ME. Quantification of Measurable Residual Disease Detection by Next-Generation Sequencing-Based Clonality Testing in B-Cell and Plasma Cell Neoplasms. J Mol Diagn 2024; 26:168-178. [PMID: 38103591 PMCID: PMC10918645 DOI: 10.1016/j.jmoldx.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023] Open
Abstract
Next-generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of various technical aspects of the MRD assays, but more studies are warranted to establish the performance characteristics and enable standardization and broad utilization in routine clinical practice. Here, the authors describe an NGS-based IGH MRD quantification assay, incorporating a spike-in calibrator for monitoring B-cell and plasma cell neoplasms based on their unique IGH rearrangement status. Comparison of MRD status (positive or undetectable) by NGS and flow cytometry (FC) assays showed high concordance (91%, 471/519 cases) and overall good linear correlation in MRD quantitation, particularly for chronic lymphocytic leukemia and B-lymphoblastic leukemia/lymphoma (R = 0.85). Quantitative correlation was lower for plasma cell neoplasms, where underestimation by FC is a known limitation. No significant effects on sequencing efficiency by the spike-in calibrator were observed, with excellent inter- and intra-assay reproducibility within the authors' laboratory, and in comparison to an external laboratory, using the same assay and protocols. Assays performed both at internal and external laboratories showed highly concordant MRD detection (100%) and quantitation (R = 0.97). Overall, this NGS-based MRD assay showed highly reproducible results with quantitation that correlated well with FC MRD assessment, particularly for B-cell neoplasms.
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Affiliation(s)
- Ying Liu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Caleb Ho
- Loxo Oncology, Inc., Stamford, Connecticut
| | - Wayne Yu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ying Huang
- Invivoscribe, Inc., San Diego, California
| | | | - Qi Gao
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mustafa Syed
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuanyuan Ma
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meiyi Wang
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lidia Maciag
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Menglei Zhu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin Durham
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark D Ewalt
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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5
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Kalinova M, Mrhalova M, Kabickova E, Svaton M, Skotnicova A, Prouzova Z, Krenova Z, Kolenova A, Divoka M, Fronkova E, Kodet R. Molecular Screening in Anaplastic Lymphoma Kinase-Positive Anaplastic Large Cell Lymphoma: Anaplastic Lymphoma Kinase Analysis, Next-Generation Sequencing Fusion Gene Detection, and T-Cell Receptor Immunoprofiling. Mod Pathol 2024; 37:100428. [PMID: 38266918 DOI: 10.1016/j.modpat.2024.100428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/08/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Anaplastic lymphoma kinase-positive anaplastic large cell lymphoma (ALK+ ALCL) originates from the T-lineage and is marked by rearrangements of the ALK gene. More than 10 fusion partners with the ALK gene are known, with the most common being the t(2;5)(p23;q35) translocation resulting in the NPM1::ALK fusion. In 10% to 20% of the ALK+ ALCL cases, the ALK gene fuses with various other partners. Modern molecular techniques, especially next-generation sequencing (NGS), have eased the identification of ALK gene fusion partners and have allowed in-depth characterization of the T-cell receptor (TCR) repertoire. We devised a real-time quantitative reverse-transcription polymerase chain reaction to measure the expression of the translocated portion of the ALK gene. Fusion partners for the ALK gene were analyzed using rapid amplification of 5'cDNA ends (RACE) method or NGS. TCR immunoprofiling was performed by amplicon NGS. We studied 96 ALK+ ALCL patients. NPM1::ALK fusion gene was observed in 71 patients, ATIC::ALK in 9, and TPM3::ALK in 3. CLTC::ALK, MYH9::ALK, and RNF213::ALK fusions were identified in 2 patients each. We also discovered the TPM4::ALK and SATB1::ALK fusion genes, plus the following 2 previously unidentified ALK+ ALCL fusions: SQSTM1::ALK and CAPRIN1::ALK. High expression of the translocated ALK gene segment was observed in all 93 analyzed samples. TCR testing was conducted on 23 patients with available DNA. In 18 (78%) patients, we discerned at least one (ranging from 1 to 4) clonal TCR rearrangement. In 59% of the patients, clonal TCR beta junctions corresponded with sequences previously observed in both healthy donors and under various pathological conditions. Reverse-transcriptase quantitative detection of ALK expression is a fast and reliable method for both diagnosing and monitoring treatment response in ALK+ ALCL patients, irrespective of the ALK gene translocation. NGS reveals new ALK translocation partners. Both malignant and reactive TCR repertoires in ALK+ ALCL patients are unique and do not consistently occur among different patients.
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Affiliation(s)
- Marketa Kalinova
- Department of Pathology, 3rd Faculty of Medicine, Charles University, Prague, Czech Republic; Central Laboratories, Faculty Hospital Kralovske Vinohrady, Prague, Czech Republic; Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Marcela Mrhalova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Edita Kabickova
- CLIP, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michael Svaton
- CLIP, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Aneta Skotnicova
- CLIP, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Zuzana Prouzova
- Department of Pathology, 3rd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pathology, 1st Faculty of Medicine, VFN, Charles University, Prague, Czech Republic
| | - Zdenka Krenova
- Department of Pediatric Oncology, University Hospital Brno, Brno, Czech Republic; Department of Pediatrics, Faculty of Medicine Masaryk University, Brno, Czech Republic
| | - Alexandra Kolenova
- Department of Pediatric Hematology and Oncology, Faculty of Medicine, Comenius University Bratislava, Bratislava, Slovak Republic
| | - Martina Divoka
- Department of Hematooncology, Faculty Hospital Olomouc, Olomouc, Czech Republic
| | - Eva Fronkova
- CLIP, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.
| | - Roman Kodet
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
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6
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Fardoos R, Christensen C, Øbro NF, Overgaard UM, Als-Nielsen B, Madsen HO, Marquart HV. Flow Sorting, Whole Genome Amplification and Next-Generation Sequencing as Combined Tools to Study Heterogeneous Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2023; 13:3306. [PMID: 37958202 PMCID: PMC10650172 DOI: 10.3390/diagnostics13213306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Next-generation sequencing (NGS) methods have been introduced for immunoglobulin (IG)/T-cell receptor (TR) gene rearrangement analysis in acute lymphoblastic leukemia (ALL) and lymphoma (LBL). These methods likely constitute faster and more sensitive approaches to analyze heterogenous cases of ALL/LBL, yet it is not known whether gene rearrangements constituting low percentages of the total sequence reads represent minor subpopulations of malignant cells or background IG/TR gene rearrangements in normal B-and T-cells. In a comparison of eight cases of B-cell precursor ALL (BCP-ALL) using both the EuroClonality NGS method and the IdentiClone multiplex-PCR/gene-scanning method, the NGS method identified between 29% and 139% more markers than the gene-scanning method, depending on whether the NGS data analysis used a threshold of 5% or 1%, respectively. As an alternative to using low thresholds, we show that IG/TR gene rearrangements in subpopulations of cancer cells can be discriminated from background IG/TR gene rearrangements in normal B-and T-cells through a combination of flow cytometry cell sorting and multiple displacement amplification (MDA)-based whole genome amplification (WGA) prior to the NGS. Using this approach to investigate the clonal evolution in a BCP-ALL patient with double relapse, clonal TR rearrangements were found in sorted leukemic cells at the time of second relapse that could be identified at the time of diagnosis, below 1% of the total sequence reads. These data emphasize that caution should be exerted when interpreting rare sequences in NGS experiments and show the advantage of employing the flow sorting of malignant cell populations in NGS clonality assessments.
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Affiliation(s)
- Rabiah Fardoos
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Claus Christensen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Nina Friesgaard Øbro
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Ulrik Malthe Overgaard
- Department of Hematology, The University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Bodil Als-Nielsen
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Hans Ole Madsen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
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7
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van den Brand M, Möbs M, Otto F, Kroeze LI, Gonzalez de Castro D, Stamatopoulos K, Davi F, Bravetti C, Kolijn PM, Vlachonikola E, Stewart JP, Pott C, Hummel M, Darzentas N, Langerak AW, Fend F, Groenen PJTA. EuroClonality-NGS Recommendations for Evaluation of B-Cell Clonality Analysis by Next-Generation Sequencing: A Structured Approach with the DEPART Algorithm. J Mol Diagn 2023; 25:729-739. [PMID: 37467928 DOI: 10.1016/j.jmoldx.2023.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/16/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Next-generation sequencing (NGS)-based clonality analysis allows in-depth assessment of the clonal composition of a sample with high sensitivity for detecting small clones. Within the EuroClonality-NGS Working Group, a protocol for NGS Ig clonality analysis was developed and validated previously. This NGS-based approach was designed to generate small amplicons, making it suitable for samples with suboptimal DNA quality, especially material derived from formalin-fixed, paraffin-embedded tissue. Using expert assessment of NGS Ig clonality results as a reference, a structured algorithmic approach to the assessment of NGS-amplicon-based B-cell clonality analysis was developed. A structured approach with the Detection of clonality through Evaluation of sample quality and assessment of Pattern, Abundance and RaTio (DEPART) algorithm was proposed, which consecutively evaluates sample quality, the pattern of the clonotypes present, the abundance of the most dominant clonotypes, and the ratio between the dominant clonotypes and the background to evaluate the different Ig gene targets. Specific issues with respect to evaluation of the various Ig targets as well as the integration of results of individual targets into a molecular clonality conclusion are discussed and illustrated with case examples. Finally, the importance of interpretation of NGS-based clonality results in clinical and histopathologic contexts is discussed. It is expected that these recommendations will have clinical utility to facilitate proper evaluation of clonality assessment.
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Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Markus Möbs
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Franziska Otto
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Gonzalez de Castro
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Frederic Davi
- Hematology Department, Hospital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - Clotilde Bravetti
- Hematology Department, Hospital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - P Martijn Kolijn
- Laboratory of Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - J Peter Stewart
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Christiane Pott
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anton W Langerak
- Laboratory of Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Patricia J T A Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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8
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Giusti GNN, Ribeiro AV, Jotta PY, Thonier F, Yunes JA, Meidanis J. Vidjil add-on for MRD quantification of samples processed using the EuroClonality-NGS protocol. EJHAEM 2023; 4:770-774. [PMID: 37601854 PMCID: PMC10435716 DOI: 10.1002/jha2.749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 08/22/2023]
Abstract
Assessment of minimal residual disease in acute lymphoblastic leukemia by immune repertoire NGS requires spiking CDR3 sequences at known quantities into the patient's sample. Recently, the EuroClonality-NGS group released one of the most comprehensive protocols for this purpose. ARResT/Interrogate is a closed-source software for processing these NGS libraries, developed by this same group. Vidjil, an open-source alternative, currently cannot handle libraries prepared using this protocol. Here, we present a Vidjil add-on to solve this issue. EuroClonality-NGS prepared samples analyzed with Vidjil and ARResT/Interrogate were highly concordant (r = 0.998) and presented low error (root-mean-square error, RMSE = 0.112).
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Affiliation(s)
- Guilherme Navarro Nilo Giusti
- Centro de Pesquisa BoldriniCentro Infantil BoldriniCampinasSão PauloBrazil
- Instituto de BiologiaUniversidade Estadual de CampinasCampinasSão PauloBrazil
| | - Antonio Vítor Ribeiro
- Instituto de MatemáticaEstatística e Computação CientíficaUniversidade Estadual de CampinasCampinasSão PauloBrazil
| | | | | | - José Andrés Yunes
- Centro de Pesquisa BoldriniCentro Infantil BoldriniCampinasSão PauloBrazil
- Faculdade de Ciências MédicasUniversidade Estadual de CampinasCampinasSão PauloBrazil
| | - João Meidanis
- Instituto de ComputaçãoUniversidade Estadual de CampinasCampinasSão PauloBrazil
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9
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Medina-Herrera A, Sarasquete ME, Jiménez C, Puig N, García-Sanz R. Minimal Residual Disease in Multiple Myeloma: Past, Present, and Future. Cancers (Basel) 2023; 15:3687. [PMID: 37509348 PMCID: PMC10377959 DOI: 10.3390/cancers15143687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Responses to treatment have improved over the last decades for patients with multiple myeloma. This is a consequence of the introduction of new drugs that have been successfully combined in different clinical contexts: newly diagnosed, transplant-eligible or ineligible patients, as well as in the relapsed/refractory setting. However, a great proportion of patients continue to relapse, even those achieving complete response, which underlines the need for updated response criteria. In 2014, the international myeloma working group established new levels of response, prompting the evaluation of minimal residual disease (MRD) for those patients already in complete or stringent complete response as defined by conventional serological assessments: the absence of tumor plasma cells in 100,000 total cells or more define molecular and immunophenotypic responses by next-generation sequencing and flow cytometry, respectively. In this review, we describe all the potential methods that may be used for MRD detection based on the evidence found in the literature, paying special attention to their advantages and pitfalls from a critical perspective.
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Affiliation(s)
- Alejandro Medina-Herrera
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - María Eugenia Sarasquete
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Cristina Jiménez
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Noemí Puig
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Ramón García-Sanz
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
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10
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Assanto GM, Del Giudice I, Della Starza I, Soscia R, Cavalli M, Cola M, Bellomarino V, Di Trani M, Guarini A, Foà R. Research Topic: Measurable Residual Disease in Hematologic Malignancies. Can digital droplet PCR improve measurable residual disease monitoring in chronic lymphoid malignancies? Front Oncol 2023; 13:1152467. [PMID: 36998457 PMCID: PMC10043164 DOI: 10.3389/fonc.2023.1152467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
Minimal/measurable residual disease (MRD) monitoring is progressively changing the management of hematologic malignancies. The possibility of detecting the persistence/reappearance of disease in patients in apparent clinical remission offers a refined risk stratification and a treatment decision making tool. Several molecular techniques are employed to monitor MRD, from conventional real-time quantitative polymerase chain reaction (RQ-PCR) to next generation sequencing and digital droplet PCR (ddPCR), in different tissues or compartments through the detection of fusion genes, immunoglobulin and T-cell receptor gene rearrangements or disease-specific mutations. RQ-PCR is still the gold standard for MRD analysis despite some limitations. ddPCR, considered the third-generation PCR, yields a direct, absolute, and accurate detection and quantification of low-abundance nucleic acids. In the setting of MRD monitoring it carries the major advantage of not requiring a reference standard curve built with the diagnostic sample dilution and of allowing to reduce the number of samples below the quantitative range. At present, the broad use of ddPCR to monitor MRD in the clinical practice is limited by the lack of international guidelines. Its application within clinical trials is nonetheless progressively growing both in acute lymphoblastic leukemia as well as in chronic lymphocytic leukemia and non-Hodgkin lymphomas. The aim of this review is to summarize the accumulating data on the use of ddPCR for MRD monitoring in chronic lymphoid malignancies and to highlight how this new technique is likely to enter into the clinical practice.
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Affiliation(s)
| | - Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
- *Correspondence: Ilaria Del Giudice, ; Robin Foà,
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
- Gruppo Italiano Malattie Ematologiche dell'Adulto (GIMEMA), Fondazione GIMEMA Franco Mandelli Onlus, Rome, Italy
| | - Roberta Soscia
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Marzia Cavalli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Mattia Cola
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Vittorio Bellomarino
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Mariangela Di Trani
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Anna Guarini
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
- *Correspondence: Ilaria Del Giudice, ; Robin Foà,
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11
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Svaton M, Skotnicova A, Reznickova L, Rennerova A, Valova T, Kotrova M, van der Velden VHJ, Brüggemann M, Darzentas N, Langerak AW, Zuna J, Stary J, Trka J, Fronkova E. NGS better discriminates true MRD positivity for the risk stratification of childhood ALL treated on an MRD-based protocol. Blood 2023; 141:529-533. [PMID: 36240445 PMCID: PMC10651772 DOI: 10.1182/blood.2022017003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/02/2022] [Accepted: 10/06/2022] [Indexed: 02/07/2023] Open
Abstract
We compared minimal/measurable residual disease (MRD) levels evaluated by routinely used real-time quantitative polymerase chain reaction (qPCR) patient-specific assays and by next-generation sequencing (NGS) approach in 780 immunoglobulin (IG) and T-cell receptor (TR) markers in 432 children with B-cell precursor acute lymphoblastic leukemia treated on the AIEOP-BFM ALL 2009 protocol. Our aim was to compare the MRD-based risk stratification at the end of induction. The results were concordant in 639 of 780 (81.9%) of these markers; 37 of 780 (4.7%) markers were detected only by NGS. In 104 of 780 (13.3%) markers positive only by qPCR, a large fraction (23/104; 22.1%) was detected also by NGS, however, owing to the presence of identical IG/TR rearrangements in unrelated samples, we classified those as nonspecific/false-positive. Risk group stratification based on the MRD results by qPCR and NGS at the end of induction was concordant in 76% of the patients; 19% of the patients would be assigned to a lower risk group by NGS, largely owing to the elimination of false-positive qPCR results, and 5% of patients would be assigned to a higher risk group by NGS. NGS MRD is highly concordant with qPCR while providing more specific results and can be an alternative in the front line of MRD evaluation in forthcoming MRD-based protocols.
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Affiliation(s)
- Michael Svaton
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Aneta Skotnicova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Leona Reznickova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Andrea Rennerova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Tatana Valova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michaela Kotrova
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Vincent H. J. van der Velden
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Monika Brüggemann
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nikos Darzentas
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anton W. Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan Zuna
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Eva Fronkova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
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12
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Detecting measurable residual disease beyond 10-4 by an IGHV leader-based NGS approach improves prognostic stratification in CLL. Blood 2023; 141:519-528. [PMID: 36084320 DOI: 10.1182/blood.2022017411] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023] Open
Abstract
The sensitivity of conventional techniques for reliable quantification of minimal/measurable residual disease (MRD) in chronic lymphocytic leukemia (CLL) is limited to MRD 10-4. Measuring MRD <10-4 could help to further distinguish between patients with CLL with durable remission and those at risk of early relapse. We herein present an academically developed immunoglobulin heavy-chain variable (IGHV) leader-based next-generation sequencing (NGS) assay for the quantification of MRD in CLL. We demonstrate, based on measurements in contrived MRD samples, that the linear range of detection and quantification of our assay reaches beyond MRD 10-5. If provided with sufficient DNA input, MRD can be detected down to MRD 10-6. There was high interassay concordance between measurements of the IGHV leader-based NGS assay and allele-specific oligonucleotide quantitative polymerase chain reaction (PCR) (r = 0.92 [95% confidence interval {CI}, 0.86-0.96]) and droplet digital PCR (r = 0.93 [95% CI, 0.88-0.96]) on contrived MRD samples. In a cohort of 67 patients from the CLL11 trial, using MRD 10-5 as a cutoff, undetectable MRD was associated with superior progression-free survival (PFS) and time to next treatment. More important, deeper MRD measurement allowed for additional stratification of patients with MRD <10-4 but ≥10-5. PFS of patients in this MRD range was significantly shorter, compared with patients with MRD <10-5 (hazard ratio [HR], 4.0 [95% CI, 1.6-10.3]; P = .004), but significantly longer, compared with patients with MRD ≥10-4 (HR, 0.44 [95% CI, 0.23-0.87]; P = .018). These results support the clinical utility of the IGHV leader-based NGS assay.
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13
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Smirnova AO, Miroshnichenkova AM, Olshanskaya YV, Maschan MA, Lebedev YB, Chudakov DM, Mamedov IZ, Komkov A. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. eLife 2023; 12:69157. [PMID: 36692004 PMCID: PMC9901932 DOI: 10.7554/elife.69157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here, we discovered a hallmark anomaly in the ratio between read count and clone count-based frequencies of non-functional clonotypes in multiplex PCR-based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5' RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches and compared with a biological spike-in-based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.
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Affiliation(s)
- Anastasia O Smirnova
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Anna M Miroshnichenkova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yulia V Olshanskaya
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Michael A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cells CenterAbu DhabiUnited Arab Emirates
| | - Ilgar Z Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
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14
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Optimizing Molecular Minimal Residual Disease Analysis in Adult Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020374. [PMID: 36672325 PMCID: PMC9856386 DOI: 10.3390/cancers15020374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Minimal/measurable residual disease (MRD) evaluation has resulted in a fundamental instrument to guide patient management in acute lymphoblastic leukemia (ALL). From a methodological standpoint, MRD is defined as any approach aimed at detecting and possibly quantifying residual neoplastic cells beyond the sensitivity level of cytomorphology. The molecular methods to study MRD in ALL are polymerase chain reaction (PCR) amplification-based approaches and are the most standardized techniques. However, there are some limitations, and emerging technologies, such as digital droplet PCR (ddPCR) and next-generation sequencing (NGS), seem to have advantages that could improve MRD analysis in ALL patients. Furthermore, other blood components, namely cell-free DNA (cfDNA), appear promising and are also being investigated for their potential role in monitoring tumor burden and response to treatment in hematologic malignancies. Based on the review of the literature and on our own data, we hereby discuss how emerging molecular technologies are helping to refine the molecular monitoring of MRD in ALL and may help to overcome some of the limitations of standard approaches, providing a benefit for the care of patients.
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15
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Darzentas F, Szczepanowski M, Kotrová M, Hartmann A, Beder T, Gökbuget N, Schwartz S, Bastian L, Baldus CD, Pál K, Darzentas N, Brüggemann M. Insights into IGH clonal evolution in BCP-ALL: frequency, mechanisms, associations, and diagnostic implications. Front Immunol 2023; 14:1125017. [PMID: 37143651 PMCID: PMC10151743 DOI: 10.3389/fimmu.2023.1125017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction The malignant transformation leading to a maturation arrest in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) occurs early in B-cell development, in a pro-B or pre-B cell, when somatic recombination of variable (V), diversity (D), and joining (J) segment immunoglobulin (IG) genes and the B-cell rescue mechanism of VH replacement might be ongoing or fully active, driving clonal evolution. In this study of newly diagnosed BCP-ALL, we sought to understand the mechanistic details of oligoclonal composition of the leukemia at diagnosis, clonal evolution during follow-up, and clonal distribution in different hematopoietic compartments. Methods Utilizing high-throughput sequencing assays and bespoke bioinformatics we identified BCP-ALL-derived clonally-related IGH sequences by their shared 'DNJ-stem'. Results We introduce the concept of 'marker DNJ-stem' to cover the entirety of, even lowly abundant, clonally-related family members. In a cohort of 280 adult patients with BCP-ALL, IGH clonal evolution at diagnosis was identified in one-third of patients. The phenomenon was linked to contemporaneous recombinant and editing activity driven by aberrant ongoing DH/VH-DJH recombination and VH replacement, and we share insights and examples for both. Furthermore, in a subset of 167 patients with molecular subtype allocation, high prevalence and high degree of clonal evolution driven by ongoing DH/VH-DJH recombination were associated with the presence of KMT2A gene rearrangements, while VH replacements occurred more frequently in Ph-like and DUX4 BCP-ALL. Analysis of 46 matched diagnostic bone marrow and peripheral blood samples showed a comparable clonal and clonotypic distribution in both hematopoietic compartments, but the clonotypic composition markedly changed in longitudinal follow-up analysis in select cases. Thus, finally, we present cases where the specific dynamics of clonal evolution have implications for both the initial marker identification and the MRD monitoring in follow-up samples. Discussion Consequently, we suggest to follow the marker DNJ-stem (capturing all family members) rather than specific clonotypes as the MRD target, as well as to follow both VDJH and DJH family members since their respective kinetics are not always parallel. Our study further highlights the intricacy, importance, and present and future challenges of IGH clonal evolution in BCP-ALL.
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Affiliation(s)
- Franziska Darzentas
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Monika Szczepanowski
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michaela Kotrová
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Alina Hartmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH-ALL” (KFO 5010/1), funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Bonn, Germany
| | - Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, Goethe University Hospital, Frankfurt/M, Germany
| | - Stefan Schwartz
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lorenz Bastian
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH-ALL” (KFO 5010/1), funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Bonn, Germany
| | - Claudia Dorothea Baldus
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH-ALL” (KFO 5010/1), funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Bonn, Germany
| | - Karol Pál
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Nikos Darzentas
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- *Correspondence: Nikos Darzentas,
| | - Monika Brüggemann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit “CATCH-ALL” (KFO 5010/1), funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Bonn, Germany
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16
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IGH Rearrangement Evolution in Adult KMT2A-rearranged B-cell Precursor ALL: Implications for Cell-of-origin and MRD Monitoring. Hemasphere 2022; 7:e820. [PMID: 36570692 PMCID: PMC9771314 DOI: 10.1097/hs9.0000000000000820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
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17
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Lee JW, Kim Y, Ahn A, Lee JM, Yoo JW, Kim S, Cho B, Chung NG, Kim M. Clinical implication of minimal residual disease assessment by next-generation sequencing-based immunoglobulin clonality assay in pediatric B-acute lymphoblastic leukemia. Front Oncol 2022; 12:957743. [PMID: 36185293 PMCID: PMC9521036 DOI: 10.3389/fonc.2022.957743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Measuring minimal residual disease (MRD) during treatment is valuable to identify acute lymphoblastic leukemia (ALL) patients who require intensified treatment to avert relapse. We performed the next-generation sequencing (NGS)-based immunoglobulin gene (Ig) clonality assay and evaluated its clinical implication in pediatric B-ALL patients to assess MRD. Fifty-five patients who were diagnosed and treated with de novo (n = 44) or relapsed/refractory B-ALL (n = 11) were enrolled. MRD assessment was performed using the LymphoTrack® Dx IGH and IGK assay panels. The percentage of the clonal sequences per total read count was calculated as MRD (% of B cells). The data were normalized as the proportion of total nucleated cells (TNC) by LymphoQuant™ Internal control or the B-cell proportion in each sample estimated by flow cytometry or immunohistochemistry. Clonal Ig rearrangement was identified in all patients. The normalized MRD value was significantly lower than the unnormalized MRD value (p < 0.001). When categorizing patients, 27 of 50 patients (54%) achieved normalized MRD <0.01%, while 6 of them did not achieve MRD <0.01% when applying the unnormalized value. The normalized post-induction MRD value of 0.01% proved to be a significant threshold value for both 3-year event-free survival (100% for MRD <0.01% vs. 60.9% ± 10.2% for MRD ≥0.01%, p = 0.007) and 3-year overall survival (100% for MRD <0.01% vs. 78.3% ± 8.6% for MRD ≥0.01%, p = 0.011). However, unnormalized MRD was not a significant factor for outcome in this cohort. Our study demonstrated that MRD assessment by NGS-based Ig clonality assay could be applied in most pediatric B-ALL patients. Normalized post-induction MRD <0.01% was a significant prognostic indicator.
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Affiliation(s)
- Jae Wook Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Ari Ahn
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jong Mi Lee
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jae Won Yoo
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Seongkoo Kim
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- *Correspondence: Nack-Gyun Chung, ; Myungshin Kim,
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- *Correspondence: Nack-Gyun Chung, ; Myungshin Kim,
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18
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Mai H, Li Q, Wang G, Wang Y, Liu S, Tang X, Chen F, Zhou G, Liu Y, Li T, Wang L, Wang C, Wen F, Liu S. Clinical application of next-generation sequencing-based monitoring of minimal residual disease in childhood acute lymphoblastic leukemia. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04151-6. [PMID: 35918464 DOI: 10.1007/s00432-022-04151-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/13/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) is an emerging technology that can comprehensively assess the diversity of the immune system. We explored the feasibility of NGS in detecting minimal residual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) based on immunoglobulin and T cell receptor. METHODS Bone marrow samples were collected pre- and post-treatment with pediatric ALL admitted to Shenzhen Children's Hospital from February 1st, 2020 to January 31st, 2021. We analyzed the MRD detected by NGS, multiparametric flow cytometry (MFC) and real-time quantitative PCR (RQ-PCR), and analyzed risk factors of positive NGS-MRD at the end of B-ALL induction chemotherapy. RESULTS A total of paired 236 bone marrow samples were collected from 64 children with ALL (58 B-ALL and 6 T-ALL). The decrease in the clonal rearrangement frequency of IGH, IGK, and IGL was generally consistent after treatment. Positive MRD was detected in 57.5% (77/134) of B-ALL and 80% (12/15) of T-ALL by NGS after chemotherapy, which was higher than those detected by MFC and RQ-PCR. In B-ALL patients, MRD results detected by NGS were consistent with MFC (r = 0.708, p < 0.001) and RQ-PCR (r = 0.618, p < 0.001). At the end of induction, NGS-MRD of 40.4% B-ALL was > 0.01% and multivariate analysis indicated that ≧2 clonal rearrangement sequences before treatment were an independent factor of negative NGS-MRD. CONCLUSIONS NGS is more sensitive than MFC and RQ-PCR for MRD measurement. B-ALL children with ≧2 clonal rearrangements detected by NGS before treatment are difficult to switch to negative MRD after chemotherapy.
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Affiliation(s)
- Huirong Mai
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Qin Li
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China.,Department of Hematology and Oncology, Shenzhen Children's Hospital, China Medical University, Shenzhen, China
| | - Guobing Wang
- Pediatrics Research Institute, Shenzhen Children's Hospital, Shenzhen, China
| | - Ying Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Shilin Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Xue Tang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Fen Chen
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Guichi Zhou
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Yi Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Tonghui Li
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Lulu Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Chunyan Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Feiqiu Wen
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China
| | - Sixi Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No. 7019, Yitian Road, Futian District, Shenzhen, China.
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19
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Fronkova E, Svaton M, Trka J. Quality Control for IG /TR Marker Identification and MRD Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:91-99. [PMID: 35622322 DOI: 10.1007/978-1-0716-2115-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Selection of the proper target is crucial for clinically relevant monitoring of minimal residual disease (MRD) in patients with acute lymphoblastic leukemia using the quantitation of clonal-specific immunoreceptor (immunoglobulin/T cell receptor) gene rearrangements. Consequently, correct interpretation of the results of the entire analysis is of utmost importance. Here we present an overview of the quality control measures that need to be implemented into the process of marker identification, selection, and subsequent quantitation of the MRD level.
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Affiliation(s)
- Eva Fronkova
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michael Svaton
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.
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20
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Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:61-77. [PMID: 35622320 DOI: 10.1007/978-1-0716-2115-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Identification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation are crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. Here we describe how RNA-Seq data can be generated and subsequently analyzed with ARResT/Interrogate to identify possible MRD markers. In addition to the procedures, possible pitfalls will be discussed. Similar strategies can be employed for other lymphoid malignancies, such as lymphoma and myeloma.
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21
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Pott C, Kotrova M, Darzentas N, Brüggemann M, Khouja M. cfDNA-Based NGS IG Analysis in Lymphoma. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:101-117. [PMID: 35622323 DOI: 10.1007/978-1-0716-2115-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Liquid biopsy is a novel diagnostic approach at first developed to characterize the molecular profile of solid tumors by analyzing body fluids. For cancer patients, it represents a noninvasive way to monitor the status of the solid tumor with respect to representative biomarkers. There is growing interest in the utilization of circulating tumor DNA (ctDNA) analysis also in the diagnostic and prognostic fields of lymphomas. Clonal immunoglobulin (IG) gene rearrangements are fingerprints of the respective lymphoid malignancy and thus are highly suited as specific molecular targets for minimal residual disease (MRD) detection. Tracing of the clonal IG rearrangement patterns in ctDNA pool during treatment can be used for MRD assessment in B-cell lymphomas. Here, we describe a reproducible next-generation sequencing assay to identify and characterize clonal IG gene rearrangements for MRD detection in cell-free DNA.
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Affiliation(s)
- Christiane Pott
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany.
| | - Michaela Kotrova
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nikos Darzentas
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Monika Brüggemann
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mouhamad Khouja
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
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22
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ARResT/Interrogate Immunoprofiling Platform: Concepts, Workflows, and Insights. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:571-584. [PMID: 35622342 DOI: 10.1007/978-1-0716-2115-8_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
ARResT/Interrogate was built within the EuroClonality-NGS working group to meet the challenge of developing and applying assays for the high-throughput sequence-based profiling of immunoglobulin (IG) and T-cell receptor (TR) repertoires. We herein present basic concepts, outline the main workflow, delve into EuroClonality-NGS-specific aspects, and share insights from our experiences with the platform.
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23
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Bonello F, Cani L, D'Agostino M. Risk Stratification Before and During Treatment in Newly Diagnosed Multiple Myeloma: From Clinical Trials to the Real-World Setting. Front Oncol 2022; 12:830922. [PMID: 35356221 PMCID: PMC8959380 DOI: 10.3389/fonc.2022.830922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/08/2022] [Indexed: 12/22/2022] Open
Abstract
Multiple Myeloma (MM) is a hematologic malignancy characterized by a wide clinical and biological heterogeneity leading to different patient outcomes. Various prognostic tools to stratify newly diagnosed (ND)MM patients into different risk groups have been proposed. At baseline, the standard-of-care prognostic score is the Revised International Staging System (R-ISS), which stratifies patients according to widely available serum markers (i.e., albumin, β 2-microglobulin, lactate dehydrogenase) and high-risk cytogenetic abnormalities detected by fluorescence in situ hybridization. Though this score clearly identifies a low-risk and a high-risk population, the majority of patients are categorized as at “intermediate risk”. Although new prognostic factors identified through molecular assays (e.g., gene expression profiling, next-generation sequencing) are now available and may improve risk stratification, the majority of them need specialized centers and bioinformatic expertise that may preclude their broad application in the real-world setting. In the last years, new tools to monitor response and measurable residual disease (MRD) with very high sensitivity after the start of treatment have been developed. MRD analyses both inside and outside the bone marrow have a strong prognostic impact, and the achievement of MRD negativity may counterbalance the high-risk behavior identified at baseline. All these techniques have been developed in clinical trials. However, their efficient application in real-world clinical practice and their potential role to guide treatment-decision making are still open issues. This mini review will cover currently known prognostic factors identified before and during first-line treatment, with a particular focus on their potential applications in real-world clinical practice.
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Affiliation(s)
- Francesca Bonello
- SSD Clinical Trial in Oncoematologia e Mieloma Multiplo, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - Lorenzo Cani
- SSD Clinical Trial in Oncoematologia e Mieloma Multiplo, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - Mattia D'Agostino
- SSD Clinical Trial in Oncoematologia e Mieloma Multiplo, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
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24
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Prognostic value of low-level MRD in adult acute lymphoblastic leukemia detected by low- and high-throughput methods. Blood Adv 2022; 6:3006-3010. [PMID: 35026836 PMCID: PMC9131918 DOI: 10.1182/bloodadvances.2021006727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/17/2021] [Indexed: 11/27/2022] Open
Abstract
Adult patients with acute lymphoblastic leukemia with low MRD positivity at week 16 form an intermediate-risk group. NGS improves the risk assignment of patients with MolNE MRD.
Persistence of minimal residual disease (MRD) after induction/consolidation therapy in acute lymphoblastic leukemia is the leading cause of relapse. The GMALL 07/2003 study used MRD detection by real-time quantitative polymerase chain reaction of clonal immune gene rearrangements with 1 × 10−4 as discriminating cutoff: levels ≥1 × 10−4 define molecular failure and MRD-negativity with an assay sensitivity of at least 1 × 10−4 defining complete molecular response. The clinical relevance of MRD results not fitting into these categories is unclear and termed “molecular not evaluable” (MolNE) toward MRD-based treatment decisions. Within the GMALL 07/03 study, 1019 consecutive bone marrow samples after first consolidation were evaluated for MRD. Patients with complete molecular response had significantly better outcome (5-year overall survival [OS] = 85% ± 2%, n = 603; 5-year disease-free survival [DFS] = 73% ± 2%, n = 599) compared with patients with molecular failure (5-year OS = 40% ± 3%, n = 238; 5-year DFS = 29% ± 3%, n = 208), with patients with MolNE in between (5-year OS = 66% ± 4%; 5-year DFS = 52% ± 4%, n = 178). Of MolNE samples reanalyzed using next-generation sequencing (NGS), patients with undetectable NGS-MRD (n = 44; 5-year OS = 88% ± 5%, 5-year DFS = 70% ± 7%) had significantly better outcome than those with positive NGS-MRD (n = 42; 5-year OS = 37% ± 8%; 5-year DFS = 33% ± 8%). MolNE MRD results not just are borderline values with questionable relevance but also form an intermediate-risk group, assignment of which can be further improved by NGS.
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25
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van Bladel DAG, van den Brand M, Rijntjes J, Pamidimarri Naga S, Haacke DLCM, Luijks JACW, Hebeda KM, van Krieken JHJM, Groenen PJTA, Scheijen B. Clonality assessment and detection of clonal diversity in classic Hodgkin lymphoma by next-generation sequencing of immunoglobulin gene rearrangements. Mod Pathol 2022; 35:757-766. [PMID: 34862451 PMCID: PMC9174053 DOI: 10.1038/s41379-021-00983-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023]
Abstract
Clonality analysis in classic Hodgkin lymphoma (cHL) is of added value for correctly diagnosing patients with atypical presentation or histology reminiscent of T cell lymphoma, and for establishing the clonal relationship in patients with recurrent disease. However, such analysis has been hampered by the sparsity of malignant Hodgkin and Reed-Sternberg (HRS) cells in a background of reactive immune cells. Recently, the EuroClonality-NGS Working Group developed a novel next-generation sequencing (NGS)-based assay and bioinformatics platform (ARResT/Interrogate) to detect immunoglobulin (IG) gene rearrangements for clonality testing in B-cell lymphoproliferations. Here, we demonstrate the improved performance of IG-NGS compared to conventional BIOMED-2/EuroClonality analysis to detect clonal gene rearrangements in 16 well-characterized primary cHL cases within the IG heavy chain (IGH) and kappa light chain (IGK) loci. This was most obvious in formalin-fixed paraffin-embedded (FFPE) tissue specimens, where three times more clonal cases were detected with IG-NGS (9 cases) compared to BIOMED-2 (3 cases). In total, almost four times more clonal rearrangements were detected in FFPE with IG-NGS (N = 23) as compared to BIOMED-2/EuroClonality (N = 6) as judged on identical IGH and IGK targets. The same clonal rearrangements were also identified in paired fresh frozen cHL samples. To validate the neoplastic origin of the detected clonotypes, IG-NGS clonality analysis was performed on isolated HRS cells, demonstrating identical clonotypes as detected in cHL whole-tissue specimens. Interestingly, IG-NGS and HRS single-cell analysis after DEPArray™ digital sorting revealed rearrangement patterns and copy number variation profiles indicating clonal diversity and intratumoral heterogeneity in cHL. Our data demonstrate improved performance of NGS-based detection of IG gene rearrangements in cHL whole-tissue specimens, providing a sensitive molecular diagnostic assay for clonality assessment in Hodgkin lymphoma.
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Affiliation(s)
- Diede A. G. van Bladel
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.461760.20000 0004 0580 1253Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Michiel van den Brand
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.415930.aPathology-DNA, Rijnstate Hospital, Arnhem, The Netherlands
| | - Jos Rijntjes
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Samhita Pamidimarri Naga
- grid.461760.20000 0004 0580 1253Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Demi L. C. M. Haacke
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen A. C. W. Luijks
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Konnie M. Hebeda
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J. Han J. M. van Krieken
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Patricia J. T. A. Groenen
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands. .,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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Halper-Stromberg E, McCall CM, Haley LM, Lin MT, Vogt S, Gocke CD, Eshleman JR, Stevens W, Martinson NA, Epeldegui M, Holdhoff M, Bettegowda C, Glantz MJ, Ambinder RF, Xian RR. CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies. Clin Chem 2021; 67:1524-1533. [PMID: 34491318 PMCID: PMC8965457 DOI: 10.1093/clinchem/hvab141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/10/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Clonal immunoglobulin and T-cell receptor rearrangements serve as tumor-specific markers that have become mainstays of the diagnosis and monitoring of lymphoid malignancy. Next-generation sequencing (NGS) techniques targeting these loci have been successfully applied to lymphoblastic leukemia and multiple myeloma for minimal residual disease detection. However, adoption of NGS for primary diagnosis remains limited. METHODS We addressed the bioinformatics challenges associated with immune cell sequencing and clone detection by designing a novel web tool, CloneRetriever (CR), which uses machine-learning principles to generate clone classification schemes that are customizable, and can be applied to large datasets. CR has 2 applications-a "validation" mode to derive a clonality classifier, and a "live" mode to screen for clones by applying a validated and/or customized classifier. In this study, CR-generated multiple classifiers using 2 datasets comprising 106 annotated patient samples. A custom classifier was then applied to 36 unannotated samples. RESULTS The optimal classifier for clonality required clonal dominance ≥4.5× above background, read representation ≥8% of all reads, and technical replicate agreement. Depending on the dataset and analysis step, the optimal algorithm yielded sensitivities of 81%-90%, specificities of 97%-100%, areas under the curve of 91%-94%, positive predictive values of 92-100%, and negative predictive values of 88%-98%. Customization of the algorithms yielded 95%-100% concordance with gold-standard clonality determination, including rescue of indeterminate samples. Application to a set of unknowns showed concordance rates of 83%-96%. CONCLUSIONS CR is an out-of-the-box ready and user-friendly software designed to identify clonal rearrangements in large NGS datasets for the diagnosis of lymphoid malignancies.
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Affiliation(s)
| | - Chad M McCall
- Department of Pathology, Duke University School of Medicine, Durham, NC
| | - Lisa M Haley
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Samantha Vogt
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - James R Eshleman
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Marta Epeldegui
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Matthias Holdhoff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Michael J Glantz
- Department of Neurosurgery, Medicine, and Neurology, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Richard F Ambinder
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Rena R Xian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
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Medina A, Jiménez C, Puig N, Sarasquete ME, Flores-Montero J, García-Álvarez M, Prieto-Conde I, Chillón C, Alcoceba M, González-Calle V, Gutiérrez NC, Jacobsen A, Vigil E, Hutt K, Huang Y, Orfao A, González M, Miller J, García-Sanz R. Interlaboratory Analytical Validation of a Next-Generation Sequencing Strategy for Clonotypic Assessment and Minimal Residual Disease Monitoring in Multiple Myeloma. Arch Pathol Lab Med 2021; 146:862-871. [PMID: 34619755 DOI: 10.5858/arpa.2021-0088-oa] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Minimal residual disease (MRD) is a major prognostic factor in multiple myeloma, although validated technologies are limited. OBJECTIVE.— To standardize the performance of the LymphoTrack next-generation sequencing (NGS) assays (Invivoscribe), targeting clonal immunoglobulin rearrangements, in order to reproduce the detection of tumor clonotypes and MRD quantitation in myeloma. DESIGN.— The quantification ability of the assay was evaluated through serial dilution experiments. Paired samples from 101 patients were tested by LymphoTrack, using Sanger sequencing and EuroFlow's next-generation flow (NGF) assay as validated references for diagnostic and follow-up evaluation, respectively. MRD studies using LymphoTrack were performed in parallel at 2 laboratories to evaluate reproducibility. RESULTS.— Sensitivity was set as 1.3 tumor cells per total number of input cells. Clonality was confirmed in 99% and 100% of cases with Sanger and NGS, respectively, showing great concordance (97.9%), although several samples had minor discordances in the nucleotide sequence of rearrangements. Parallel NGS was performed in 82 follow-up cases, achieving a median sensitivity of 0.001%, while for NGF, median sensitivity was 0.0002%. Reproducibility of LymphoTrack-based MRD studies (85.4%) and correlation with NGF (R2 > 0.800) were high. Bland-Altman tests showed highly significant levels of agreement between flow and sequencing. CONCLUSIONS.— Taken together, we have shown that LymphoTrack is a suitable strategy for clonality detection and MRD evaluation, with results comparable to gold standard procedures.
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Affiliation(s)
- Alejandro Medina
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Cristina Jiménez
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Noemí Puig
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - María Eugenia Sarasquete
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Juan Flores-Montero
- Departamento de Citometría de Flujo, Laboratorio 11, Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00400, Salamanca, Spain (Flores-Montero, Orfao)
| | - María García-Álvarez
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Isabel Prieto-Conde
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Carmen Chillón
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Miguel Alcoceba
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Verónica González-Calle
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Norma C Gutiérrez
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Austin Jacobsen
- Invivoscribe, Inc, San Diego, California (Jacobsen, Vigil, Hutt, Huang, Miller)
| | - Edgar Vigil
- Invivoscribe, Inc, San Diego, California (Jacobsen, Vigil, Hutt, Huang, Miller)
| | - Kasey Hutt
- Invivoscribe, Inc, San Diego, California (Jacobsen, Vigil, Hutt, Huang, Miller)
| | - Ying Huang
- Invivoscribe, Inc, San Diego, California (Jacobsen, Vigil, Hutt, Huang, Miller)
| | - Alberto Orfao
- Departamento de Citometría de Flujo, Laboratorio 11, Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00400, Salamanca, Spain (Flores-Montero, Orfao)
| | - Marcos González
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
| | - Jeffrey Miller
- Invivoscribe, Inc, San Diego, California (Jacobsen, Vigil, Hutt, Huang, Miller)
| | - Ramón García-Sanz
- From Departamento de Hematología, Hospital Universitario de Salamanca (HUSAL/IBSAL), Centro de Investigación del Cáncer - IBMCC (USAL-CSIC), CIBERONC-CB16/12/00233, Salamanca, Spain (Medina, Jiménez, Puig, Sarasquete, García-Álvarez, Prieto-Conde, Chillón, Alcoceba, González-Calle, Gutiérrez, González, García-Sanz)
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28
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Targeting pediatric leukemia-propagating cells with anti-CD200 antibody therapy. Blood Adv 2021; 5:3694-3708. [PMID: 34470052 DOI: 10.1182/bloodadvances.2020003534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/09/2021] [Indexed: 11/20/2022] Open
Abstract
Treating refractory pediatric acute lymphoblastic leukemia (ALL) remains a challenge despite impressive remission rates (>90%) achieved in the last decade. The use of innovative immunotherapeutic approaches such as anti-CD19 chimeric antigen receptor T cells does not ensure durable remissions, because leukemia-propagating cells (LPCs) that lack expression of CD19 can cause relapse, which signifies the need to identify new markers of ALL. Here we investigated expression of CD58, CD97, and CD200, which were previously shown to be overexpressed in B-cell precursor ALL (BCP-ALL) in CD34+/CD19+, CD34+/CD19-, CD34-/CD19+, and CD34-/CD19- LPCs, to assess their potential as therapeutic targets. Whole-genome microarray and flow cytometric analyses showed significant overexpression of these molecules compared with normal controls. CD58 and CD97 were mainly co-expressed with CD19 and were not a prerequisite for leukemia engraftment in immune deficient mice. In contrast, expression of CD200 was essential for engraftment and serial transplantation of cells in measurable residual disease (MRD) low-risk patients. Moreover, these CD200+ LPCs could be targeted by using the monoclonal antibody TTI-CD200 in vitro and in vivo. Treating mice with established disease significantly reduced disease burden and extended survival. These findings demonstrate that CD200 could be an attractive target for treating low-risk ALL, with minimal off-tumor effects that beset current immunotherapeutic approaches.
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29
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Ceppi F, Rizzati F, Colombini A, Conter V, Cazzaniga G. Utilizing the prognostic impact of minimal residual disease in treatment decisions for pediatric acute lymphoblastic leukemia. Expert Rev Hematol 2021; 14:795-807. [PMID: 34374613 DOI: 10.1080/17474086.2021.1967137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Acute lymphoblastic leukemia (ALL) is the first pediatric cancer where the assessment of early response to therapy by minimal residual disease (MRD) monitoring has demonstrated its importance to improve risk-based treatment approaches. The most standardized tools to study MRD in ALL are multiparametric flow cytometry and realtime-quantitative polymerase chain reaction amplification-based methods. In recent years, MRD measurement has reached greater levels of sensitivity and standardization through international laboratory networks collaboration. AREAS COVERED We herewith describe how to assess and apply the prognostic impact of MRD in treatment decisions, with specific focus on pediatric ALL. We also highlight the role of MRD monitoring in the context of genetically homogeneous subgroups of pediatric ALL. However, some queries remain to be addressed and emerging technologies hold the promise of improving MRD detection in ALL patients. EXPERT OPINION Emerging technologies, like next generation flow cytometry, droplet digital PCR, and next generation sequencing appear to be important methods for assessing MRD in pediatric ALL. These more specific and/or sensitive MRD monitoring methods may help to predict relapse with greater accuracy, and are currently being used in clinical trials to improve pediatric ALL outcome by optimizing patient stratification and earlier MRD-based interventional therapy.
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Affiliation(s)
- Francesco Ceppi
- Pediatric Hematology-Oncology Unit, Division of Pediatrics, Woman-Mother-Child Department, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Frida Rizzati
- Pediatric Hematology-Oncology Unit, Division of Pediatrics, Woman-Mother-Child Department, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Antonella Colombini
- Pediatric Hematology-Oncology, University Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Valentino Conter
- Pediatric Hematology-Oncology, University Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Pediatrics, School of Medicine, University of Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy.,Medical Genetics, School of Medicine, University of Milano Bicocca, Monza, Italy
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30
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Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood Adv 2021; 5:3188-3198. [PMID: 34424321 DOI: 10.1182/bloodadvances.2020004056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
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.
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31
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Ho C, Rothberg PG. Next-Generation Sequencing-Based Antigen-Receptor Gene Clonality Assays: Will They Become the Clinical Standard? J Mol Diagn 2021; 23:1043-1046. [PMID: 34293488 DOI: 10.1016/j.jmoldx.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 07/14/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Caleb Ho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Paul G Rothberg
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York.
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32
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Immune Gene Rearrangements: Unique Signatures for Tracing Physiological Lymphocytes and Leukemic Cells. Genes (Basel) 2021; 12:genes12070979. [PMID: 34198966 PMCID: PMC8329920 DOI: 10.3390/genes12070979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
The tremendous diversity of the human immune repertoire, fundamental for the defense against highly heterogeneous pathogens, is based on the ingenious mechanism of immune gene rearrangements. Rearranged immune genes encoding the immunoglobulins and T-cell receptors and thus determining each lymphocyte's antigen specificity are very valuable molecular markers for tracing malignant or physiological lymphocytes. One of their most significant applications is tracking residual leukemic cells in patients with lymphoid malignancies. This so called 'minimal residual disease' (MRD) has been shown to be the most important prognostic factor across various leukemia subtypes and has therefore been given enormous attention. Despite the current rapid development of the molecular methods, the classical real-time PCR based approach is still being regarded as the standard method for molecular MRD detection due to the cumbersome standardization of the novel approaches currently in progress within the EuroMRD and EuroClonality NGS Consortia. Each of the molecular methods, however, poses certain benefits and it is therefore expectable that none of the methods for MRD detection will clearly prevail over the others in the near future.
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33
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van den Brand M, Rijntjes J, Möbs M, Steinhilber J, van der Klift MY, Heezen KC, Kroeze LI, Reigl T, Porc J, Darzentas N, Luijks JACW, Scheijen B, Davi F, ElDaly H, Liu H, Anagnostopoulos I, Hummel M, Fend F, Langerak AW, Groenen PJTA. Next-Generation Sequencing-Based Clonality Assessment of Ig Gene Rearrangements: A Multicenter Validation Study by EuroClonality-NGS. J Mol Diagn 2021; 23:1105-1115. [PMID: 34186174 DOI: 10.1016/j.jmoldx.2021.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Ig gene (IG) clonality analysis has an important role in the distinction of benign and malignant B-cell lymphoid proliferations and is mostly performed with the conventional EuroClonality/BIOMED-2 multiplex PCR protocol and GeneScan fragment size analysis. Recently, the EuroClonality-NGS Working Group developed a method for next-generation sequencing (NGS)-based IG clonality analysis. Herein, we report the results of an international multicenter biological validation of this novel method compared with the gold standard EuroClonality/BIOMED-2 protocol, based on 209 specimens of reactive and neoplastic lymphoproliferations. NGS-based IG clonality analysis showed a high interlaboratory concordance (99%) and high concordance with conventional clonality analysis (98%) for the molecular conclusion. Detailed analysis of the individual IG heavy chain and kappa light chain targets showed that NGS-based clonality analysis was more often able to detect a clonal rearrangement or yield an interpretable result. NGS-based and conventional clonality analysis detected a clone in 96% and 95% of B-cell neoplasms, respectively, and all but one of the reactive cases were scored polyclonal. We conclude that NGS-based IG clonality analysis performs comparable to conventional clonality analysis. We provide critical parameters for interpretation and discuss a first step toward a quantitative scoring approach for NGS clonality results. Considering the advantages of NGS-based clonality analysis, including its high sensitivity and possibilities for accurate clonal comparison, this supports implementation in diagnostic practice.
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Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Markus Möbs
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Julia Steinhilber
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Michèle Y van der Klift
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kim C Heezen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tomas Reigl
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Jakub Porc
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Nikos Darzentas
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic; Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jeroen A C W Luijks
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frédéric Davi
- Hematology Department, Hospital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - Hesham ElDaly
- Histopathology Department, Coventry University Hospitals National Health Service Trust, Coventry, United Kingdom; Clinical Pathology Department, Cairo University, Cairo, Egypt
| | - Hongxiang Liu
- Haematopathology and Oncology Diagnostics Service, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom
| | | | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Navrkalova V, Plevova K, Hynst J, Pal K, Mareckova A, Reigl T, Jelinkova H, Vrzalova Z, Stranska K, Pavlova S, Panovska A, Janikova A, Doubek M, Kotaskova J, Pospisilova S. LYmphoid NeXt-Generation Sequencing (LYNX) Panel: A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. J Mol Diagn 2021; 23:959-974. [PMID: 34082072 DOI: 10.1016/j.jmoldx.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine II - Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrea Mareckova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tomas Reigl
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Zuzana Vrzalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Andrea Janikova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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35
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Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community’s Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
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Affiliation(s)
- Johannes Trück
- University Children's Hospital and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi), Paris, France
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, United States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Davide Bagnara
- University of Genoa, Department of Experimental Medicine, Genoa, Italy
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, United States
| | - Jacob S Sherkow
- College of Law, University of Illinois, Champaign, United States.,Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of Law, Copenhagen, Denmark.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States
| | - Aimee S Payne
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France.,Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of Montpellier, Montpellier, France.,Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
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Leenders AM, Kroeze LI, Rijntjes J, Luijks J, Hebeda KM, Darzentas N, Langerak AW, van den Brand M, Groenen PJTA. Multiple Immunoglobulin κ Gene Rearrangements within a Single Clone Unraveled by Next-Generation Sequencing-Based Clonality Assessment. J Mol Diagn 2021; 23:1097-1104. [PMID: 34020040 DOI: 10.1016/j.jmoldx.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/14/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
Clonality assessment of the Ig heavy- and light-chain genes (IGH and IGK) using GeneScan analysis is an important supplemental assay in diagnostic testing for lymphoma. Occasionally cases with an IGK rearrangement pattern that cannot readily be assigned to a monoclonal lymphoma are encountered, whereas the occurrence of biclonal lymphomas is rare, and the result of the IGH locus of these cases is in line with monoclonality. Three such ambiguous cases were assessed for clonality using next-generation sequencing. Information on the sequences of the rearrangements, combined with knowledge of the complex organization of the IGK locus, pointed to two explanations that can attribute seemingly biclonal IGK rearrangements to a single clone. In two cases, this explanation involved inversion rearrangements on the IGK locus, whereas in the third case, the cross-reactivity of primers generated an additional clonal product. In conclusion, next-generation sequencing-based clonality assessment allows for the detection of both inversion rearrangements and the cross-reactivity of primers, and can therefore facilitate the interpretation of cases of lymphoma with complex IGK rearrangement patterns.
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Affiliation(s)
- A Meilinde Leenders
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jeroen Luijks
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Konnie M Hebeda
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory for Medical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Michiel van den Brand
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
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Bertamini L, D'Agostino M, Gay F. MRD Assessment in Multiple Myeloma: Progress and Challenges. Curr Hematol Malig Rep 2021; 16:162-171. [PMID: 33950462 DOI: 10.1007/s11899-021-00633-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Over the last decade, the development of effective treatment approaches for multiple myeloma (MM) has been associated with higher response rates and longer survival. In patients who achieve complete response, several high sensitivity techniques have been studied to assess minimal residual disease (MRD) and detect residual neoplastic cells within the bone marrow (by flow cytometry or molecular biology techniques) or outside the bone marrow (by imaging or circulating disease markers in the peripheral blood). This is of utmost importance, since residual disease can drive clinical relapse. This review focuses on the progress made in the assessment of MRD in MM. RECENT FINDINGS The achievement of MRD negativity after therapy is considered prognostically important for MM patients, and data from clinical trials and meta-analyses have confirmed that it is strongly associated with better survival. Along with well-known techniques, such as next-generation sequencing (NGS), next-generation flow (NGF), and positron emission tomography/computed tomography (PET/CT), other methods such as mass spectrometry (MS) and circulating tumor cells are under study. Intensive treatment regimens at diagnosis can lead up to 70% of MRD negativity in MM patients, although the current proportion of curable patients is still unknown. Today, clinicians who treat MM deal with MRD assessment in routine clinical practice. Its appropriate use in therapeutic decision making may be the most fascinating and challenging issue to be addressed over the next few years.
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Affiliation(s)
- Luca Bertamini
- Myeloma Unit, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, via Genova 3, 10126, Torino, Italy
| | - Mattia D'Agostino
- Myeloma Unit, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, via Genova 3, 10126, Torino, Italy
| | - Francesca Gay
- Myeloma Unit, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, via Genova 3, 10126, Torino, Italy.
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38
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Tosi M, Spinelli O, Leoncin M, Cavagna R, Pavoni C, Lussana F, Intermesoli T, Frison L, Perali G, Carobolante F, Viero P, Skert C, Rambaldi A, Bassan R. MRD-Based Therapeutic Decisions in Genetically Defined Subsets of Adolescents and Young Adult Philadelphia-Negative ALL. Cancers (Basel) 2021; 13:cancers13092108. [PMID: 33925541 PMCID: PMC8123823 DOI: 10.3390/cancers13092108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/05/2022] Open
Abstract
Simple Summary In acute lymphoblastic leukemia (ALL), once a complete remission is achieved following induction chemotherapy, the study of submicroscopic minimal residual disease (MRD) represents a highly sensitive tool to assess the efficacy of early chemotherapy courses and predict outcome. Because of the significant therapeutic progress occurred in adolescent and young adult (AYA) ALL, the importance of MRD in this peculiar age setting has grown considerably, to refine individual prognostic scores within different genetic subsets and support specific risk and MRD-oriented programs. The evidence coming from the most recent MRD-based studies and the new therapeutic directions for AYA ALL are critically reviewed according to ALL subset and risk category. Abstract In many clinical studies published over the past 20 years, adolescents and young adults (AYA) with Philadelphia chromosome negative acute lymphoblastic leukemia (Ph− ALL) were considered as a rather homogeneous clinico-prognostic group of patients suitable to receive intensive pediatric-like regimens with an improved outcome compared with the use of traditional adult ALL protocols. The AYA group was defined in most studies by an age range of 18–40 years, with some exceptions (up to 45 years). The experience collected in pediatric ALL with the study of post-induction minimal residual disease (MRD) was rapidly duplicated in AYA ALL, making MRD a widely accepted key factor for risk stratification and risk-oriented therapy with or without allogeneic stem cell transplantation and experimental new drugs for patients with MRD detectable after highly intensive chemotherapy. This combined strategy has resulted in long-term survival rates of AYA patients of 60–80%. The present review examines the evidence for MRD-guided therapies in AYA’s Ph− ALL, provides a critical appraisal of current treatment pitfalls and illustrates the ways of achieving further therapeutic improvement according to the massive knowledge recently generated in the field of ALL biology and MRD/risk/subset-specific therapy
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Affiliation(s)
- Manuela Tosi
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Orietta Spinelli
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Matteo Leoncin
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Roberta Cavagna
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Chiara Pavoni
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Federico Lussana
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Tamara Intermesoli
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Luca Frison
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Giulia Perali
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Francesca Carobolante
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Piera Viero
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Cristina Skert
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Alessandro Rambaldi
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
- Department of Oncology-Hematology, University of Milan, 20122 Milan, Italy
| | - Renato Bassan
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
- Correspondence: ; Tel.: +39-041-965-7362
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Tumor and microenvironment response but no cytotoxic T-cell activation in classic Hodgkin lymphoma treated with anti-PD1. Blood 2021; 136:2851-2863. [PMID: 33113552 DOI: 10.1182/blood.2020008553] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/02/2020] [Indexed: 12/15/2022] Open
Abstract
Classic Hodgkin lymphoma (cHL) is the cancer type most susceptible to antibodies targeting programmed cell death protein 1 (PD1) and is characterized by scarce Hodgkin and Reed-Sternberg cells (HRSCs), perpetuating a unique tumor microenvironment (TME). Although anti-PD1 effects appear to be largely mediated by cytotoxic CD8+ T cells in solid tumors, HRSCs frequently lack major histocompatibility complex expression, and the mechanism of anti-PD1 efficacy in cHL is unclear. Rapid clinical responses and high interim complete response rates to anti-PD1 based first-line treatment were recently reported for patients with early-stage unfavorable cHL treated in the German Hodgkin Study Group phase 2 NIVAHL trial. To investigate the mechanisms underlying this very early response to anti-PD1 treatment, we analyzed paired biopsies and blood samples obtained from NIVAHL patients before and during the first days of nivolumab first-line cHL therapy. Mirroring the rapid clinical response, HRSCs had disappeared from the tissue within days after the first nivolumab application. The TME already shows a reduction in type 1 regulatory T cells and PD-L1+ tumor-associated macrophages at this early time point of treatment. Interestingly, a cytotoxic immune response and a clonal T-cell expansion were not observed in the tumors or peripheral blood. These early changes in the TME were distinct from alterations found in a separate set of cHL biopsies at relapse during anti-PD1 therapy. We identify a unique very early histologic response pattern to anti-PD1 therapy in cHL that is suggestive of withdrawal of prosurvival factors, rather than induction of an adaptive antitumor immune response, as the main mechanism of action.
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Hansen MH, Cédile O, Larsen TS, Abildgaard N, Nyvold CG. Perspective: sensitive detection of residual lymphoproliferative disease by NGS and clonal rearrangements-how low can you go? Exp Hematol 2021; 98:14-24. [PMID: 33823225 DOI: 10.1016/j.exphem.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/12/2023]
Abstract
Malignant lymphoproliferative disorders collectively constitute a large fraction of the hematological cancers, ranging from indolent to highly aggressive neoplasms. Being a diagnostically important hallmark, clonal gene rearrangements of the immunoglobulins enable the detection of residual disease in the clinical course of patients down to a minute fraction of malignant cells. The introduction of next-generation sequencing (NGS) has provided unprecedented assay specificity, with a sensitivity matching that of polymerase chain reaction-based measurable residual disease (MRD) detection down to the 10-6 level. Although reaching 10-6 to 10-7 is theoretically feasible, employing a sufficient amount of DNA and sequencing coverage is placed in the perspective of the practical challenges when relying on clinical samples in contrast to controlled serial dilutions. As we discuss, the randomness of subsampling must be taken into account to accommodate the sensitivity threshold-in terms of both the required number of cells and sequencing coverage. As a substantial part of the reviewed studies do not state the depth of coverage or even amount of DNA in some cases, we call for increased transparency to enable critical assessment of the MRD assays for clinical implementation and feasibility.
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Affiliation(s)
- Marcus H Hansen
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark.
| | - Oriane Cédile
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Thomas S Larsen
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Niels Abildgaard
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Charlotte G Nyvold
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
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41
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Potential and pitfalls of whole transcriptome-based immunogenetic marker identification in acute lymphoblastic leukemia; a EuroMRD and EuroClonality-NGS Working Group study. Leukemia 2021; 35:924-928. [PMID: 33608635 PMCID: PMC7932924 DOI: 10.1038/s41375-021-01154-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/15/2020] [Accepted: 01/22/2021] [Indexed: 11/08/2022]
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42
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Barennes P, Quiniou V, Shugay M, Egorov ES, Davydov AN, Chudakov DM, Uddin I, Ismail M, Oakes T, Chain B, Eugster A, Kashofer K, Rainer PP, Darko S, Ransier A, Douek DC, Klatzmann D, Mariotti-Ferrandiz E. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat Biotechnol 2021; 39:236-245. [PMID: 32895550 DOI: 10.1038/s41587-020-0656-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter.
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Affiliation(s)
- Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Valentin Quiniou
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Mikhail Shugay
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
| | - Anne Eugster
- DFG-Centre for Regenerative Therapies Dresden, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Peter P Rainer
- Division of Cardiology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France.
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Yao Q, Bai Y, Kumar S, Au E, Orfao A, Chim CS. Minimal Residual Disease Detection by Next-Generation Sequencing in Multiple Myeloma: A Comparison With Real-Time Quantitative PCR. Front Oncol 2021; 10:611021. [PMID: 33585233 PMCID: PMC7878533 DOI: 10.3389/fonc.2020.611021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Here we compared clonotype identification by allele-specific oligonucleotide real-time quantitative-PCR (ASO RQ-PCR) and next-generation sequencing (NGS) in 80 multiple myeloma patients. ASO RQ-PCR was applicable in 49/55 (89%) and NGS in 62/78 (80%). Clonotypes identified by both methods were identical in 33/35 (94%). Sensitivity of 10-5 was confirmed in 28/29 (96%) by NGS while sensitivity of RQ-PCR was 10-5 in 7 (24%), 5 × 10-5 in 15 (52%), and 10-4 in 7 (24%). Among 14 samples quantifiable by ASO RQ-PCR, NGS yielded comparable results in 12 (86%). Applicability of NGS can be improved if immunoglobulin heavy-chain incomplete DJ primers are included.
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Affiliation(s)
- Qiumei Yao
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yinlei Bai
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Shaji Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, United States
| | - Elaine Au
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong
| | - Alberto Orfao
- Department of Medicine and Cytometry Service (Nucleus), Cancer Research Centre (IBMCC, USAL-CSIC) and CIBERONC, Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Salamanca, Spain
| | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong
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Merli P, Ifversen M, Truong TH, Marquart HV, Buechner J, Wölfl M, Bader P. Minimal Residual Disease Prior to and After Haematopoietic Stem Cell Transplantation in Children and Adolescents With Acute Lymphoblastic Leukaemia: What Level of Negativity Is Relevant? Front Pediatr 2021; 9:777108. [PMID: 34805054 PMCID: PMC8602790 DOI: 10.3389/fped.2021.777108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/14/2021] [Indexed: 12/18/2022] Open
Abstract
Minimal residual disease (MRD) assessment plays a central role in risk stratification and treatment guidance in paediatric patients with acute lymphoblastic leukaemia (ALL). As such, MRD prior to haematopoietic stem cell transplantation (HSCT) is a major factor that is independently correlated with outcome. High burden of MRD is negatively correlated with post-transplant survival, as both the risk of leukaemia recurrence and non-relapse mortality increase with greater levels of MRD. Despite growing evidence supporting these findings, controversies still exist. In particular, it is still not clear whether multiparameter flow cytometry and real-time quantitative polymerase chain reaction, which is used to recognise immunoglobulin and T-cell receptor gene rearrangements, can be employed interchangeably. Moreover, the higher sensitivity in MRD quantification offered by next-generation sequencing techniques may further refine the ability to stratify transplant-associated risks. While MRD quantification from bone marrow prior to HSCT remains the state of the art, heavily pre-treated patients may benefit from additional staging, such as using 18F-fluorodeoxyglucose positron emission tomography/computed tomography to detect focal residues of disease. Additionally, the timing of MRD detection (i.e., immediately before administration of the conditioning regimen or weeks before) is a matter of debate. Pre-transplant MRD negativity has previously been associated with superior outcomes; however, in the recent For Omitting Radiation Under Majority age (FORUM) study, pre-HSCT MRD positivity was associated with neither relapse risk nor survival. In this review, we discuss the level of MRD that may require pre-transplant therapy intensification, risking time delay and complications (as well as losing the window for HSCT if disease progression occurs), as opposed to an adapted post-transplant strategy to achieve long-term remission. Indeed, MRD monitoring may be a valuable tool to guide individualised treatment decisions, including tapering of immunosuppression, cellular therapies (such as donor lymphocyte infusions) or additional immunotherapy (such as bispecific T-cell engagers or chimeric antigen receptor T-cell therapy).
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Affiliation(s)
- Pietro Merli
- Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marianne Ifversen
- Pediatric Stem Cell Transplant and Immune Deficiency, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Tony H Truong
- Division of Pediatric Oncology and Bone Marrow Transplant, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Hanne V Marquart
- Section for Diagnostic Immunology, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jochen Buechner
- Department of Pediatric Hematology and Oncology, Oslo University Hospital, Oslo, Norway
| | - Matthias Wölfl
- Pediatric Hematology, Oncology and Stem Cell Transplantation, Children's Hospital, Würzburg University Hospital, Würzburg, Germany
| | - Peter Bader
- Division for Stem Cell Transplantation, Immunology and Intensive Care Medicine, Department for Children and Adolescents, Goethe University, University Hospital Frankfurt, Frankfurt, Germany
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45
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Kotrova M, Darzentas N, Pott C, Brüggemann M. Next-Generation Sequencing Technology to Identify Minimal Residual Disease in Lymphoid Malignancies. Methods Mol Biol 2021; 2185:95-111. [PMID: 33165845 DOI: 10.1007/978-1-0716-0810-4_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Next-generation sequencing (NGS) of immunoglobulin (IG) and T cell receptor (TR) rearrangements represents a modern alternative to classical RQ-PCR-based minimal residual disease (MRD) detection. The same primer sets and conditions can be used for all patients, which is undoubtedly one of the most important benefits of NGS, not only reducing the labor required to perform the analysis but also enabling the assay to comply with the upcoming EU IVD regulation. So far, only one standardized academic protocol for this task has been published, developed, and validated within the EuroClonality-NGS working group. In this chapter we describe the materials and methods for amplicon library preparation for sequencing on Illumina MiSeq, and the bioinformatic pipeline for this protocol.
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Affiliation(s)
- Michaela Kotrova
- Unit for Hematological Diagnostics, Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nikos Darzentas
- Unit for Hematological Diagnostics, Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christiane Pott
- Unit for Hematological Diagnostics, Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany.
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Abstract
Although new techniques (i.e., droplet digital-PCR, next-generation sequencing, advanced flow cytometry) are being developed, DNA-based allele-specific real-time quantitative (RQ)-PCR is still the gold standard for sensitive and accurate immunoglobulin/T cell receptor (IG/TR)-based minimal residual disease (MRD) monitoring, allowing the detection of up to 1 leukemic cell in 100,000 normal lymphoid cells. We herewith describe the standard PCR procedure which has been developed and standardized (with minor modification in single labs) through the last 20 years of activity of the EuroMRD Consortium, a volunteer activity of expert laboratories that is continuously providing education, standardization, quality control rounds, and guidelines for interpretation of RQ-PCR data.
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Affiliation(s)
- Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Fondazione Tettamanti, Pediatrics, Monza, Italy.
- Department of Medicine and Surgery, University of Milan Bicocca, Monza, Italy.
| | - Simona Songia
- Centro Ricerca Tettamanti, Fondazione Tettamanti, Pediatrics, Monza, Italy
| | - Andrea Biondi
- Department of Medicine and Surgery, University of Milan Bicocca, Monza, Italy
- Pediatrics, Ospedale San Gerardo/Fondazione MBBM, Italy
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47
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Mendoza H, Tormey CA, Rinder HM, Howe JG, Siddon AJ. The utility and limitations of B- and T-cell gene rearrangement studies in evaluating lymphoproliferative disorders. Pathology 2020; 53:157-165. [PMID: 33358756 DOI: 10.1016/j.pathol.2020.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/05/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022]
Abstract
A hallmark of lymphoid malignancies is the presence of a monoclonal lymphocyte population. Monoclonality of B- and T-cell populations can be established through immunoglobulin (IG) or T-cell receptor (TCR) gene rearrangement analysis, respectively. The biological rationale of IG and TCR gene rearrangement analysis is that due to the extensive combinatorial repertoire made possible by V(D)J recombination in lymphocytes, it is unlikely that any substantive lymphocyte population would share the same IG or TCR gene rearrangement pattern unless there is an underlying neoplastic or reactive origin. Modern IG and TCR gene rearrangement analysis is typically performed by polymerase chain reaction (PCR) using commercially available primer sets followed by gel capillary electrophoresis. This process is highly sensitive in the detection of nearly all lymphoid malignancies. Several pitfalls and limitations, both biological and technical, apply to IG/TCR gene rearrangement analysis, but these can be minimised with high quality controls, performance of assays in duplicate, and adherence to strict criteria for interpreting and reporting results. Next generation sequencing (NGS) will likely replace PCR based methods of IG/TCR gene rearrangement analysis but is not yet widespread due to the absence of standardised protocols and multicentre validation.
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Affiliation(s)
- Hadrian Mendoza
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Henry M Rinder
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Hematology Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John G Howe
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Alexa J Siddon
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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48
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Lay L, Stroup B, Payton JE. Validation and interpretation of IGH and TCR clonality testing by Ion Torrent S5 NGS for diagnosis and disease monitoring in B and T cell cancers. Pract Lab Med 2020; 22:e00191. [PMID: 33304977 PMCID: PMC7718169 DOI: 10.1016/j.plabm.2020.e00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/17/2020] [Indexed: 01/02/2023] Open
Abstract
Cancers of B and T lymphocytes are the most common hematologic malignancies in the US. Molecular assays for assessing clonal rearrangements of the immunoglobulin receptor (IGH) and T-cell receptor (TCR), commonly referred to as B- and T-cell clonality, as well as determination of IGH somatic mutation status, enables improved diagnostic accuracy and disease monitoring. Here we describe validation of NGS LymphoTrack (IGH, TCRG, Invivoscribe, Inc) with Ion Torrent S5 sequencing, which employs a different sequencing chemistry and has not been previously reported for NGS clonality to our knowledge. We also demonstrate the concordance of clonality by LymphoTrack with S5 sequencing with other molecular methodologies and with clinical measurements of disease. We show that LymphoTrack with S5 sequencing identifies previously detected IGH and TCRG clonal sequences across matched biopsy specimens and clinical timepoints, enabling more precise and sensitive disease monitoring for B- and T-cell cancers compared to PCR fragment or capillary sequencing. In sum, our study demonstrates that the LymphoTrack assays with Ion Torrent S5 sequencing 1) can be used successfully for IGH and TCR clonality with reproducible results; 2) generates and quantifies clonal sequences to enable highly precise comparison of samples; 3) are substantially more sensitive than PCR fragment and return clonality results in specimens that failed PCR fragment assays; and 4) the TCRG assays are highly concordant with clinical and histopathologic diagnoses. Taken together, the LymphoTrack with Ion S5 NGS clonality assays offer a sensitive and precise method for diagnostic testing and disease monitoring in B- and T-cell cancers.
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Affiliation(s)
| | | | - Jacqueline E. Payton
- Washington University School of Medicine, St. Louis, MO, USA
- Corresponding author.
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Kim M, Park CJ. Minimal Residual Disease Detection in Pediatric Acute Lymphoblastic Leukemia. CLINICAL PEDIATRIC HEMATOLOGY-ONCOLOGY 2020. [DOI: 10.15264/cpho.2020.27.2.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Miyoung Kim
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University Medical Center, Hallym University College of Medicine, Anyang, Korea
| | - Chan-Jeoung Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
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Stadler R, Hain C, Cieslak C, Stranzenbach R. Molecular pathogenesis of cutaneous lymphoma-Future directions. Exp Dermatol 2020; 29:1062-1068. [PMID: 33090576 DOI: 10.1111/exd.14211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022]
Abstract
The pathogenesis of cutaneous T-cell lymphomas is not clear. In recent years, the genetic changes in CTCL were explored. The detected mutations showed a great deal of heterogeneity between individual patients. The studies documented various copy number variations (CNV) and single nucleotide variations (SNV) in multiple genes involved in multiple signalling pathways. Recurrently mutated signalling pathways include JAK-STAT, MAPK, T-cell receptor, TNF receptor and NFκB signalling. In the period between 2018 and today, additional studies towards the genetic changes in CTCL were carried out. Genetic changes in gamma delta T-cell lymphoma are also shown in genes of the JAK-STAT, MAPK, MYC and chromatin signalling pathways. These studies might indicate a shift away from targeted sequencing approaches towards whole-genome sequencing. This approach demands additional resources in terms of funding but has the advantage of finding mutations in non-coding regions. These mutations were neglected for a long time, but as shown in contemporary research these regions harbour highly recurrent mutations affecting gene expression and regulation. Nevertheless, the detection of specific molecular changes in known pathways enables considerations for targeted therapies.
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Affiliation(s)
- Rudolf Stadler
- University Clinic for Dermatology, Johannes Wesling Medical Centre, UKRUB, University of Bochum, Minden, Germany
| | - Carsten Hain
- Center of Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Cassandra Cieslak
- University Clinic for Dermatology, Johannes Wesling Medical Centre, UKRUB, University of Bochum, Minden, Germany
| | - René Stranzenbach
- University Clinic for Dermatology, Johannes Wesling Medical Centre, UKRUB, University of Bochum, Minden, Germany
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