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Dyshlovoy SA, Paigin S, Afflerbach AK, Lobermeyer A, Werner S, Schüller U, Bokemeyer C, Schuh AH, Bergmann L, von Amsberg G, Joosse SA. Applications of Nanopore sequencing in precision cancer medicine. Int J Cancer 2024. [PMID: 39031959 DOI: 10.1002/ijc.35100] [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: 03/09/2024] [Revised: 04/25/2024] [Accepted: 06/25/2024] [Indexed: 07/22/2024]
Abstract
Oxford Nanopore Technologies sequencing, also referred to as Nanopore sequencing, stands at the forefront of a revolution in clinical genetics, offering the potential for rapid, long read, and real-time DNA and RNA sequencing. This technology is currently making sequencing more accessible and affordable. In this comprehensive review, we explore its potential regarding precision cancer diagnostics and treatment. We encompass a critical analysis of clinical cases where Nanopore sequencing was successfully applied to identify point mutations, splice variants, gene fusions, epigenetic modifications, non-coding RNAs, and other pivotal biomarkers that defined subsequent treatment strategies. Additionally, we address the challenges of clinical applications of Nanopore sequencing and discuss the current efforts to overcome them.
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Affiliation(s)
- Sergey A Dyshlovoy
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefanie Paigin
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Ann-Kristin Afflerbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annabelle Lobermeyer
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Paediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
| | - Lina Bergmann
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Hansen MH, Maagaard M, Cédile O, Nyvold CG. SWIGH-SCORE: A translational light-weight approach in computational detection of rearranged immunoglobulin heavy chain to be used in monoclonal lymphoproliferative disorders. MethodsX 2024; 12:102741. [PMID: 38846434 PMCID: PMC11154698 DOI: 10.1016/j.mex.2024.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/23/2024] [Accepted: 05/02/2024] [Indexed: 06/09/2024] Open
Abstract
We present a lightweight tool for clonotyping and measurable residual disease (MRD) assessment in monoclonal lymphoproliferative disorders. It is a translational method that enables computational detection of rearranged immunoglobulin heavy chain gene sequences.•The swigh-score clonotyping tool emphasizes parallelization and applicability across sequencing platforms.•The algorithm is based on an adaptation of the Smith-Waterman algorithm for local alignment of reads generated by 2nd and 3rd generation of sequencers.For method validation, we demonstrate the targeted sequences of immunoglobulin heavy chain genes from diagnostic bone marrow using serial dilutions of CD138+ plasma cells from a patient with multiple myeloma. Sequencing libraries from diagnostic samples were prepared for the three sequencing platforms, Ion S5 (Thermo Fisher Scientific), MiSeq (Illumina), and MinION (Oxford Nanopore), using the LymphoTrack assay. Basic quality filtering was performed, and a Smith-Waterman-based swigh-score algorithm was developed in shell and C for clonotyping and MRD assessment using FASTQ data files. Performance is demonstrated across the three different sequencing platforms.
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Affiliation(s)
- Marcus Høy Hansen
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Markus Maagaard
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Oriane Cédile
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
- OPEN, Odense Patient data Explorative Network, Haematology-Pathology Research Laboratory, Odense University Hospital, Odense, Denmark
| | - Charlotte Guldborg Nyvold
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
- OPEN, Odense Patient data Explorative Network, Haematology-Pathology Research Laboratory, Odense University Hospital, Odense, Denmark
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Hansen MH, Cédile O, Abildgaard N, Nyvold CG. The potential of 3rd-generation nanopore sequencing for B-cell clonotyping in lymphoproliferative disorders. EJHAEM 2024; 5:290-293. [PMID: 38406528 PMCID: PMC10887334 DOI: 10.1002/jha2.815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 02/27/2024]
Abstract
Lymphoid malignancies are characterized by clonal cell expansion, often identifiable by unique immunoglobulin rearrangements. Heavy (IGH) and light-chain gene usage offers diagnostic insights and enables sensitive residual disease detection via next-generation sequencing. With its adaptable throughput and variable read lengths, Oxford Nanopore thirdgeneration sequencing now holds promise for clonotyping. This study analyzed CD138+ plasma-cell DNA from eight multiple myeloma patients, comparing clonotyping performance between Nanopore sequencing, Illumina MiSeq, and Ion Torrent S5. We demonstrated clonotype consistency across platforms through Smith-Waterman local alignment of nanopore reads. The mean clonal percentage of IGH V and J gene usage in the CD138+ cells was 69% for Nanopore, 67% for S5, and 76% for MiSeq. When aligned with known clonotypes, clonal cells averaged a 91% similarity, exceeding 85%. In summary, Nanopore sequencing, with its capacity for generating millions of high-quality reads, proves effective for detecting clonal IGH rearrangements. This versatile platform offers the potential for measuring residual disease down to a sensitivity level of 10-6 at a lower cost, marking a significant advancement in clonotyping techniques.
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Affiliation(s)
- Marcus H. Hansen
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
| | - Oriane Cédile
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
- OPEN, Odense Patient data Explorative Network, Odense University HospitalOdenseDenmark
| | - Niels Abildgaard
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
| | - Charlotte G. Nyvold
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
- OPEN, Odense Patient data Explorative Network, Odense University HospitalOdenseDenmark
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Levkova M, Chervenkov T, Angelova L, Dzenkov D. Oxford Nanopore Technology and its Application in Liquid Biopsies. Curr Genomics 2023; 24:337-344. [PMID: 38327653 PMCID: PMC10845067 DOI: 10.2174/0113892029286632231127055733] [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: 10/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 02/09/2024] Open
Abstract
Advanced medical technologies are transforming the future of healthcare, in particular, the screening and detection of molecular-genetic changes in patients suspected of having a neoplasm. They are based on the assumption that neoplasms release small amounts of various neoplasm-specific molecules, such as tumor DNA, called circulating DNA (cirDNA), into the extracellular space and subsequently into the blood. The detection of tumor-specific molecules and specific molecular changes in body fluids in a noninvasive or minimally invasive approach is known as "liquid biopsy." The aim of this review is to summarize the current knowledge of the application of ONT for analyzing circulating DNA in the field of liquid biopsies among cancer patients. Databases were searched using the keywords "nanopore" and "liquid biopsy" and by applying strict inclusion criteria. This technique can be used for the detection of neoplastic disease, including metastases, guiding precision therapy, and monitoring its effects. There are many challenges, however, for the successful implementation of this technology into the clinical practice. The first one is the low amount of tumor-specific molecules in the body fluids. Secondly, a tumor molecular signature should be discriminated from benign conditions like clonal hematopoiesis of unknown significance. Oxford Nanopore Technology (ONT) is a third-generation sequencing technology that seems particularly promising to complete these tasks. It offers rapid sequencing thanks to its ability to detect changes in the density of the electric current passing through nanopores. Even though ONT still needs validation technology, it is a promising approach for early diagnosis, therapy guidance, and monitoring of different neoplasms based on analyzing the cirDNA.
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Affiliation(s)
- Mariya Levkova
- Department of Medical Genetics, Medical University Varna, Marin Drinov Str 55, Varna, 9000, Bulgaria
- Laboratory of Medical Genetics, St. Marina Hospital, Hristo Smirnenski Blv 1, Varna, 9000, Bulgaria
| | - Trifon Chervenkov
- Department of Medical Genetics, Medical University Varna, Marin Drinov Str 55, Varna, 9000, Bulgaria
- Laboratory of Clinical immunology, St. Marina Hospital, Hristo Smirnenski Blv 1, Varna, 9000, Bulgaria
| | - Lyudmila Angelova
- Department of Medical Genetics, Medical University Varna, Marin Drinov Str 55, Varna, 9000, Bulgaria
| | - Deyan Dzenkov
- Department of General and Clinical Pathology, Forensic Medicine and Deontology, Division of General and Clinical Pathology, Medical University Varna, Marin Drinov Str 55, Varna, 9000, Bulgaria
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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Dekker SE, Rea D, Cayuela JM, Arnhardt I, Leonard J, Heuser M. Using Measurable Residual Disease to Optimize Management of AML, ALL, and Chronic Myeloid Leukemia. Am Soc Clin Oncol Educ Book 2023; 43:e390010. [PMID: 37311155 DOI: 10.1200/edbk_390010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this review, we discuss the use of measurable residual disease (MRD) in AML, ALL, and chronic myeloid leukemia (CML). Our aims were to review the different methodologies for MRD assessment; describe the clinical relevance and medical decision making on the basis of MRD; compare and contrast the usage of MRD across AML, ALL, and CML; and discuss what patients need to know about MRD as it relates to their disease status and treatment. Finally, we discuss ongoing challenges and future directions with the goal of optimizing MRD usage in leukemia management.
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Affiliation(s)
- Simone E Dekker
- Department of Medicine, Oregon Health & Science University, Portland, OR
| | - Delphine Rea
- France Intergroupe des Leucémies Myéloïdes chroniques FiLMC, Hôpital Saint-Louis APHP, Paris, France
- Service d'Hématologie Adulte, Hôpital Saint-Louis APHP, Paris, France
| | - Jean-Michel Cayuela
- France Intergroupe des Leucémies Myéloïdes chroniques FiLMC, Hôpital Saint-Louis APHP, Paris, France
- Laboratoire de Biologie Moléculaire, Hôpital Saint-Louis APHP, Paris, France
| | - Isabell Arnhardt
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Jessica Leonard
- Division of Hematology-Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- Comprehensive Cancer Center Lower Saxony, Hannover, Germany
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