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Fu Y, Xu Y, Liu W, Zhang J, Wang F, Jian Q, Huang G, Zou C, Xie X, Kim AH, Mathios D, Pang F, Li F, Wang K, Shen J, Yin J. Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma. EClinicalMedicine 2024; 73:102697. [PMID: 39022798 PMCID: PMC11252770 DOI: 10.1016/j.eclinm.2024.102697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Background Current surveillance modalities of osteosarcoma relapse exhibit limited sensitivity and specificity. Although circulating tumor DNA (ctDNA) has been established as a biomarker of minimal residual disease (MRD) in many solid tumors, a sensitive ctDNA detection technique has not been thoroughly explored for longitudinal MRD detection in osteosarcoma. Methods From August 2019 to June 2023, 59 patients diagnosed with osteosarcoma at the First Affiliated Hospital of Sun Yat-sen University were evaluated in this study. Tumor-informed MRD panels were developed through whole exome sequencing (WES) of tumor tissues. Longitudinal blood samples were collected during treatment and subjected to multiplex PCR-based next-generation sequencing (NGS). Kaplan-Meier curves and Log-rank tests were used to compare outcomes, and Cox regression analysis was performed to identify prognostic factors. Findings WES analysis of 83 patients revealed substantial mutational heterogeneity, with non-recurrent mutated genes accounting for 58.1%. Tumor-informed MRD panels were successfully obtained for 85.5% of patients (71/83). Among 59 patients with successful MRD panel customization and available blood samples, 13 patients exhibited positive ctDNA detection after surgery. Patients with negative post-operative ctDNA had better event-free survival (EFS) compared to those with positive ctDNA, at 1-6 months after surgery, after adjuvant chemotherapy, and more than 6 months after surgery (p < 0.05). In both univariate and multivariate Cox regression analysis, ctDNA results emerged as a significant predictor of EFS (p < 0.05). ctDNA detection preceded positive imaging in 5 patients, with an average lead time of 92.6 days. Thirty-nine patients remained disease-free, with ctDNA results consistently negative or turning negative during follow-up. Interpretation Our study underscores the applicability of tumor-informed deep sequencing of ctDNA in osteosarcoma MRD surveillance and, to our knowledge, represents the largest cohort to date. ctDNA detection is a significant prognostic factor, enabling the early identification of tumor relapse and progression compared to standard imaging, thus offering valuable insights in guiding osteosarcoma patient management. Funding The Grants of National Natural Science Foundation of China (No. 82072964, 82072965, 82203798, 82203026), the Natural Science Foundation of Guangdong (No. 2023A1515012659, 2023A1515010302), and the Regional Combination Project of Basic and Applied Basic Research Foundation of Guangdong (No. 2020A1515110010).
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Affiliation(s)
- Yiwei Fu
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Yu Xu
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Weihai Liu
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiajun Zhang
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Fen Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | | | - Gang Huang
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Changye Zou
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Xianbiao Xie
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Albert H. Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dimitrios Mathios
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Fei Pang
- OrigiMed, Shanghai, 201124, China
| | - Feng Li
- OrigiMed, Shanghai, 201124, China
| | - Kai Wang
- OrigiMed, Shanghai, 201124, China
| | - Jingnan Shen
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Junqiang Yin
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
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2
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Chea M, Rigolot L, Canali A, Vergez F. Minimal Residual Disease in Acute Myeloid Leukemia: Old and New Concepts. Int J Mol Sci 2024; 25:2150. [PMID: 38396825 PMCID: PMC10889505 DOI: 10.3390/ijms25042150] [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: 12/31/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Minimal residual disease (MRD) is of major importance in onco-hematology, particularly in acute myeloid leukemia (AML). MRD measures the amount of leukemia cells remaining in a patient after treatment, and is an essential tool for disease monitoring, relapse prognosis, and guiding treatment decisions. Patients with a negative MRD tend to have superior disease-free and overall survival rates. Considerable effort has been made to standardize MRD practices. A variety of techniques, including flow cytometry and molecular methods, are used to assess MRD, each with distinct strengths and weaknesses. MRD is recognized not only as a predictive biomarker, but also as a prognostic tool and marker of treatment efficacy. Expected advances in MRD assessment encompass molecular techniques such as NGS and digital PCR, as well as optimization strategies such as unsupervised flow cytometry analysis and leukemic stem cell monitoring. At present, there is no perfect method for measuring MRD, and significant advances are expected in the future to fully integrate MRD assessment into the management of AML patients.
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Affiliation(s)
- Mathias Chea
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
| | - Lucie Rigolot
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Alban Canali
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Francois Vergez
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
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3
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Rosenquist R, Bernard E, Erkers T, Scott DW, Itzykson R, Rousselot P, Soulier J, Hutchings M, Östling P, Cavelier L, Fioretos T, Smedby KE. Novel precision medicine approaches and treatment strategies in hematological malignancies. J Intern Med 2023; 294:413-436. [PMID: 37424223 DOI: 10.1111/joim.13697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Genetic testing has been applied for decades in clinical routine diagnostics of hematological malignancies to improve disease (sub)classification, prognostication, patient management, and survival. In recent classifications of hematological malignancies, disease subtypes are defined by key recurrent genetic alterations detected by conventional methods (i.e., cytogenetics, fluorescence in situ hybridization, and targeted sequencing). Hematological malignancies were also one of the first disease areas in which targeted therapies were introduced, the prime example being BCR::ABL1 inhibitors, followed by an increasing number of targeted inhibitors hitting the Achilles' heel of each disease, resulting in a clear patient benefit. Owing to the technical advances in high-throughput sequencing, we can now apply broad genomic tests, including comprehensive gene panels or whole-genome and whole-transcriptome sequencing, to identify clinically important diagnostic, prognostic, and predictive markers. In this review, we give examples of how precision diagnostics has been implemented to guide treatment selection and improve survival in myeloid (myelodysplastic syndromes and acute myeloid leukemia) and lymphoid malignancies (acute lymphoblastic leukemia, diffuse large B-cell lymphoma, and chronic lymphocytic leukemia). We discuss the relevance and potential of monitoring measurable residual disease using ultra-sensitive techniques to assess therapy response and detect early relapses. Finally, we bring up the promising avenue of functional precision medicine, combining ex vivo drug screening with various omics technologies, to provide novel treatment options for patients with advanced disease. Although we are only in the beginning of the field of precision hematology, we foresee rapid development with new types of diagnostics and treatment strategies becoming available to the benefit of our patients.
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Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Elsa Bernard
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
- PRISM Center for Personalized Medicine, Gustave Roussy, Villejuif, France
| | - Tom Erkers
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
| | - David W Scott
- BC Cancer's Centre for Lymphoid Cancer, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Raphael Itzykson
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, Paris, France
- Département Hématologie et Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Philippe Rousselot
- Department of Hematology, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Jean Soulier
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, Paris, France
- Hématologie Biologique, APHP, Hôpital Saint-Louis, Paris, France
| | - Martin Hutchings
- Department of Haematology and Phase 1 Unit, Rigshospitalet, Copenhagen, Denmark
| | - Päivi Östling
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Karin E Smedby
- Department of Hematology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Division of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
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4
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Kim JJ, Jang JE, Lee HA, Park MR, Kook HW, Lee ST, Choi JR, Min YH, Shin S, Cheong JW. Development of a Next-generation Sequencing-based Gene Panel Test to Detect Measurable Residual Disease in Acute Myeloid Leukemia. Ann Lab Med 2023; 43:328-336. [PMID: 36843401 PMCID: PMC9989530 DOI: 10.3343/alm.2023.43.4.328] [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: 08/25/2022] [Revised: 12/04/2022] [Accepted: 01/27/2023] [Indexed: 02/28/2023] Open
Abstract
Background AML is a heterogeneous disease, and despite intensive therapy, recurrence is still high in AML patients who achieve the criterion for cytomorphologic remission (residual tumor burden [measurable residual disease, MRD]<5%). This study aimed to develop a targeted next-generation sequencing (NGS) panel to detect MRD in AML patients and validate its performance. Methods We designed an error-corrected, targeted MRD-NGS panel without using physical molecular barcodes, including 24 genes. Fifty-four bone marrow and peripheral blood samples from 23 AML patients were sequenced using the panel. The panel design was validated using reference material, and accuracy was assessed using droplet digital PCR. Results Dilution tests showed excellent linearity and a strong correlation between expected and observed clonal frequencies (R>0.99). The test reproducibly detected MRD in three dilution series samples, with a sensitivity of 0.25% for single-nucleotide variants. More than half of samples from patients with morphologic remission after one month of chemotherapy had detectable mutations. NGS-MRD positivity for samples collected after one month of chemotherapy tended to be associated with poor overall survival and progression-free survival. Conclusions Our highly sensitive and accurate NGS-MRD panel can be readily used to monitor most AML patients in clinical practice, including patients without gene rearrangement. In addition, this NGS-MRD panel may allow the detection of newly emerging clones during clinical relapse, leading to more reliable prognoses of AML.
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Affiliation(s)
- Jin Ju Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Ji Eun Jang
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Hyeon Ah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Korea
| | - Mi Ri Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Hye Won Kook
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea.,Dxome Co. Ltd., Seongnam, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea.,Dxome Co. Ltd., Seongnam, Korea
| | - Yoo Hong Min
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
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5
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Bieler J, Kubik S, Macheret M, Pozzorini C, Willig A, Xu Z. Benefits of applying molecular barcoding systems are not uniform across different genomic applications. J Transl Med 2023; 21:305. [PMID: 37147717 PMCID: PMC10163729 DOI: 10.1186/s12967-023-04160-0] [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: 02/08/2023] [Accepted: 04/25/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Despite the wide variety of Next Generation Sequencing (NGS)-based methods, it remains challenging to detect mutations present at very low frequencies. This problem is particularly relevant in oncology, where the limiting amount of input material, and its low quality, often limit the performance of the assays. Unique Molecular Identifiers (UMIs) are a molecular barcoding system often coupled with computational methods of noise suppression to improve the reliability of detection of rare variants. Although widely adopted, UMI inclusion imposes additional technical complexity and sequencing cost. Currently, there are no guidelines on UMI usage nor a comprehensive evaluation of their advantage across different applications. METHODS We used DNA sequencing data generated by molecular barcoding and hybridization-based enrichment, from various types and quantities of input material (fresh frozen, formaldehyde-treated and cell-free DNA), to evaluate the performance of variant calling in different clinically relevant contexts. RESULTS Noise suppression achieved by read grouping based on fragment mapping positions ensures reliable variant calling for many experimental designs even without exogenous UMIs. Exogenous barcodes significantly improve performance only when mapping position collisions occur, which is common in cell-free DNA. CONCLUSIONS We demonstrate that UMI usage is not universally beneficial across experimental designs and that it is worthwhile to critically consider the comparative advantage of UMI usage for a given NGS application prior to experimental design.
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Affiliation(s)
- Jonathan Bieler
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Slawomir Kubik
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Morgane Macheret
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Christian Pozzorini
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Adrian Willig
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland
| | - Zhenyu Xu
- Data Science Department, SOPHiA GENETICS, Rue du Centre 172, CH-1025, Saint Sulpice, Switzerland.
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6
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Puzo CJ, Tormey CA, Rinder HM, Siddon AJ. Optimizing Donor Chimerism Threshold for Next Generation Sequencing Monitoring of Measurable Residual Disease Post-Allogeneic Stem Cell Transplant for Myeloid Neoplasms. Transplant Cell Ther 2023:S2666-6367(23)01237-X. [PMID: 37062510 DOI: 10.1016/j.jtct.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND Next-Generation Sequencing (NGS) is used to monitor genetically-measurable residual disease (gMRD) following allogeneic stem cell transplant (aSCT). It is unknown whether an upper limit of chimerism exists such that gMRD NGS testing can be safely forgone. METHODS We reviewed 61 AML and 24 MDS patients between 2016-2020 with at least 1 NGS panel before and after aSCT. Donor chimerism was quantified. Logistic regression characterized which factors predicted gMRD. Receiver operator curves (ROC) determined the optimal chimerism threshold for which gMRD would not be detected. Data from an additional 22 patients with follow-up NGS testing in 2022, was also analyzed to validate our proposed threshold. RESULTS Donor chimerism (OR= 0.38, 95% CI[0.10,0.62], p=0.02), as expected, was a significant predictor of gMRD. Age, gender, conditioning regimen, presence of a related donor, and diagnosis were not associated with gMRD. A chimerism threshold of 92.5% optimized sensitivity (97.7) and specificity (95.4) such that values >92.5% strongly predicted absence of gMRD (AUC= .986). The validation cohort demonstrated similar strongly predictive capability (AUC= .974) with appropriate sensitivity (100%) and specificity (90.9%). CONCLUSION NGS monitoring of gMRD is redundant at chimerism values greater than a more conservative threshold of 92.5% after stem cell transplant.
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Affiliation(s)
| | | | - Henry M Rinder
- Yale School of Medicine, Department of Laboratory Medicine, New Haven CT, USA
| | - Alexa J Siddon
- Yale School of Medicine, Department of Laboratory Medicine, New Haven CT, USA; Yale School of Medicine, Department of Pathology, New Haven CT, USA.
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7
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Shimony S, Stahl M, Stone RM. Acute myeloid leukemia: 2023 update on diagnosis, risk-stratification, and management. Am J Hematol 2023; 98:502-526. [PMID: 36594187 DOI: 10.1002/ajh.26822] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023]
Abstract
DISEASE OVERVIEW Acute myeloid leukemia (AML) is a frequently fatal bone marrow stem cell cancer characterized by unbridled proliferation of malignant marrow stem cells with associated infection, anemia, and bleeding. An improved understanding of pathophysiology, improvements in measurement technology and at least 10 recently approved therapies have led to revamping the diagnostic, prognostic, and therapeutic landscape of AML. DIAGNOSIS One updated and one new classification system were published in 2022, both emphasizing the integration of molecular analysis into daily practice. Differences between the International Consensus Classification and major revisions from the previous 2016 WHO system provide both challenges and opportunities for care and clinical research. RISK ASSESSMENT AND MONITORING The European Leukemia Net 2022 risk classification integrates knowledge from novel molecular findings and recent trial results, as well as emphasizing dynamic risk based on serial measurable residual disease assessment. However, how to leverage our burgeoning ability to measure a small number of potentially malignant myeloid cells into therapeutic decision making is controversial. RISK ADAPTED THERAPY The diagnostic and therapeutic complexity plus the availability of newly approved agents requires a nuanced therapeutic algorithm which should integrate patient goals of care, comorbidities, and disease characteristics including the specific mutational profile of the patient's AML. The framework we suggest only represents the beginning of the discussion.
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Affiliation(s)
- Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Rabin Medical Center and Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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8
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Turner SA, Abou Shaar R, Yang Z. The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology. Diagn Cytopathol 2023; 51:83-94. [PMID: 36345929 PMCID: PMC10098847 DOI: 10.1002/dc.25067] [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: 08/09/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.
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Affiliation(s)
- Scott A Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Rand Abou Shaar
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zhongbo Yang
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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9
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Wästerlid T, Cavelier L, Haferlach C, Konopleva M, Fröhling S, Östling P, Bullinger L, Fioretos T, Smedby KE. Application of precision medicine in clinical routine in haematology-Challenges and opportunities. J Intern Med 2022; 292:243-261. [PMID: 35599019 PMCID: PMC9546002 DOI: 10.1111/joim.13508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Precision medicine is revolutionising patient care in cancer. As more knowledge is gained about the impact of specific genetic lesions on diagnosis, prognosis and treatment response, diagnostic precision and the possibility for optimal individual treatment choice have improved. Identification of hallmark genetic aberrations such as the BCR::ABL1 gene fusion in chronic myeloid leukaemia (CML) led to the rapid development of efficient targeted therapy and molecular follow-up, vastly improving survival for patients with CML during recent decades. The assessment of translocations, copy number changes and point mutations are crucial for the diagnosis and risk stratification of acute myeloid leukaemia and myelodysplastic syndromes. Still, the often heterogeneous and complex genetic landscape of haematological malignancies presents several challenges for the implementation of precision medicine to guide diagnosis, prognosis and treatment choice. This review provides an introduction and overview of the important molecular characteristics and methods currently applied in clinical practice to guide clinical decision making in haematological malignancies of myeloid and lymphoid origin. Further, experimental ways to guide the choice of targeted therapy for refractory patients are reviewed, such as functional precision medicine using drug profiling. An example of the use of pipeline studies where the treatment is chosen according to the molecular characteristics in rare solid malignancies is also provided. Finally, the future opportunities and remaining challenges of precision medicine in the real world are discussed.
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Affiliation(s)
- Tove Wästerlid
- Department of Medicine Solna, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Marina Konopleva
- Department of Leukemia, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Päivi Östling
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Consortium (DKTK) Berlin Site, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Science for Life Laboratory, Lund University and Clinical Genomics Lund, Lund, Sweden
| | - Karin E Smedby
- Department of Medicine Solna, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
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10
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Cluzeau T, Lemoli RM, McCloskey J, Cooper T. Measurable Residual Disease in High-Risk Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:cancers14051278. [PMID: 35267586 PMCID: PMC8909238 DOI: 10.3390/cancers14051278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Assessment of measurable residual disease (MRD) identifies small numbers of acute myeloid leukemia (AML) cells that may remain after initiating treatment. The achievement of MRD negativity (no detectable AML cells remaining) typically predicts better outcomes for patients with AML. Some patients with AML have disease characteristics that put them at a higher risk of treatment failure or relapse; while outcomes for patients with high-risk AML are historically poor with traditional chemotherapy regimens, newer chemotherapy formulations (i.e., CPX-351) and targeted therapies may be more effective in achieving MRD negativity in these patients. Currently, there is no agreement on the best method for determining whether a patient has achieved MRD negativity, and the use of several different methods makes it difficult to compare outcomes across studies. Despite these challenges, regular monitoring of patients for the achievement of MRD negativity will become increasingly important in the routine management of patients with high-risk AML. Abstract Mounting evidence suggests measurable residual disease (MRD) assessments are prognostic in acute myeloid leukemia (AML). High-risk AML encompasses a subset of AML with poor response to therapy and prognosis, with features such as therapy-related AML, an antecedent hematologic disorder, extramedullary disease (in adults), and selected mutations and cytogenetic abnormalities. Historically, few patients with high-risk AML achieved deep and durable remission with conventional chemotherapy; however, newer agents might be more effective in achieving MRD-negative remission. CPX-351 (dual-drug liposomal encapsulation of daunorubicin/cytarabine at a synergistic ratio) demonstrated MRD-negativity rates of 36–64% across retrospective studies in adults with newly diagnosed high-risk AML and 84% in pediatric patients with first-relapse AML. Venetoclax (BCL2 inhibitor) demonstrated MRD-negativity rates of 33–53% in combination with hypomethylating agents for high-risk subgroups in studies of older adults with newly diagnosed AML who were ineligible for intensive therapy and 65% in combination with chemotherapy in pediatric patients with relapsed/refractory AML. However, there is no consensus on optimal MRD methodology in AML, and the use of different techniques, sample sources, sensitivity thresholds, and the timing of assessments limit comparisons across studies. Robust MRD analyses are needed in future clinical studies, and MRD monitoring should become a routine aspect of AML management.
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Affiliation(s)
- Thomas Cluzeau
- Service d’hématologie, Université Cote d’Azur, CHU de Nice, 06200 Nice, France
- Correspondence: ; Tel.: +33-492035841; Fax: +33-492035895
| | - Roberto M. Lemoli
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
- Clinic of Hematology, Department of Internal Medicine (DIMI), University of Genoa, 16132 Genoa, Italy
| | - James McCloskey
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA;
| | - Todd Cooper
- Division of Hematology/Oncology, Cancer and Blood Disorders Center, Seattle Children’s Hospital, Seattle, WA 98105, USA;
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11
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Georgi JA, Stasik S, Bornhäuser M, Platzbecker U, Thiede C. Analysis of Subset Chimerism for MRD-Detection and Pre-Emptive Treatment in AML. Front Oncol 2022; 12:841608. [PMID: 35252010 PMCID: PMC8892234 DOI: 10.3389/fonc.2022.841608] [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: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (alloHCT) represents the only potentially curative treatment in high-risk AML patients, but up to 40% of patients suffer from relapse after alloHCT. Treatment of overt relapse poses a major therapeutic challenge and long-term disease control is achieved only in a minority of patients. In order to avoid post-allograft relapse, maintenance as well as pre-emptive therapy strategies based on MRD-detection have been used. A prerequisite for the implementation of pre-emptive therapy is the accurate identification of patients at risk for imminent relapse. Detection of measurable residual disease (MRD) represents an effective tool for early relapse prediction in the post-transplant setting. However, using established MRD methods such as multicolor flow cytometry or quantitative PCR, sensitive MRD monitoring is only applicable in about half of the patients with AML and advanced MDS undergoing alloHCT. Donor chimerism analysis, in particular when performed on enriched leukemic stem and progenitor cells, e.g. CD34+ cells, is a sensitive method and has emerged as an alternative option in the post alloHCT setting. In this review, we will focus on the current strategies for lineage specific chimerism analysis, results of pre-emptive treatment using this technology as well as future developments in this field.
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Affiliation(s)
- Julia-Annabell Georgi
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der Technischen Universität, Dresden, Germany
| | - Sebastian Stasik
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der Technischen Universität, Dresden, Germany
| | - Martin Bornhäuser
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der Technischen Universität, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- *Correspondence: Martin Bornhäuser ,
| | - Uwe Platzbecker
- Klinik und Poliklinik für Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der Technischen Universität, Dresden, Germany
- AgenDix GmbH, Dresden, Germany
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12
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Vonk CM, Al Hinai ASA, Hanekamp D, Valk PJM. Molecular Minimal Residual Disease Detection in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:5431. [PMID: 34771594 PMCID: PMC8582498 DOI: 10.3390/cancers13215431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Initial induction chemotherapy to eradicate the bulk of acute myeloid leukemia (AML) cells results in complete remission (CR) in the majority of patients. However, leukemic cells persisting in the bone marrow below the morphologic threshold remain unaffected and have the potential to proliferate and re-emerge as AML relapse. Detection of minimal/measurable residual disease (MRD) is a promising prognostic marker for AML relapse as it can assess an individual patients' risk profile and evaluate their response to treatment. With the emergence of molecular techniques, such as next generation sequencing (NGS), a more sensitive assessment of molecular MRD markers is available. In recent years, the detection of MRD by molecular assays and its association with AML relapse and survival has been explored and verified in multiple studies. Although most studies show that the presence of MRD leads to a worse clinical outcome, molecular-based methods face several challenges including limited sensitivity/specificity, and a difficult distinction between mutations that are representative of AML rather than clonal hematopoiesis. This review describes the studies that have been performed using molecular-based assays for MRD detection in the context of other MRD detection approaches in AML, and discusses limitations, challenges and opportunities.
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Affiliation(s)
- Christian M Vonk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
| | - Adil S A Al Hinai
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- National Genetic Center, Ministry of Health, Muscat 111, Oman
| | - Diana Hanekamp
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- Department of Hematology, Cancer Center VU University Medical Center, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
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13
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Qin D. Molecular testing for acute myeloid leukemia. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0734. [PMID: 34347394 PMCID: PMC8763005 DOI: 10.20892/j.issn.2095-3941.2020.0734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/02/2021] [Indexed: 11/11/2022] Open
Abstract
In the era of personalized medicine, information on molecular change at the gene level is important for patient care. Such information has been used for disease classification, diagnosis, prognosis, risk stratification, and treatment, which is especially important in cancer patient care. Many molecular tests exist and can be used to detect the molecular changes at gene level. These tests include, but are not limited to, karyotyping, endpoint polymerase chain reaction (PCR), real-time PCR, Sanger sequencing, pyrosequencing, next-generation sequencing, and so forth. How to use the right tests for the right patients at the right time is essential for optimal patient outcome. This review puts together some information on molecular testing for acute myeloid leukemia.
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Affiliation(s)
- Dahui Qin
- Moffitt Cancer Center, Tampa, FL 33612-9416, USA
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14
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Tsagiopoulou M, Maniou MC, Pechlivanis N, Togkousidis A, Kotrová M, Hutzenlaub T, Kappas I, Chatzidimitriou A, Psomopoulos F. UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction. Front Genet 2021; 12:660366. [PMID: 34122513 PMCID: PMC8193862 DOI: 10.3389/fgene.2021.660366] [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: 01/29/2021] [Accepted: 04/08/2021] [Indexed: 11/17/2022] Open
Abstract
A recent refinement in high-throughput sequencing involves the incorporation of unique molecular identifiers (UMIs), which are random oligonucleotide barcodes, on the library preparation steps. A UMI adds a unique identity to different DNA/RNA input molecules through polymerase chain reaction (PCR) amplification, thus reducing bias of this step. Here, we propose an alignment free framework serving as a preprocessing step of fastq files, called UMIc, for deduplication and correction of reads building consensus sequences from each UMI. Our approach takes into account the frequency and the Phred quality of nucleotides and the distances between the UMIs and the actual sequences. We have tested the tool using different scenarios of UMI-tagged library data, having in mind the aspect of a wide application. UMIc is an open-source tool implemented in R and is freely available from https://github.com/BiodataAnalysisGroup/UMIc.
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Affiliation(s)
- Maria Tsagiopoulou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Maria Christina Maniou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasis Togkousidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Michaela Kotrová
- Unit for Hematological Diagnostics, Department of Internal Medicine II, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Tobias Hutzenlaub
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | - Ilias Kappas
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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15
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Walter RB, Ofran Y, Wierzbowska A, Ravandi F, Hourigan CS, Ngai LL, Venditti A, Buccisano F, Ossenkoppele GJ, Roboz GJ. Measurable residual disease as a biomarker in acute myeloid leukemia: theoretical and practical considerations. Leukemia 2021; 35:1529-1538. [PMID: 33758317 DOI: 10.1038/s41375-021-01230-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/19/2021] [Accepted: 03/11/2021] [Indexed: 12/20/2022]
Abstract
Several methodologies that rely on the detection of immunophenotypic or molecular abnormalities of the neoplastic cells are now available to quantify measurable ("minimal") residual disease (MRD) in acute myeloid leukemia (AML). Although the perfect MRD test does not (yet) exist, the strong association between MRD and adverse patient outcomes has provided the impetus to use measures of MRD as biomarker in the routine care of AML patients and during clinical trials. MRD test results may inform the selection of postremission therapy in some patients but evidence supporting the use of MRD as predictive biomarker is still limited. Several retrospective studies have shown that conversion from undetectable to detectable MRD or increasing MRD over time is associated with overt disease recurrence, and MRD testing may therefore be valuable as a monitoring biomarker for early detection of relapse. Interpreting serial MRD data is complex, with open questions regarding the optimal timing and frequency of testing, as well as the identification of test-specific thresholds to define relapse. Importantly, it is unknown whether intervening at the time of MRD detection, rather than at overt disease recurrence, improves outcomes. Finally, using MRD as a surrogate efficacy-response biomarker to accelerate drug development/approval has already been accepted by regulatory authorities in other diseases and is of great interest as a potential strategy in AML. While the prognostic value of MRD in AML is well established, data from prospective clinical trials confirming that treatment effects on MRD directly relate to clinical outcomes are needed to further establish the role of MRD as a surrogate endpoint in AML.
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Affiliation(s)
- Roland B Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA. .,Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA. .,Department of Epidemiology, University of Washington, Seattle, WA, USA.
| | - Yishai Ofran
- Department of Hematology, Sharee Zedeq Medical Center, Jerusalem, Israel
| | | | - Farhad Ravandi
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lok Lam Ngai
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Adriano Venditti
- Department of Biomedicine and Prevention, Hematology, University Tor Vergata, Rome, Italy
| | - Francesco Buccisano
- Department of Biomedicine and Prevention, Hematology, University Tor Vergata, Rome, Italy
| | - Gert J Ossenkoppele
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Gail J Roboz
- Hematology and Oncology, Weill Cornell Medicine and NewYork-Presbyterian Hospital, Cornell University, New York, NY, USA
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16
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Rimando JC, Christopher MJ, Rettig MP, DiPersio JF. Biology of Disease Relapse in Myeloid Disease: Implication for Strategies to Prevent and Treat Disease Relapse After Stem-Cell Transplantation. J Clin Oncol 2021; 39:386-396. [PMID: 33434062 PMCID: PMC8462627 DOI: 10.1200/jco.20.01587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/05/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Joseph C. Rimando
- Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Matthew J. Christopher
- Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Michael P. Rettig
- Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO
| | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO
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17
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Ngai LL, Kelder A, Janssen JJWM, Ossenkoppele GJ, Cloos J. MRD Tailored Therapy in AML: What We Have Learned So Far. Front Oncol 2021; 10:603636. [PMID: 33575214 PMCID: PMC7871983 DOI: 10.3389/fonc.2020.603636] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/16/2020] [Indexed: 12/22/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous clonal disease associated with a dismal survival, partly due to the frequent occurrence of relapse. Many patient- and leukemia-specific characteristics, such as age, cytogenetics, mutations, and measurable residual disease (MRD) after intensive chemotherapy, have shown to be valuable prognostic factors. MRD has become a rich field of research where many advances have been made regarding technical, biological, and clinical aspects, which will be the topic of this review. Since many laboratories involved in AML diagnostics have experience in immunophenotyping, multiparameter flow cytometry (MFC) based MRD is currently the most commonly used method. Although molecular, quantitative PCR based techniques may be more sensitive, their disadvantage is that they can only be applied in a subset of patients harboring the genetic aberration. Next-generation sequencing can assess and quantify mutations in many genes but currently does not offer highly sensitive MRD measurements on a routine basis. In order to provide reliable MRD results, MRD assay optimization and standardization is essential. Different techniques for MRD assessment are being evaluated, and combinations of the methods have shown promising results for improving its prognostic value. In this regard, the load of leukemic stem cells (LSC) has also been shown to add to the prognostic value of MFC-MRD. At this moment, MRD after intensive chemotherapy is most often used as a prognostic factor to help stratify patients, but also to select the most appropriate consolidation therapy. For example, to guide post-remission treatment for intermediate-risk patients where MRD positive patients receive allogeneic stem cell transplantation and MRD negative receive autologous stem cell transplantation. Other upcoming uses of MRD that are being investigated include: selecting the type of allogeneic stem cell transplantation therapy (donor, conditioning), monitoring after stem cell transplantation (to allow intervention), and determining drug efficacy for the use of a surrogate endpoint in clinical trials.
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Affiliation(s)
| | | | | | | | - Jacqueline Cloos
- Department of Hematology, Amsterdam UMC, Cancer Center Amsterdam, Vrije Universiteit, Amsterdam, Netherlands
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18
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Carlsen ED, Aggarwal N, Bailey NG. Molecular methods for measurable residual disease in acute myeloid leukemia: where are we and where are we going? J Hematop 2021. [DOI: 10.1007/s12308-020-00440-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Patkar N, Kakirde C, Shaikh AF, Salve R, Bhanshe P, Chatterjee G, Rajpal S, Joshi S, Chaudhary S, Kodgule R, Ghoghale S, Deshpande N, Shetty D, Khizer SH, Jain H, Bagal B, Menon H, Khattry N, Sengar M, Tembhare P, Subramanian P, Gujral S. Clinical impact of panel-based error-corrected next generation sequencing versus flow cytometry to detect measurable residual disease (MRD) in acute myeloid leukemia (AML). Leukemia 2021; 35:1392-1404. [PMID: 33558666 PMCID: PMC8102181 DOI: 10.1038/s41375-021-01131-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/30/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
We accrued 201 patients of adult AML treated with conventional therapy, in morphological remission, and evaluated MRD using sensitive error-corrected next generation sequencing (NGS-MRD) and multiparameter flow cytometry (FCM-MRD) at the end of induction (PI) and consolidation (PC). Nearly 71% of patients were PI NGS-MRD+ and 40.9% PC NGS-MRD+ (median VAF 0.76%). NGS-MRD+ patients had a significantly higher cumulative incidence of relapse (p = 0.003), inferior overall survival (p = 0.001) and relapse free survival (p < 0.001) as compared to NGS-MRD- patients. NGS-MRD was predictive of inferior outcome in intermediate cytogenetic risk and demonstrated potential in favorable cytogenetic risk AML. PI NGS-MRD- patients had a significantly improved survival as compared to patients who became NGS-MRD- subsequently indicating that kinetics of NGS-MRD clearance was of paramount importance. NGS-MRD identified over 80% of cases identified by flow cytometry at PI time point whereas FCM identified 49.3% identified by NGS. Only a fraction of cases were NGS-MRD- but FCM-MRD+. NGS-MRD provided additional information of the risk of relapse when compared to FCM-MRD. We demonstrate a widely applicable, scalable NGS-MRD approach that is clinically informative and synergistic to FCM-MRD in AML treated with conventional therapies. Maximum clinical utility may be leveraged by combining FCM and NGS-MRD modalities.
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Affiliation(s)
- Nikhil Patkar
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Chinmayee Kakirde
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Anam Fatima Shaikh
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rakhi Salve
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Bhanshe
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Gaurav Chatterjee
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sweta Rajpal
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Swapnali Joshi
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shruti Chaudhary
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rohan Kodgule
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Sitaram Ghoghale
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Nilesh Deshpande
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Dhanalaxmi Shetty
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Syed Hasan Khizer
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hasmukh Jain
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Bhausaheb Bagal
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hari Menon
- Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Navin Khattry
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Manju Sengar
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Papagudi Subramanian
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sumeet Gujral
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
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20
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Thakral D, Gupta R, Sahoo RK, Verma P, Kumar I, Vashishtha S. Real-Time Molecular Monitoring in Acute Myeloid Leukemia With Circulating Tumor DNA. Front Cell Dev Biol 2020; 8:604391. [PMID: 33363162 PMCID: PMC7759522 DOI: 10.3389/fcell.2020.604391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
The clonal evolution of acute myeloid leukemia (AML), an oligoclonal hematological malignancy, is driven by a plethora of cytogenetic abnormalities, gene mutations, abnormal epigenetic patterns, and aberrant gene expressions. These alterations in the leukemic blasts promote clinically diverse manifestations with common characteristics of high relapse and drug resistance. Defining and real-time monitoring of a personalized panel of these predictive genetic biomarkers is rapidly being adapted in clinical setting for diagnostic, prognostic, and therapeutic decision-making in AML. A major challenge remains the frequency of invasive biopsy procedures that can be routinely performed for monitoring of AML disease progression. Moreover, a single-site biopsy is not representative of the tumor heterogeneity as it is spatially and temporally constrained and necessitates the understanding of longitudinal and spatial subclonal dynamics in AML. Hematopoietic cells are a major contributor to plasma cell-free DNA, which also contain leukemia-specific aberrations as the circulating tumor-derived DNA (ctDNA) fraction. Plasma cell-free DNA analysis holds immense potential as a minimally invasive tool for genomic profiling at diagnosis as well as clonal evolution during AML disease progression. With the technological advances and increasing sensitivity for detection of ctDNA, both genetic and epigenetic aberrations can be qualitatively and quantitatively evaluated. However, challenges remain in validating the utility of liquid biopsy tools in clinics, and universal recommendations are still awaited towards reliable diagnostics and prognostics. Here, we provide an overview on the scope of ctDNA analyses for prognosis, assessment of response to treatment and measurable residual disease, prediction of disease relapse, development of acquired resistance and beyond in AML.
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Affiliation(s)
- Deepshi Thakral
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ranjit Kumar Sahoo
- Department of Medical Oncology, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Pramod Verma
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Indresh Kumar
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sangeeta Vashishtha
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
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Haferlach T. Advancing leukemia diagnostics: Role of Next Generation Sequencing (NGS) in acute myeloid leukemia. Hematol Rep 2020; 12:8957. [PMID: 33042506 PMCID: PMC7520852 DOI: 10.4081/hr.2020.8957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
AML diagnostics, initially based solely on morphological evaluation, now relies on multiple disciplines to reach its full potential. Only by integrating the results of cytomorphology, cytochemistry, immunophenotyping, cytogenetics and molecular genetics it is possible to fulfil WHO classification and ELN prognostication systems. Especially molecular genetics has gained a lot of interest over the last decade, mainly through the introduction of next generation sequencing (NGS). NGS application ranges from the investigation of single genes and panels to even whole exomes, transcriptomes and genomes. In routine AML diagnostics panels are the preferred NGS methodology. Here, we will review the power and limitations of NGS in the context of diagnosis, prognosis and precision medicine. Due to high dimensionality, NGS data interpretation is challenging but it also offers a unique investigatory chance and the opportunity to apply data mining techniques such as artificial intelligence. We will also reflect on how the incorporation of the improved knowledge base into routine diagnostics can pave the way for better treatment and more cure in AML.
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