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Saisaard W, Owattanapanich W. Comparative analysis of BCR::ABL1 p210 mRNA transcript quantification and ratio to ABL1 control gene converted to the International Scale by chip digital PCR and droplet digital PCR for monitoring patients with chronic myeloid leukemia. Clin Chem Lab Med 2024; 0:cclm-2024-0456. [PMID: 39167824 DOI: 10.1515/cclm-2024-0456] [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: 04/13/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024]
Abstract
OBJECTIVES Chronic myeloid leukemia (CML) is characterized by the Philadelphia chromosome, leading to the BCR::ABL1 fusion gene and hyper-proliferation of granulocytes. Tyrosine kinase inhibitors (TKIs) are effective, and minimal residual disease (MRD) monitoring is crucial. Digital PCR platforms offer increased precision compared to quantitative PCR but lack comparative studies. METHODS Eighty CML patient samples were analyzed in parallel using digital droplet PCR (ddPCR) (QXDx™ BCR-ABL %IS Kit) and chip digital PCR (cdPCR) (Dr. PCR™ BCR-ABL1 Major IS Detection Kit). RESULTS Overall, qualitative and quantitative agreement was good. Sensitivity analysis showed positive percentage agreement and negative percentage agreement were both ≥90 %, and the quadratic weighted kappa index for molecular response (MR) level categorization was 0.94 (95 %CI 0.89, 0.98). MR levels subgroup analysis showed perfect categorical agreement on MR level at MR3 or above, while 35.4 % (17/48) of patient samples with MR4 or below showed discordant categorizations. Overall, Lin's concordance correlation coefficient (CCC) for the ratio of %BCR::ABL1/ABL1 converted to the International Scale (BCR::ABL1 IS) was almost perfect quantitative agreement (Lin's CCC=0.99). By subgroups of MR levels, Lin's CCC showed a quantitative agreement of BCR::ABL1 IS decreased as MR deepened. CONCLUSIONS Both cdPCR and ddPCR demonstrated comparable performance in detecting BCR::ABL1 transcripts with high concordance in MR3 level or above. Choosing between platforms may depend on cost, workflow, and sensitivity requirements.
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Affiliation(s)
- Wannachai Saisaard
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Weerapat Owattanapanich
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Center of Excellence of Siriraj Adult Acute Myeloid/Lymphoblastic Leukemia (SiAML), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Whang K, Min J, Shin Y, Hwang I, Lee H, Kwak T, La JA, Kim S, Kim D, Lee LP, Kang T. Capillarity-Driven Enrichment and Hydrodynamic Trapping of Trace Nucleic Acids by Plasmonic Cavity Membrane for Rapid and Sensitive Detections. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2403896. [PMID: 38663435 DOI: 10.1002/adma.202403896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Small-reactor-based polymerase chain reaction (PCR) has attracted considerable attention. A significant number of tiny reactors must be prepared in parallel to capture, amplify, and accurately quantify few target genes in clinically relevant large volume, which, however, requires sophisticated microfabrication and longer sample-to-answer time. Here, single plasmonic cavity membrane is reported that not only enriches and captures few nucleic acids by taking advantage of both capillarity and hydrodynamic trapping but also quickly amplifies them for sensitive plasmonic detection. The plasmonic cavity membrane with few nanoliters in a void volume is fabricated by self-assembling gold nanorods with SiO2 tips. Simulations reveal that hydrodynamic stagnation between the SiO2 tips is mainly responsible for the trapping of the nucleic acid in the membrane. Finally, it is shown that the plasmonic cavity membrane is capable of enriching severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes up to 20 000-fold within 1 min, amplifying within 3 min, and detecting the trace genes as low as a single copy µL-1. It is anticipated that this work not only expands the utility of PCR but also provides an innovative way of the enrichment and detection of trace biomolecules in a variety of point-of-care testing applications.
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Affiliation(s)
- Keumrai Whang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Junwon Min
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Yonghee Shin
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Inhyeok Hwang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Hyunjoo Lee
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Taejin Kwak
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Ju A La
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Sungbong Kim
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
- Department of Chemistry, Military Academy, Seoul, 01805, South Korea
| | - Dongchoul Kim
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Luke P Lee
- Harvard Institute of Medicine, Harvard Medical School, Brigham and Women's Hospital, Harvard University, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwonsi, Gyeonggi-do, 16419, South Korea
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
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3
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Lee SJ, Lee J, Ahn A, Lee S, Hong Y, Lee GD, Song H, Song M, Shin S, Kim M, Kim Y. Analytical Performance Evaluation of a Digital Real-Time PCR for Quantifying Major BCR::ABL1 Transcripts. J Clin Lab Anal 2024; 38:e25034. [PMID: 38525919 PMCID: PMC11033343 DOI: 10.1002/jcla.25034] [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: 09/27/2023] [Revised: 02/09/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Accurate quantification of the BCR::ABL1 transcripts is essential for measurable residual disease (MRD) monitoring in chronic myeloid leukemia (CML) after tyrosine kinase inhibitor (TKI) treatment. This study evaluated the newly developed digital real-time PCR method, Dr. PCR, as an alternative reverse transcription-PCR (qRT-PCR) for MRD detection. METHODS The performance of Dr. PCR was assessed using reference and clinical materials. Precision, linearity, and correlation with qRT-PCR were evaluated. MRD levels detected by Dr. PCR were compared with qRT-PCR, and practical advantages were investigated. RESULTS Dr. PCR detected MRD up to 0.0032%IS (MR4.5) with excellent precision and linearity and showed a strong correlation with qRT-PCR results. Notably, Dr. PCR identified higher levels of MRD in 12.7% (29/229) of patients than qRT-PCR, including six cases of MR4, which is a critical level for TKI discontinuation. Dr. PCR also allowed for sufficient ABL1 copies in all cases, while qRT-PCR necessitated multiple repeat tests in 3.5% (8/229) of cases. CONCLUSION Our study provides a body of evidence supporting the clinical application of Dr. PCR as a rapid and efficient method for assessing MRD in patients with CML under the current treatment regimen.
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Affiliation(s)
- Soo Jung Lee
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
| | - Jong‐Mi Lee
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
| | - Ari Ahn
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Sung‐Eun Lee
- Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Yuna Hong
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
- Department of Biomedicine & Health Sciences, Graduate SchoolThe Catholic University of KoreaSeoulKorea
| | - Gun Dong Lee
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
| | - Hyun‐Woo Song
- Bio Institute, Optolane Technologies Inc.PangyoSeong‐Nam‐SiKorea
| | - Min‐Sik Song
- Bio Institute, Optolane Technologies Inc.PangyoSeong‐Nam‐SiKorea
| | - Seung‐Shick Shin
- Bio Institute, Optolane Technologies Inc.PangyoSeong‐Nam‐SiKorea
| | - Myungshin Kim
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Yonggoo Kim
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
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Russo D, Malagola M, Polverelli N, Farina M, Re F, Bernardi S. Twenty years of evolution of CML therapy: how the treatment goal is moving from disease to patient. Ther Adv Hematol 2023; 14:20406207231216077. [PMID: 38145059 PMCID: PMC10748527 DOI: 10.1177/20406207231216077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/19/2023] [Indexed: 12/26/2023] Open
Abstract
The introduction of imatinib in 2000 opened the era of tyrosine kinase inhibitors (TKIs) for CML therapy and has revolutionized the life expectancy of CML patients, which is now quite like the one of the healthy aged population. Over the last 20 years, both the TKI therapy itself and the objectives have undergone evolutions highlighted and discussed in this review. The main objective of the CML therapy in the first 10 years after TKI introduction was to abolish the disease progression from the chronic to the blastic phase and guarantee the long-term survival of the great majority of patients. In the second 10 years (from 2010 to the present), the main objective of CML therapy moved from survival, considered achieved as a goal, to treatment-free remission (TFR). Two phenomena emerged: no more than 50-60% of CML patients could be candidates for discontinuation and over 50% of them molecularly relapse. The increased cumulative incidence of specific TKI off-target side effects was such relevant to compel to discontinue or reduce the TKI administration in a significant proportion of patients and to avoid a specific TKI in particular settings of patients. Therefore, the treatment strategy must be adapted to each category of patients. What about the patients who do not get or fail the TFR? Should they be compelled to continue the TKIs at the maximum tolerated dose? Alternative strategies based on the principle of minimal effective dose have been tested with success and they are now re-evaluated with more attention, since they guarantee survival and probably a better quality of life, too. Moving from treating the disease to treating the patient is an important change of paradigm. We can say that we are entering a personalized CML therapy, which considers the patients' age, their comorbidities, tolerability, and specific objectives. In this scenario, the new techniques supporting the monitoring of the patients, such as the digital PCR, must be considered. In the present review, we present in deep this evolution and comment on the future perspectives of CML therapy.
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Affiliation(s)
- Domenico Russo
- Unit of Blood Diseases and Cell Therapies, Department of Clinical and Experimental Sciences, ASST-Spedali Civili Hospital of Brescia, Piazzale Spedali Civili 1, 25123, Brescia, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Michele Malagola
- Unit of Blood Diseases and Cell Therapies, Department of Clinical and Experimental Sciences, ASST-Spedali Civili Hospital of Brescia, University of Brescia, Brescia, Italy
| | - Nicola Polverelli
- Unit of Blood Diseases and Cell Therapies, Department of Clinical and Experimental Sciences, ASST-Spedali Civili Hospital of Brescia, University of Brescia, Brescia, Italy
| | - Mirko Farina
- Unit of Blood Diseases and Cell Therapies, Department of Clinical and Experimental Sciences, ASST-Spedali Civili Hospital of Brescia, University of Brescia, Brescia, Italy
| | - Federica Re
- Unit of Blood Diseases and Cell Therapies, Department of Clinical and Experimental Sciences, ASST-Spedali Civili Hospital of Brescia, University of Brescia, Brescia, Italy
- Centro di Ricerca Emato-oncologico AIL (CREA), ASST-Spedali Civili Hospital of Brescia, Brescia, Italy
| | - Simona Bernardi
- Unit of Blood Diseases and Cell Therapies, Department of Clinical and Experimental Sciences, ASST-Spedali Civili Hospital of Brescia, University of Brescia, Brescia, Italy
- Centro di Ricerca Emato-oncologico AIL (CREA), ASST-Spedali Civili Hospital of Brescia, Brescia, Italy
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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6
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Gao HL, Hao Y, Chen WM, Li LD, Wang X, Qin YZ, Jiang Q. [Comparison of BCR::ABL (P210) mRNA levels detected by dPCR and qPCR methods in patients with chronic myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:906-910. [PMID: 38185519 PMCID: PMC10753264 DOI: 10.3760/cma.j.issn.0253-2727.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 01/09/2024]
Abstract
Objective: To compare digital polymerase chain reaction (dPCR) and real-time quantitative PCR (qPCR) measurements of BCR::ABL (P210) mRNA expression in patients with chronic myeloid leukemia (CML) . Methods: In this non-interventional, cross-sectional study, BCR::ABL (P210) mRNA was simultaneously measured by dPCR and qPCR in peripheral blood samples collected from patients with CML who underwent tyrosine kinase inhibitor therapy and who achieved at least a complete cytogenetic response from September 2021 to February 2023 at Peking University People's Hospital. The difference, correlation, and agreement between the two methods were evaluated using the Wilcoxon signed-rank test, Spearman's correlation, and Bland-Altman analysis, respectively. Results: In total, 459 data pairs for BCR::ABL mRNA expression measured by dPCR and qPCR from 356 patients with CML were analyzed. There was a significant difference in BCR::ABL mRNA expression between the two methods (P<0.001). When analyzed by the depth of the molecular response (MR), a significant difference only existed for patients with ≥MR4.5 (P<0.001). No significant difference was observed for those who did not achieve a major MR (no MMR; P=0.922) or for those who achieved a major MR (MMR; P=0.723) or MR4 (P=0.099). There was a moderate correlation between the BCR::ABL mRNA expression between the two methods (r=0.761, P<0.001). However, the correlation gradually weakened or disappeared as the depth of the MR increased (no MMR: r=0.929, P<0.001; MMR: r=0.815, P<0.001; MR4: r=0.408, P<0.001; MR4.5: r=0.176, P=0.176). In addition, the agreement in BCR::ABL mRNA expression between the two methods in those with MR4.5 was weaker than other groups (no MMR: ▉= 0.042, P=0.846; MMR:▉=0.054, P=0.229; MR4:▉=-0.020, P=0.399; MR4.5:▉=-0.219, P<0.001) . Conclusions: dPCR is more accurate than qPCR for measuring BCR::ABL (P210) mRNA expression in patients with CML who achieve a stable deep MR.
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Affiliation(s)
- H L Gao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Y Hao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - W M Chen
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - L D Li
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - X Wang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Y Z Qin
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Q Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
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7
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Cross NCP, Ernst T, Branford S, Cayuela JM, Deininger M, Fabarius A, Kim DDH, Machova Polakova K, Radich JP, Hehlmann R, Hochhaus A, Apperley JF, Soverini S. European LeukemiaNet laboratory recommendations for the diagnosis and management of chronic myeloid leukemia. Leukemia 2023; 37:2150-2167. [PMID: 37794101 PMCID: PMC10624636 DOI: 10.1038/s41375-023-02048-y] [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: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
From the laboratory perspective, effective management of patients with chronic myeloid leukemia (CML) requires accurate diagnosis, assessment of prognostic markers, sequential assessment of levels of residual disease and investigation of possible reasons for resistance, relapse or progression. Our scientific and clinical knowledge underpinning these requirements continues to evolve, as do laboratory methods and technologies. The European LeukemiaNet convened an expert panel to critically consider the current status of genetic laboratory approaches to help diagnose and manage CML patients. Our recommendations focus on current best practice and highlight the strengths and pitfalls of commonly used laboratory tests.
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Affiliation(s)
| | - Thomas Ernst
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Susan Branford
- Centre for Cancer Biology and SA Pathology, Adelaide, SA, Australia
| | - Jean-Michel Cayuela
- Laboratory of Hematology, University Hospital Saint-Louis, AP-HP and EA3518, Université Paris Cité, Paris, France
| | | | - Alice Fabarius
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | | | | | - Rüdiger Hehlmann
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
- ELN Foundation, Weinheim, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Jane F Apperley
- Centre for Haematology, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Simona Soverini
- Department of Medical and Surgical Sciences, Institute of Hematology "Lorenzo e Ariosto Seràgnoli", University of Bologna, Bologna, Italy
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8
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Kim SY, Huh HJ. Measurable Residual Disease Testing Using Next-Generation Sequencing in Acute Myeloid Leukemia. Ann Lab Med 2023; 43:323-324. [PMID: 36843399 PMCID: PMC9989539 DOI: 10.3343/alm.2023.43.4.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Affiliation(s)
- Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Hee Jin Huh
- Department of Laboratory Medicine, Dongguk University Ilsan Hospital, Goyang, Korea
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9
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Marin AM, Wosniaki DK, Sanchuki HBS, Munhoz EC, Nardin JM, Soares GS, Espinace DC, de Holanda Farias JS, Veroneze B, Becker LF, Costa GL, Beltrame OC, de Oliveira JC, Cambri G, Zanette DL, Aoki MN. Molecular BCR::ABL1 Quantification and ABL1 Mutation Detection as Essential Tools for the Clinical Management of Chronic Myeloid Leukemia Patients: Results from a Brazilian Single-Center Study. Int J Mol Sci 2023; 24:10118. [PMID: 37373266 DOI: 10.3390/ijms241210118] [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: 04/27/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a well-characterized oncological disease in which virtually all patients possess a translocation (9;22) that generates the tyrosine kinase BCR::ABL1 protein. This translocation represents one of the milestones in molecular oncology in terms of both diagnostic and prognostic evaluations. The molecular detection of the BCR::ABL1 transcription is a required factor for CML diagnosis, and its molecular quantification is essential for assessing treatment options and clinical approaches. In the CML molecular context, point mutations on the ABL1 gene are also a challenge for clinical guidelines because several mutations are responsible for tyrosine kinase inhibitor resistance, indicating that a change may be necessary in the treatment protocol. So far, the European LeukemiaNet and the National Comprehensive Cancer Network (NCCN) have presented international guidelines on CML molecular approaches, especially those related to BCR::ABL1 expression. In this study, we show almost three years' worth of data regarding the clinical treatment of CML patients at the Erasto Gaertner Hospital, Curitiba, Brazil. These data primarily comprise 155 patients and 532 clinical samples. BCR::ABL1 quantification by a duplex-one-step RT-qPCR and ABL1 mutations detection were conducted. Furthermore, digital PCR for both BCR::ABL1 expression and ABL1 mutations were conducted in a sub-cohort. This manuscript describes and discusses the clinical importance and relevance of molecular biology testing in Brazilian CML patients, demonstrating its cost-effectiveness.
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Affiliation(s)
- Anelis Maria Marin
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Denise Kusma Wosniaki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | | | | | - Gabriela Silva Soares
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Dhienifer Caroline Espinace
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | | | | | | | | | | | | | - Geison Cambri
- Instituto de Biologia Molecular do Paraná (IBMP), Curitiba 81350-010, Brazil
| | - Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
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10
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Oliveira BB, Costa B, Morão B, Faias S, Veigas B, Pereira LP, Albuquerque C, Maio R, Cravo M, Fernandes AR, Baptista PV. Combining the amplification refractory mutation system and high-resolution melting analysis for KRAS mutation detection in clinical samples. Anal Bioanal Chem 2023; 415:2849-2863. [PMID: 37097304 PMCID: PMC10185647 DOI: 10.1007/s00216-023-04696-6] [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: 02/10/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
The success of personalized medicine depends on the discovery of biomarkers that allow oncologists to identify patients that will benefit from a particular targeted drug. Molecular tests are mostly performed using tumor samples, which may not be representative of the tumor's temporal and spatial heterogeneity. Liquid biopsies, and particularly the analysis of circulating tumor DNA, are emerging as an interesting means for diagnosis, prognosis, and predictive biomarker discovery. In this study, the amplification refractory mutation system (ARMS) coupled with high-resolution melting analysis (HRMA) was developed for detecting two of the most relevant KRAS mutations in codon 12. After optimization with commercial cancer cell lines, KRAS mutation screening was validated in tumor and plasma samples collected from patients with pancreatic ductal adenocarcinoma (PDAC), and the results were compared to those obtained by Sanger sequencing (SS) and droplet digital polymerase chain reaction (ddPCR). The developed ARMS-HRMA methodology stands out for its simplicity and reduced time to result when compared to both SS and ddPCR but showing high sensitivity and specificity for the detection of mutations in tumor and plasma samples. In fact, ARMS-HRMA scored 3 more mutations compared to SS (tumor samples T6, T7, and T12) and one more compared to ddPCR (tumor sample T7) in DNA extracted from tumors. For ctDNA from plasma samples, insufficient genetic material prevented the screening of all samples. Still, ARMS-HRMA allowed for scoring more mutations in comparison to SS and 1 more mutation in comparison to ddPCR (plasma sample P7). We propose that ARMS-HRMA might be used as a sensitive, specific, and simple method for the screening of low-level mutations in liquid biopsies, suitable for improving diagnosis and prognosis schemes.
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Affiliation(s)
- Beatriz B Oliveira
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Beatriz Costa
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | | | | | - Bruno Veigas
- AlmaScience, Campus de Caparica, 2829-519, Caparica, Portugal
| | - Lucília Pebre Pereira
- Unidade de Investigação Em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Rua Prof Lima Basto, 1099-023, Lisbon, Portugal
| | - Cristina Albuquerque
- Unidade de Investigação Em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Rua Prof Lima Basto, 1099-023, Lisbon, Portugal
| | - Rui Maio
- Hospital da Luz-Lisboa, Lisbon, Portugal
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Marília Cravo
- Hospital da Luz-Lisboa, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
| | - Pedro Viana Baptista
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
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11
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Lee H, Seo J, Shin S, Lee ST, Choi JR. Development and validation of sensitive BCR::ABL1 fusion gene quantitation using next-generation sequencing. Cancer Cell Int 2023; 23:106. [PMID: 37248544 DOI: 10.1186/s12935-023-02938-2] [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: 11/30/2022] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND BCR::ABL1 fusion has significant prognostic value and is screened for chronic myeloid leukemia (CML) disease monitoring as a part of routine molecular testing. To overcome the limitations of the current standard real-time quantitative polymerase chain reaction (RQ-PCR), we designed and validated a next-generation sequencing (NGS)-based assay to quantify BCR::ABL1 and ABL1 transcript copy numbers. METHODS After PCR amplification of the target sequence, deep sequencing was performed using an Illumina Nextseq 550Dx sequencer and in-house-designed bioinformatics pipeline. The Next-generation Quantitative sequencing (NQ-seq) assay was validated for its analytical performance, including precision, linearity, and limit of detection, using serially diluted control materials. A comparison with conventional RQ-PCR was performed with 145 clinical samples from 77 patients. RESULTS The limit of detection of the NQ-seq was the molecular response (MR) 5.6 [BCR::ABL1 0.00028% international scale (IS)]. The NQ-seq exhibited excellent precision and linear range from MR 2.0 to 5.0. The IS value from the NQ-seq was highly correlated with conventional RQ-PCR. CONCLUSIONS We conclude that the NQ-seq is an effective tool for monitoring BCR::ABL1 transcripts in CML patients with high sensitivity and reliability. Prospective assessment of the unselected large series is required to validate the clinical impact of this NGS-based monitoring strategy.
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Affiliation(s)
- Hyeonah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Seo
- Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
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12
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Bou Zerdan M, Kassab J, Saba L, Haroun E, Bou Zerdan M, Allam S, Nasr L, Macaron W, Mammadli M, Abou Moussa S, Chaulagain CP. Liquid biopsies and minimal residual disease in lymphoid malignancies. Front Oncol 2023; 13:1173701. [PMID: 37228488 PMCID: PMC10203459 DOI: 10.3389/fonc.2023.1173701] [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: 02/25/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Minimal residual disease (MRD) assessment using peripheral blood instead of bone marrow aspirate/biopsy specimen or the biopsy of the cancerous infiltrated by lymphoid malignancies is an emerging technique with enormous interest of research and technological innovation at the current time. In some lymphoid malignancies (particularly ALL), Studies have shown that MRD monitoring of the peripheral blood may be an adequate alternative to frequent BM aspirations. However, additional studies investigating the biology of liquid biopsies in ALL and its potential as an MRD marker in larger patient cohorts in treatment protocols are warranted. Despite the promising data, there are still limitations in liquid biopsies in lymphoid malignancies, such as standardization of the sample collection and processing, determination of timing and duration for liquid biopsy analysis, and definition of the biological characteristics and specificity of the techniques evaluated such as flow cytometry, molecular techniques, and next generation sequencies. The use of liquid biopsy for detection of minimal residual disease in T-cell lymphoma is still experimental but it has made significant progress in multiple myeloma for example. Recent attempt to use artificial intelligence may help simplify the algorithm for testing and may help avoid inter-observer variation and operator dependency in these highly technically demanding testing process.
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Affiliation(s)
- Maroun Bou Zerdan
- Department of Internal Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Joseph Kassab
- Cleveland Clinic, Research Institute, Cleveland, OH, United States
| | - Ludovic Saba
- Department of Hematology-Oncology, Myeloma and Amyloidosis Program, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
| | - Elio Haroun
- Department of Medicine, State University of New York (SUNY) Upstate Medical University, New York, NY, United States
| | | | - Sabine Allam
- Department of Medicine and Medical Sciences, University of Balamand, Balamand, Lebanon
| | - Lewis Nasr
- University of Texas MD Anderson Cancer Center, Texas, TX, United States
| | - Walid Macaron
- University of Texas MD Anderson Cancer Center, Texas, TX, United States
| | - Mahinbanu Mammadli
- Department of Internal Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | | | - Chakra P. Chaulagain
- Department of Hematology-Oncology, Myeloma and Amyloidosis Program, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
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13
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Digital PCR as a New Method for Minimal Residual Disease Monitoring and Treatment Free Remission Management in Chronic Myeloid Leukemia Patients: Is It Reliable? HEMATO 2022. [DOI: 10.3390/hemato4010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effective and sensitive monitoring of Minimal Residual Disease or Measurable Residual Disease (MRD) is a very important aspect in the management of patients affected by hematologic malignancies. The recent availability of new technologies has opened to the improvement of MRD monitoring. It is particularly relevant in patients affected by Chronic Myeloid Leukemia (CML). MRD monitoring is key in the management of CML patients thanks to the efficacy of TKIs therapy. Moreover, the policies of TKIs discontinuation aimed at treatment free remission are strongly based on the good selection of patients eligible for stopping TKIs therapy. The recently described application of digital PCR in CML patients monitoring seems to improve the accuracy and precision in the identification of optimal responders. The present review reports an overview on the application of digital PCR in the monitoring of MRD in CML and its impact on TKIs discontinuation trials and, consequently, on TFR success.
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14
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Galimberti S, Balducci S, Guerrini F, Del Re M, Cacciola R. Digital Droplet PCR in Hematologic Malignancies: A New Useful Molecular Tool. Diagnostics (Basel) 2022; 12:1305. [PMID: 35741115 PMCID: PMC9221914 DOI: 10.3390/diagnostics12061305] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Digital droplet PCR (ddPCR) is a recent version of quantitative PCR (QT-PCR), useful for measuring gene expression, doing clonality assays and detecting hot spot mutations. In respect of QT-PCR, ddPCR is more sensitive, does not need any reference curve and can quantify one quarter of samples already defined as "positive but not quantifiable". In the IgH and TCR clonality assessment, ddPCR recapitulates the allele-specific oligonucleotide PCR (ASO-PCR), being not adapt for detecting clonal evolution, that, on the contrary, does not represent a pitfall for the next generation sequencing (NGS) technique. Differently from NGS, ddPCR is not able to sequence the whole gene, but it is useful, cheaper, and less time-consuming when hot spot mutations are the targets, such as occurs with IDH1, IDH2, NPM1 in acute leukemias or T315I mutation in Philadelphia-positive leukemias or JAK2 in chronic myeloproliferative neoplasms. Further versions of ddPCR, that combine different primers/probes fluorescences and concentrations, allow measuring up to four targets in the same PCR reaction, sparing material, time, and money. ddPCR is also useful for quantitating BCR-ABL1 fusion gene, WT1 expression, donor chimerism, and minimal residual disease, so helping physicians to realize that "patient-tailored therapy" that is the aim of the modern hematology.
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Affiliation(s)
- Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Serena Balducci
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Marzia Del Re
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Rossella Cacciola
- Department of Clinical and Experimental Medicine, Section of Hemostasis, University of Catania, 95123 Catania, Italy
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15
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Dide-Agossou C, Rossmassler K, Reid J, Purohit J, Savic RM, Nahid P, Phillips PP, Moore CM, Walter ND. MOVER approximated CV: A tool for quantifying precision in ratiometric droplet digital PCR assays. J Pharm Biomed Anal 2022; 212:114664. [PMID: 35192991 PMCID: PMC8923918 DOI: 10.1016/j.jpba.2022.114664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 10/19/2022]
Abstract
Droplet digital PCR is a particularly valuable tool for ratiometric assays because it provides simultaneous absolute quantification of two target sequences in a single assay. This manuscript addresses a challenge in establishing a new ratiometric droplet digital PCR assay for use in sputum, the rRNA synthesis ratio. In principle, the methods established to evaluate precision and determine the limit of quantification for a single measurand cannot be applied to a ratiometric assay. The precision of a ratio depends on precision in both the numerator and denominator. Here, we evaluated the MOVER approximated coefficient of variation as indicator of assay precision that does not require technical replicates. We estimated the MOVER approximated coefficient of variation in dilution series and routine assays and evaluated its agreement with the traditional coefficient of variation. We found that the MOVER approximated coefficient of variation was able to recapitulate the traditional coefficient of variation without the requirement for replicate assays. We also demonstrated that the MOVER approximated coefficient of variation threshold can be used to define the limit of quantification of the rRNA synthesis Ratio. In conclusion, the MOVER approximated coefficient of variation may be useful not only for the rRNA synthesis ratio but for other assays that measure ratios via droplet digital PCR.
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16
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Shelton DN, Bhagavatula P, Sepulveda N, Beppu L, Gandhi S, Qin D, Hauenstein S, Radich J. Performance characteristics of the first Food and Drug Administration (FDA)-cleared digital droplet PCR (ddPCR) assay for BCR::ABL1 monitoring in chronic myelogenous leukemia. PLoS One 2022; 17:e0265278. [PMID: 35298544 PMCID: PMC8929598 DOI: 10.1371/journal.pone.0265278] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/27/2022] [Indexed: 11/19/2022] Open
Abstract
Chronic myelogenous leukemia (CML) is a hematopoietic stem cell malignancy that accounts for 15-20% of all cases of leukemia. CML is caused by a translocation between chromosomes 9 and 22 which creates an abnormal fusion gene, BCR::ABL1. The amount of BCR::ABL1 transcript RNA is a marker of disease progression and the effectiveness of tyrosine kinase inhibitor (TKI) treatment. This study determined the analytical and clinical performance of a droplet digital PCR based assay (QXDx BCR-ABL %IS Kit; Bio-Rad) for BCR::ABL1 quantification. The test has a limit of detection of MR4.7 (0.002%) and a linear range of MR0.3-4.7 (50-0.002%IS). Reproducibility of results across multiple sites, days, instruments, and users was evaluated using panels made from BCR::ABL1 positive patient samples. Clinical performance of the assay was evaluated on patient samples and compared to an existing FDA-cleared test. The reproducibility study noted negligible contributions to variance from site, instrument, day, and user for samples spanning from MR 0.7-4.2. The assay demonstrated excellent clinical correlation with the comparator test using a Deming regression with a Pearson R of 0.99, slope of 1.037 and intercept of 0.1084. This data establishes that the QXDx™ BCR-ABL %IS Kit is an accurate, precise, and sensitive system for the diagnosis and monitoring of CML.
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MESH Headings
- Fusion Proteins, bcr-abl/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Polymerase Chain Reaction/methods
- Protein Kinase Inhibitors/therapeutic use
- Reproducibility of Results
- United States
- United States Food and Drug Administration
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Affiliation(s)
- Dawne N. Shelton
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Prasanthi Bhagavatula
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Nathan Sepulveda
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Lan Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Shital Gandhi
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Dahui Qin
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Scott Hauenstein
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Jerald Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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17
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Kim Y, Kim S, Lee JM, Ahn A, Yoo JW, Lee JW, Cho B, Chung NG, Kim Y, Kim M. Discontinuation of tyrosine kinase inhibitors based on BCR-ABL1 monitoring by digital droplet PCR in pediatric chronic myeloid leukemia. Front Pediatr 2022; 10:928136. [PMID: 35967571 PMCID: PMC9363655 DOI: 10.3389/fped.2022.928136] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Lifelong treatment of pediatric chronic myeloid leukemia (CML) patients with tyrosine kinase inhibitors (TKIs) can affect their growth and development. For these reasons, clinical trials have explored the feasibility of TKI discontinuation in children with a sufficient TKI response. We evaluated the analytical performance of digital droplet PCR (ddPCR) to quantify BCR-ABL1 and compared the results with reverse transcription quantitative polymerase chain reaction (RT-qPCR). We further investigated whether ddPCR could be used to determine TKI discontinuation in a clinical setting. Performance of ddPCR was evaluated using standard materials for BCR-ABL1, and a total of 197 clinical samples from 45 pediatric CML patients was included for comparison with RT-qPCR. ddPCR showed excellent analytical sensitivity with 0.001% international scale (IS) and linearity with R 2 > 0.99 in log scale. BCR-ABL1 % IS results correlated well with those of RT-qPCR (R 2 = 0.9435), however, they showed a moderate strength for agreement with a Cohen's kappa of 0.41 due to higher sensitivity of ddPCR. Among 45 pediatric CML patients, 42 were treated with first-line TKIs including imatinib (n = 27, 64%) and dasatinib (n = 12, 29%), and three patients that were started with imatinib were switched to dasatinib. When we evaluated whether follow-up samples fulfilled ABL1 copies ≥ 10,000 required for deep molecular response (DMR), all samples were acceptable by ddPCR, whereas 18% by RT-qPCR did not reached acceptable ABL1 copies. Moreover, 52 and 13% reached ABL1 copies ≥ 32,000 required for MR4.5 by ddPCR and RT-qPCR, respectively. Seven patients discontinued TKI and the median TKI treatment duration was 73 months prior to discontinuation. Prior to discontinuation, the median duration of sustained undetected BCR-ABL1 was 60 months. Two patients experienced loss of major MR (MMR) during follow-up and restarted dasatinib 5 months after discontinuation. They achieved MMR again and maintained better than DMR afterward. Results from those patients demonstrated that RT-qPCR did not match the need for adequate ABL1 copies for MR4.5 while majority of ddPCR could. Therefore, ddPCR was technically more acceptable to decide and monitor pediatric CML patients before and after TKI discontinuation.
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Affiliation(s)
- Yeojae Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, South Korea
| | - Seongkoo Kim
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Jong Mi Lee
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Laboratory Medicine, 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
| | - Jae Won Yoo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Jae Wook Lee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Bin Cho
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Nack-Gyun Chung
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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18
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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19
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Droplet Digital PCR for BCR-ABL1 Monitoring in Diagnostic Routine: Ready to Start? Cancers (Basel) 2021; 13:cancers13215470. [PMID: 34771634 PMCID: PMC8582412 DOI: 10.3390/cancers13215470] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The introduction to clinical practice of a treatment-free remission approach in chronic myeloid leukemia patients with a stable deep molecular response highlighted how crucial it is to monitor the molecular levels of BCR–ABL1 as accurately and precisely as possible. In this context, the droplet digital PCR (ddPCR) presents an alternative methodology for such quantification. To hypothesize the introduction of this technology in routine practice, we performed a multicentric study that compares ddPCR with the standard methodology currently used. Our results demonstrate that the use of ddPCR in clinical practice is feasible and could be beneficial. Abstract BCR–ABL1 mRNA levels represent the key molecular marker for the evaluation of minimal residual disease (MRD) in chronic myeloid leukemia (CML) patients and real-time quantitative PCR (RT-qPCR) is currently the standard method to monitor it. In the era of tyrosine kinase inhibitors (TKIs) discontinuation, droplet digital PCR (ddPCR) has emerged to provide a more precise detection of MRD. To hypothesize the use of ddPCR in clinical practice, we designed a multicentric study to evaluate the potential value of ddPCR in the diagnostic routine. Thirty-seven RNA samples from CML patients and five from healthy donors were analyzed using both ddPCR QXDxTMBCR-ABL %IS Kit and LabNet-approved RT-qPCR methodologies in three different Italian laboratories. Our results show that ddPCR has a good agreement with RT-qPCR, but it is more precise to quantify BCR–ABL1 transcript levels. Furthermore, we did not find differences between duplicate or quadruplicate analysis in terms of BCR–ABL1% IS values. Droplet digital PCR could be confidently introduced into the diagnostic routine as a complement to the RT-qPCR.
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20
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Resistance to Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia-From Molecular Mechanisms to Clinical Relevance. Cancers (Basel) 2021; 13:cancers13194820. [PMID: 34638304 PMCID: PMC8508378 DOI: 10.3390/cancers13194820] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Chronic myeloid leukemia (CML) is a myeloproliferative neoplasia associated with a molecular alteration, the fusion gene BCR-ABL1, that encodes the tyrosine kinase oncoprotein BCR-ABL1. This led to the development of tyrosine kinase inhibitors (TKI), with Imatinib being the first TKI approved. Although the vast majority of CML patients respond to Imatinib, resistance to this targeted therapy contributes to therapeutic failure and relapse. Here we review the molecular mechanisms and other factors (e.g., patient adherence) involved in TKI resistance, the methodologies to access these mechanisms, and the possible therapeutic approaches to circumvent TKI resistance in CML. Abstract Resistance to targeted therapies is a complex and multifactorial process that culminates in the selection of a cancer clone with the ability to evade treatment. Chronic myeloid leukemia (CML) was the first malignancy recognized to be associated with a genetic alteration, the t(9;22)(q34;q11). This translocation originates the BCR-ABL1 fusion gene, encoding the cytoplasmic chimeric BCR-ABL1 protein that displays an abnormally high tyrosine kinase activity. Although the vast majority of patients with CML respond to Imatinib, a tyrosine kinase inhibitor (TKI), resistance might occur either de novo or during treatment. In CML, the TKI resistance mechanisms are usually subdivided into BCR-ABL1-dependent and independent mechanisms. Furthermore, patients’ compliance/adherence to therapy is critical to CML management. Techniques with enhanced sensitivity like NGS and dPCR, the use of artificial intelligence (AI) techniques, and the development of mathematical modeling and computational prediction methods could reveal the underlying mechanisms of drug resistance and facilitate the design of more effective treatment strategies for improving drug efficacy in CML patients. Here we review the molecular mechanisms and other factors involved in resistance to TKIs in CML and the new methodologies to access these mechanisms, and the therapeutic approaches to circumvent TKI resistance.
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21
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Kim B, Chi HY, Yoon YA, Choi YJ. Promyelocytic Blast Phase of Chronic Myeloid Leukemia, BCR-ABL1-Positive: Points to be Considered at Diagnosis. Ann Lab Med 2021; 41:328-332. [PMID: 33303719 PMCID: PMC7748100 DOI: 10.3343/alm.2021.41.3.328] [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: 06/22/2020] [Revised: 07/13/2020] [Accepted: 11/11/2020] [Indexed: 11/19/2022] Open
Affiliation(s)
- Bohyun Kim
- Department of Laboratory Medicine, Soonchunhyang University Cheonan Hospital, Soonchunhyang University College of Medicine, Cheonan, Korea
| | | | - Young Ahn Yoon
- Department of Laboratory Medicine, Soonchunhyang University Cheonan Hospital, Soonchunhyang University College of Medicine, Cheonan, Korea
| | - Young-Jin Choi
- Department of Laboratory Medicine, Soonchunhyang University Cheonan Hospital, Soonchunhyang University College of Medicine, Cheonan, Korea
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22
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Nucleophosmin1 and isocitrate dehydrogenase 1 and 2 as measurable residual disease markers in acute myeloid leukemia. PLoS One 2021; 16:e0253386. [PMID: 34153064 PMCID: PMC8216517 DOI: 10.1371/journal.pone.0253386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/03/2021] [Indexed: 11/19/2022] Open
Abstract
Monitoring measurable residual disease (MRD) in acute myeloid leukemia (AML) plays an important role in predicting relapse and outcome. The applicability of the leukemia-initiating nucleophosmin1 (NPM1) gene mutations in MRD detection is well-established, while that of isocitrate dehydrogenase1/2 (IDH1/2) mutations are matter of debate. The aim of this study was to investigate the stability of NPM1 and IDH1/2 mutations at diagnosis and relapse retrospectively in 916 adult AML patients. The prognostic value of MRD was evaluated by droplet digital PCR on the DNA level in a selected subgroup of patients in remission. NPM1 re-emerged at relapse in 91% (72/79), while IDH1/2 in 87% (20/23) of mutation-positive cases at diagnosis. NPM1 mutation did not develop at relapse, on the contrary novel IDH1/2 mutations occurred in 3% (3/93) of previously mutation-negative cases. NPM1 MRD-positivity after induction (n = 116) proved to be an independent, adverse risk factor (MRDpos 24-month OS: 39.3±6.2% versus MRDneg: 58.5±7.5%, p = 0.029; HR: 2.16; 95%CI: 1.25–3.74, p = 0.006). In the favorable subgroup of mutated NPM1 without fms-like tyrosine kinase 3 internal tandem duplication (FLT3-ITD) or with low allelic ratio, NPM1 MRD provides a valuable prognostic biomarker (NPM1 MRDpos versus MRDneg 24-month OS: 42.9±6.7% versus 66.7±8.6%; p = 0.01). IDH1/2 MRD-positivity after induction (n = 62) was also associated with poor survival (MRDpos 24-month OS: 41.3±9.2% versus MRDneg: 62.5±9.0%, p = 0.003; HR 2.81 95%CI 1.09–7.23, p = 0.032). While NPM1 variant allele frequency decreased below 2.5% in remission in all patients, IDH1/2 mutations (typically IDH2 R140Q) persisted in 24% of cases. Our results support that NPM1 MRD even at DNA level is a reliable prognostic factor, while IDH1/2 mutations may represent pre-leukemic, founder or subclonal drivers.
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23
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Moncada A, Pancrazzi A. Lab tests for MPN. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 366:187-220. [PMID: 35153004 DOI: 10.1016/bs.ircmb.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular laboratory investigations for myeloproliferative neoplasm (MPN) can ideally be divided into two distincts groups, those for the detection of the BCR-ABL rearrangement (suspect of chronic myeloid leukemia) and those for the variants determination of the driver genes of the negative Philadelphia forms (MPN Ph neg). The BCR-ABL detection is based on RT-Polymerase Chain Reaction techniques and more recently on droplet digital PCR (ddPCR). For this type of analysis, combined with chromosome banding analysis (CBA) and Fluorescent in situ hybridization (FISH), it is essential to quantify BCR-ABL mutated copies by standard curve method. The investigation on driver genes for MPN Ph neg forms includes activity for erythroid forms such as Polycythemia Vera (test JAK2V617F and JAK2 exon 12), for non-erythroid forms such as essential thrombocythemia and myelofibrosis (test JAK2V617F, CALR exon 9, MPL exon 10), for "atypical" ones such as mastocytosis (cKIT D816V test) and for hypereosinophilic syndrome (FIP1L1-PDGFRalpha test). It's crucial to assign prognosis value through calculating allelic burden of JAK2 V617F variant and determining CALR esone 9 variants (type1/1like, type2/2like and atypical ones). A fundamental innovation for investigating triple negative cases for JAK2, CALR, MPL and for providing prognostic score is the use of Next Generation Sequencing panels containing high molecular risk genes as ASXL1, EZH2, TET2, IDH1/IDH2, SRSF2. This technique allows to detect additional or subclonal mutations which are usually acquired in varying sized sub-clones of hematopoietic progenitors. These additional variants have a prognostic significance and should be indagated to exclude false negative cases.
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Affiliation(s)
- Alice Moncada
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy
| | - Alessandro Pancrazzi
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy.
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24
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Branford S. Why is it critical to achieve a deep molecular response in chronic myeloid leukemia? Haematologica 2020; 105:2730-2737. [PMID: 33054104 PMCID: PMC7716360 DOI: 10.3324/haematol.2019.240739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The primary goal of tyrosine kinase inhibitor (TKI) therapy for patients with chronic myeloid leukemia is survival, which is achieved by the vast majority of patients. The initial response to therapy provides a sensitive measure of future clinical outcome. Measurement of BCR-ABL1 transcript levels using real-time quantitative polymerase chain reaction standardized to the international reporting scale is now the principal recommended monitoring strategy. The method is used to assess early milestone responses and provides a guide for therapeutic intervention. When patients successfully traverse the critical first 12 months of TKI therapy, most will head towards another milestone response, deep molecular response (DMR, BCR-ABL1 ≤0.01%). DMR is essential for patients aiming to achieve treatment-free remission and a prerequisite for a trial of TKI discontinuation. The success of discontinuation trials has led to new treatment strategies in order for more patients to reach this milestone response. DMR has been incorporated into endpoints of clinical trials and is considered by some expert groups as the optimal treatment response. But is DMR a stable response and does it provide the ultimate protection against TKI resistance and death? Do we need to increase the sensitivity of detection of BCR-ABL1 to better identify the patients who would likely remain in treatment-free remission after TKI discontinuation? Is it necessary to switch current TKI therapy to a more potent inhibitor if the goal is to achieve DMR? These are issues that I will explore in this review.
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Affiliation(s)
- Susan Branford
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology; School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia; School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide and School of Biological Sciences, University of Adelaide, Adelaide.
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25
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Kockerols CC, Valk PJ, Levin MD, Pallisgaard N, Cornelissen JJ, Westerweel PE. Digital PCR for BCR-ABL1 Quantification in CML: Current Applications in Clinical Practice. Hemasphere 2020; 4:e496. [PMID: 33283168 PMCID: PMC7710259 DOI: 10.1097/hs9.0000000000000496] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular monitoring of the BCR-ABL1 transcript for patients with chronic phase chronic myeloid leukemia (CML) has become increasingly demanding. Real-time quantitative PCR (qPCR) is the routinely used method, but has limitations in quantification accuracy due to its inherent technical variation. Treatment recommendations rely on specific BCR-ABL1 values set at timed response milestones, making precise measurement of BCR-ABL1 a requisite. Furthermore, the sensitivity of qPCR may be insufficient to reliably quantify low levels of residual BCR-ABL1 in patients in deep molecular response (DMR) who could qualify for an attempt to discontinue Tyrosine Kinase Inhibitor (TKI) therapy. We reviewed the current use of digital PCR (dPCR) as a promising alternative for response monitoring in CML. dPCR offers an absolute BCR-ABL1 quantification at various disease levels with remarkable precision and a clinical sensitivity reaching down to at least MR5.0. Moreover, dPCR has been validated in multiple studies as prognostic marker for successful TKI treatment discontinuation, while this could not be achieved using classical qPCR. dPCR may thus prospectively be the preferred method to reliably identify patients achieving treatment milestones after initiation of TKI therapy as well as for the selection and timing for TKI discontinuation.
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Affiliation(s)
| | - Peter J.M. Valk
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark-David Levin
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | | | - Jan J. Cornelissen
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter E. Westerweel
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
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26
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Soverini S, Bernardi S, Galimberti S. Molecular Testing in CML between Old and New Methods: Are We at a Turning Point? J Clin Med 2020; 9:E3865. [PMID: 33261150 PMCID: PMC7760306 DOI: 10.3390/jcm9123865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular monitoring of minimal residual disease (MRD) and BCR-ABL1 kinase domain (KD) mutation testing have a well consolidated role in the routine management of chronic myeloid leukemia (CML) patients, as they provide precious information for therapeutic decision-making. Molecular response levels are used to define whether a patient has an "optimal", "warning", or "failure" response to tyrosine kinase inhibitor (TKI) therapy. Mutation status may be useful to decide whether TKI therapy should be changed and which alternative TKI (or TKIs) are most likely to be effective. Real-time quantitative polymerase chain reaction (RQ-qPCR) and Sanger sequencing are currently the gold standard for molecular response monitoring and mutation testing, respectively. However, in recent years, novel technologies such as digital PCR (dPCR) and next-generation sequencing (NGS) have been evaluated. Here, we critically describe the main features of these old and novel technologies, provide an overview of the recently published studies assessing the potential clinical value of dPCR and NGS, and discuss how the state of the art might evolve in the next years.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology “Lorenzo e Ariosto Seràgnoli”, University of Bologna, 40138 Bologna, Italy;
| | - Simona Bernardi
- Department of Clinical and Experimental Sciences, University of Brescia, Bone Marrow Transplant Unit, ASST Spedali Civili, 25123 Brescia, Italy
- Centro di Ricerca Emato-Oncologica AIL (CREA), ASST Spedali Civili, 25123 Brescia, Italy
| | - Sara Galimberti
- Department of Clinical and Experimental Medicine, Hematology Unit, University of Pisa, 56126 Pisa, Italy;
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27
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Jovanovski A, Petiti J, Giugliano E, Gottardi EM, Saglio G, Cilloni D, Fava C. Standardization of BCR-ABL1 p210 Monitoring: From Nested to Digital PCR. Cancers (Basel) 2020; 12:cancers12113287. [PMID: 33172063 PMCID: PMC7694607 DOI: 10.3390/cancers12113287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The introduction of tyrosine kinase inhibitors in 2001 as a targeted anticancer therapy has significantly improved the quality of life and survival of patients with chronic myeloid leukemia. At the same time, with the introduction of tyrosine kinase inhibitors, the need for precise monitoring of the molecular response to therapy has emerged. Starting with a qualitative polymerase chain reaction, followed by the introduction of a quantitative polymerase chain reaction to determine the exact quantity of the transcript of interest-p210 BCR-ABL1, molecular monitoring in patients with chronic myeloid leukemia was internationally standardized. This enabled precise monitoring of the therapeutic response, unification of therapeutic protocols, and comparison of results between different laboratories. This review aims to summarize the steps in the diagnosis and molecular monitoring of p210 BCR-ABL1, as well as to consider the possible future application of a more sophisticated method such as digital polymerase chain reaction.
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Affiliation(s)
- Aleksandar Jovanovski
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
- Correspondence: (A.J.); (J.P.); Tel.: +39-0119026800 (A.J. & J.P.)
| | - Jessica Petiti
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
- Correspondence: (A.J.); (J.P.); Tel.: +39-0119026800 (A.J. & J.P.)
| | - Emilia Giugliano
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, Orbassano, 10043 Turin, Italy; (E.G.); (E.M.G.)
| | - Enrico Marco Gottardi
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, Orbassano, 10043 Turin, Italy; (E.G.); (E.M.G.)
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
| | - Carmen Fava
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
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28
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Treatment-Free Remission in Chronic Myeloid Leukemia Harboring Atypical BCR-ABL1 Transcripts. Mediterr J Hematol Infect Dis 2020; 12:e2020066. [PMID: 32952977 PMCID: PMC7485467 DOI: 10.4084/mjhid.2020.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/14/2020] [Indexed: 11/08/2022] Open
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29
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Zenner K, Jensen DM, Cook TT, Dmyterko V, Bly RA, Ganti S, Mirzaa GM, Dobyns WB, Perkins JA, Bennett JT. Cell-free DNA as a diagnostic analyte for molecular diagnosis of vascular malformations. Genet Med 2020; 23:123-130. [PMID: 32884133 PMCID: PMC7796969 DOI: 10.1038/s41436-020-00943-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
Purpose: Vascular malformations (VM) are primarily caused by somatic activating pathogenic variants in oncogenes. Targeted pharmacotherapies are emerging but require molecular diagnosis. Since variants are currently only detected in malformation tissue, patients may be ineligible for clinical trials prior to surgery. We hypothesized that cell-free DNA (cfDNA) could provide molecular diagnoses for patients with isolated VM. Methods: cfDNA was isolated from plasma or cyst fluid from patients with arteriovenous malformations (AVM), venous malformations (VeM), or lymphatic malformations (LM), and assayed for known pathogenic variants using droplet digital PCR (ddPCR). Cyst fluid cfDNA from an independent cohort of LM patients was prospectively screened for variants using a multiplex ddPCR assay. Results: Variants were detected in plasma cfDNA in patients with AVM (2/8) and VeM (1/3). Variants were detected in cyst fluid cfDNA (7/7) but not plasma (0/26) in LM patients. Prospective testing of cyst fluid cfDNA with multiplex ddPCR identified variants in LM patients who had never undergone surgery (4/5). Conclusion: Variants were detected in plasma from AVM and VeM patients, and in cyst fluid from patients with LM. These data support investigation of cfDNA-based molecular diagnostics for VM patients which may provide opportunities to initiate targeted pharmacotherapies without prior surgery.
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Affiliation(s)
- Kaitlyn Zenner
- Seattle Children's Hospital, Division of Pediatric Otolaryngology, Department of Otolaryngology/Head and Neck Surgery, University of Washington, Seattle, WA, USA.,Vascular Anomalies Program, Seattle Children's Hospital, Seattle, WA, USA
| | - Dana M Jensen
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Tori T Cook
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Victoria Dmyterko
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Randall A Bly
- Seattle Children's Hospital, Division of Pediatric Otolaryngology, Department of Otolaryngology/Head and Neck Surgery, University of Washington, Seattle, WA, USA.,Vascular Anomalies Program, Seattle Children's Hospital, Seattle, WA, USA
| | - Sheila Ganti
- Seattle Children's Hospital, Division of Pediatric Otolaryngology, Department of Otolaryngology/Head and Neck Surgery, University of Washington, Seattle, WA, USA.,Vascular Anomalies Program, Seattle Children's Hospital, Seattle, WA, USA.,Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Seattle Children's Hospital, Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Seattle Children's Hospital, Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jonathan A Perkins
- Seattle Children's Hospital, Division of Pediatric Otolaryngology, Department of Otolaryngology/Head and Neck Surgery, University of Washington, Seattle, WA, USA.,Vascular Anomalies Program, Seattle Children's Hospital, Seattle, WA, USA
| | - James T Bennett
- Vascular Anomalies Program, Seattle Children's Hospital, Seattle, WA, USA. .,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA. .,Seattle Children's Hospital, Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
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30
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Comparison of Droplet Digital PCR versus qPCR Measurements on the International Scale for the Molecular Monitoring of Chronic Myeloid Leukemia Patients. Mol Diagn Ther 2020; 24:593-600. [PMID: 32875515 DOI: 10.1007/s40291-020-00485-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND BCR-ABL1/ABL1 p210 measurement by quantitative polymerase chain reaction (qPCR) is used worldwide to monitor the molecular response in chronic myeloid leukemia (CML) patients. Droplet digital polymerase chain reaction (ddPCR) seems to show a greater sensitivity than qPCR, probably due to the high number of replicates analyzed in ddPCR for the comparison. Additionally, in a recently published comparison, ddPCR measurements were not adequately transformed into International Scale (IS). METHOD We have analyzed 50 CML patients and ten non-CML donors in parallel by qPCR and ddPCR. To the best of our knowledge, this is the first study comparing both techniques under similar conditions, with BCR-ABL1/ABL1 measurements performed via both techniques transformed into IS. RESULTS Qualitative and quantitative comparisons showed excellent results. The qualitative correlation showed a Kappa index of 0.94 (95% confidence interval [CI] 0.90-0.98) (P < 0.001). In the quantitative comparison, the absolute intra-class correlation coefficient was 0.868 (95% CI 0.734-0.937; P < 0.001), and Lin's concordance correlation coefficient was 0.863. The Passing-Bablock test indicated a slight proportional difference between qPCR and ddPCR. A quantitative and qualitative subanalysis including 40 patients with a molecular response of 3.0 or deeper showed similar results in every test. In addition, the proportional difference in the Passing-Bablock test disappeared. There were no differences in the sensitivity for BCR-ABL1 detection between qPCR and ddPCR (McNemar test, P = 0.5). CONCLUSIONS In conclusion, our results show very good quantitative and qualitative correlations between BCR-ABL1/ABL1 p210 results obtained by qPCR and by ddPCR and confirm previous scarce data regarding the lack of an increase in sensitivity of ddPCR over qPCR in this setting.
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31
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Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots. Nat Commun 2020; 11:2971. [PMID: 32532990 PMCID: PMC7293259 DOI: 10.1038/s41467-020-16802-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/26/2020] [Indexed: 02/07/2023] Open
Abstract
APOBEC3A is a cytidine deaminase driving mutagenesis, DNA replication stress and DNA damage in cancer cells. While the APOBEC3A-induced vulnerability of cancers offers an opportunity for therapy, APOBEC3A protein and mRNA are difficult to quantify in tumors due to their low abundance. Here, we describe a quantitative and sensitive assay to measure the ongoing activity of APOBEC3A in tumors. Using hotspot RNA mutations identified from APOBEC3A-positive tumors and droplet digital PCR, we develop an assay to quantify the RNA-editing activity of APOBEC3A. This assay is superior to APOBEC3A protein- and mRNA-based assays in predicting the activity of APOBEC3A on DNA. Importantly, we demonstrate that the RNA mutation-based APOBEC3A assay is applicable to clinical samples from cancer patients. Our study presents a strategy to follow the dysregulation of APOBEC3A in tumors, providing opportunities to investigate the role of APOBEC3A in tumor evolution and to target the APOBEC3A-induced vulnerability in therapy. The DNA cytosine deaminases APOBEC3A and APOBEC3B have emerged from cancer genomics studies as drivers of mutation in cancers and tumor heterogeneity. Here the authors present a computational approach to identify the RNA mutations specifically driven by APOBEC3A, and developed an RNA mutation-based assay to quantify ongoing APOBEC3A activity in tumor cells.
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32
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Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
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