1
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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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2
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Behrens YL, Pietzsch S, Antić Ž, Zhang Y, Bergmann AK. The landscape of cytogenetic and molecular genetic methods in diagnostics for hematologic neoplasia. Best Pract Res Clin Haematol 2024; 37:101539. [PMID: 38490767 DOI: 10.1016/j.beha.2024.101539] [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: 12/05/2023] [Accepted: 01/28/2024] [Indexed: 03/17/2024]
Abstract
Improvements made during the last decades in the management of patients with hematologic neoplasia have resulted in increase of overall survival. These advancements have become possible through progress in our understanding of genetic basis of different hematologic malignancies and their role in the current risk-adapted treatment protocols. In this review, we provide an overview of current cytogenetic and molecular genetic methods, commonly used in the genetic characterization of hematologic malignancies, describe the current developments in the cytogenetic and molecular diagnostics, and give an outlook into their future development. Furthermore, we give a brief overview of the most important public databases and guidelines for sequence variant interpretation.
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Affiliation(s)
- Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Stefan Pietzsch
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany.
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3
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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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4
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Oehler JB, Wright H, Stark Z, Mallett AJ, Schmitz U. The application of long-read sequencing in clinical settings. Hum Genomics 2023; 17:73. [PMID: 37553611 PMCID: PMC10410870 DOI: 10.1186/s40246-023-00522-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
Long-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large and complex regions of the genome makes them ideal for clinical applications in molecular diagnosis and therapy selection, thereby providing a valuable tool for precision medicine. In the third-generation sequencing duopoly, Oxford Nanopore Technologies and Pacific Biosciences work towards increasing the accuracy, throughput, and portability of long-read sequencing methods while trying to keep costs low. These trades have made long-read sequencing an attractive tool for use in research and clinical settings. This article provides an overview of current clinical applications and limitations of long-read sequencing and explores its potential for point-of-care testing and health care in remote settings.
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Affiliation(s)
- Josephine B Oehler
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Townsville, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
| | - Helen Wright
- Nursing and Midwifery, College of Healthcare Sciences, James Cook University, Townsville, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Australian Genomics, Melbourne, Australia
| | - Andrew J Mallett
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Ulf Schmitz
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Townsville, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
- Computational BioMedicine Lab Centenary Institute, The University of Sydney, Camperdown, Australia.
- Faculty of Medicine & Health, The University of Sydney, Camperdown, Australia.
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5
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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6
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Chowdhury T, Cressiot B, Parisi C, Smolyakov G, Thiébot B, Trichet L, Fernandes FM, Pelta J, Manivet P. Circulating Tumor Cells in Cancer Diagnostics and Prognostics by Single-Molecule and Single-Cell Characterization. ACS Sens 2023; 8:406-426. [PMID: 36696289 DOI: 10.1021/acssensors.2c02308] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Circulating tumor cells (CTCs) represent an interesting source of biomarkers for diagnosis, prognosis, and the prediction of cancer recurrence, yet while they are extensively studied in oncobiology research, their diagnostic utility has not yet been demonstrated and validated. Their scarcity in human biological fluids impedes the identification of dangerous CTC subpopulations that may promote metastatic dissemination. In this Perspective, we discuss promising techniques that could be used for the identification of these metastatic cells. We first describe methods for isolating patient-derived CTCs and then the use of 3D biomimetic matrixes in their amplification and analysis, followed by methods for further CTC analyses at the single-cell and single-molecule levels. Finally, we discuss how the elucidation of mechanical and morphological properties using techniques such as atomic force microscopy and molecular biomarker identification using nanopore-based detection could be combined in the future to provide patients and their healthcare providers with a more accurate diagnosis.
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Affiliation(s)
- Tafsir Chowdhury
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France
| | | | - Cleo Parisi
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France.,Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Georges Smolyakov
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France
| | | | - Léa Trichet
- Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Francisco M Fernandes
- Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Juan Pelta
- CY Cergy Paris Université, CNRS, LAMBE, 95000 Cergy, France.,Université Paris-Saclay, Université d'Evry, CNRS, LAMBE, 91190 Evry, France
| | - Philippe Manivet
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France.,Université Paris Cité, Inserm, NeuroDiderot, F-75019 Paris, France
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7
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Chen P, Sun Z, Wang J, Liu X, Bai Y, Chen J, Liu A, Qiao F, Chen Y, Yuan C, Sha J, Zhang J, Xu LQ, Li J. Portable nanopore-sequencing technology: Trends in development and applications. Front Microbiol 2023; 14:1043967. [PMID: 36819021 PMCID: PMC9929578 DOI: 10.3389/fmicb.2023.1043967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.
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Affiliation(s)
- Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zepeng Sun
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Jiawei Wang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Xinlong Liu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Feng Qiao
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chenyan Yuan
- Clinical Laboratory, Southeast University Zhongda Hospital, Nanjing, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, China
| | - Jinghui Zhang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Li-Qun Xu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China,*Correspondence: Li-Qun Xu, ✉
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China,Jian Li, ✉
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8
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Enhancing Molecular Testing for Effective Delivery of Actionable Gene Diagnostics. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120745. [PMID: 36550951 PMCID: PMC9774983 DOI: 10.3390/bioengineering9120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
There is a deep need to navigate within our genomic data to find, understand and pave the way for disease-specific treatments, as the clinical diagnostic journey provides only limited guidance. The human genome is enclosed in every nucleated cell, and yet at the single-cell resolution many unanswered questions remain, as most of the sequencing techniques use a bulk approach. Therefore, heterogeneity, mosaicism and many complex structural variants remain partially uncovered. As a conceptual approach, nanopore-based sequencing holds the promise of being a single-molecule-based, long-read and high-resolution technique, with the ability of uncovering the nucleic acid sequence and methylation almost in real time. A key limiting factor of current clinical genetics is the deciphering of key disease-causing genomic sequences. As the technological revolution is expanding regarding genetic data, the interpretation of genotype-phenotype correlations should be made with fine caution, as more and more evidence points toward the presence of more than one pathogenic variant acting together as a result of intergenic interplay in the background of a certain phenotype observed in a patient. This is in conjunction with the observation that many inheritable disorders manifest in a phenotypic spectrum, even in an intra-familial way. In the present review, we summarized the relevant data on nanopore sequencing regarding clinical genomics as well as highlighted the importance and content of pre-test and post-test genetic counselling, yielding a complex approach to phenotype-driven molecular diagnosis. This should significantly lower the time-to-right diagnosis as well lower the time required to complete a currently incomplete genotype-phenotype axis, which will boost the chance of establishing a new actionable diagnosis followed by therapeutical approach.
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9
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Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer. Genes (Basel) 2022; 13:genes13091583. [PMID: 36140751 PMCID: PMC9498802 DOI: 10.3390/genes13091583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the success of clinical genomics, employing third-generation sequencing. Different variant calling techniques have been used and recommended by both Oxford Nanopore Technologies (ONT) and Nanopore communities. A thorough examination of the variant callers might give critical guidance for third-generation sequencing-based clinical genomics. In this study, two reference genome sample datasets (NA12878) and (NA24385) and the set of high-confidence variant calls provided by the Genome in a Bottle (GIAB) were used to allow the evaluation of the performance of six variant calling tools, including Human-SNP-wf, Clair3, Clair, NanoCaller, Longshot, and Medaka, as an integral step in the in-house variant detection workflow. Out of the six variant callers understudy, Clair3 and Human-SNP-wf that has Clair3 incorporated into it achieved the highest performance rates in comparison to the other variant callers. Evaluation of the results for the tool was expressed in terms of Precision, Recall, and F1-score using Hap.py tools for the comparison. In conclusion, our findings give important insights for identifying accurate variants from third-generation sequencing of personal genomes using different variant detection tools available for long-read sequencing.
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10
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Tanimoto IMF, Cressiot B, Greive SJ, Le Pioufle B, Bacri L, Pelta J. Focus on using nanopore technology for societal health, environmental, and energy challenges. NANO RESEARCH 2022; 15:9906-9920. [PMID: 35610982 PMCID: PMC9120803 DOI: 10.1007/s12274-022-4379-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
With an increasing global population that is rapidly ageing, our society faces challenges that impact health, environment, and energy demand. With this ageing comes an accumulation of cellular changes that lead to the development of diseases and susceptibility to infections. This impacts not only the health system, but also the global economy. As the population increases, so does the demand for energy and the emission of pollutants, leading to a progressive degradation of our environment. This in turn impacts health through reduced access to arable land, clean water, and breathable air. New monitoring approaches to assist in environmental control and minimize the impact on health are urgently needed, leading to the development of new sensor technologies that are highly sensitive, rapid, and low-cost. Nanopore sensing is a new technology that helps to meet this purpose, with the potential to provide rapid point-of-care medical diagnosis, real-time on-site pollutant monitoring systems to manage environmental health, as well as integrated sensors to increase the efficiency and storage capacity of renewable energy sources. In this review we discuss how the powerful approach of nanopore based single-molecule, or particle, electrical promises to overcome existing and emerging societal challenges, providing new opportunities and tools for personalized medicine, localized environmental monitoring, and improved energy production and storage systems.
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Affiliation(s)
- Izadora Mayumi Fujinami Tanimoto
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
- LuMIn, CNRS, Institut d’Alembert, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | | | | | - Bruno Le Pioufle
- LuMIn, CNRS, Institut d’Alembert, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Laurent Bacri
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
| | - Juan Pelta
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
- LAMBE, CNRS, CY Cergy Paris Université, 95000 Cergy, France
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11
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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12
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Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.
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13
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Hewat TI, Johnson MB, Flanagan SE. Congenital Hyperinsulinism: Current Laboratory-Based Approaches to the Genetic Diagnosis of a Heterogeneous Disease. Front Endocrinol (Lausanne) 2022; 13:873254. [PMID: 35872984 PMCID: PMC9302115 DOI: 10.3389/fendo.2022.873254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
Congenital hyperinsulinism is characterised by the inappropriate release of insulin during hypoglycaemia. This potentially life-threatening disorder can occur in isolation, or present as a feature of syndromic disease. Establishing the underlying aetiology of the hyperinsulinism is critical for guiding medical management of this condition especially in children with diazoxide-unresponsive hyperinsulinism where the underlying genetics determines whether focal or diffuse pancreatic disease is present. Disease-causing single nucleotide variants affecting over 30 genes are known to cause persistent hyperinsulinism with mutations in the KATP channel genes (ABCC8 and KCNJ11) most commonly identified in children with severe persistent disease. Defects in methylation, changes in chromosome number, and large deletions and duplications disrupting multiple genes are also well described in congenital hyperinsulinism, further highlighting the genetic heterogeneity of this condition. Next-generation sequencing has revolutionised the approach to genetic testing for congenital hyperinsulinism with targeted gene panels, exome, and genome sequencing being highly sensitive methods for the analysis of multiple disease genes in a single reaction. It should though be recognised that limitations remain with next-generation sequencing with no single application able to detect all reported forms of genetic variation. This is an important consideration for hyperinsulinism genetic testing as comprehensive screening may require multiple investigations.
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14
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Bartalucci N, Romagnoli S, Vannucchi AM. A blood drop through the pore: nanopore sequencing in hematology. Trends Genet 2021; 38:572-586. [PMID: 34906378 DOI: 10.1016/j.tig.2021.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
Abstract
The development of new sequencing platforms, technologies, and bioinformatics tools in the past decade fostered key discoveries in human genomics. Among the most recent sequencing technologies, nanopore sequencing (NS) has caught the interest of researchers for its intriguing potential and flexibility. This up-to-date review highlights the recent application of NS in the hematology field, focusing on progress and challenges of the technological approaches employed for the identification of pathologic alterations. The molecular and analytic pipelines developed for the analysis of the whole-genome, target regions, and transcriptomics provide a proof of evidence of the unparalleled amount of information that could be retrieved by an innovative approach based on long-read sequencing.
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Affiliation(s)
- Niccolò Bartalucci
- CRIMM, Center of Research and Innovation of Myeloproliferative Neoplasms, Careggi University Hospital and Department of Experimental and Clinical Medicine, University of Florence, DENOTHE Excellence Center, Florence, Italy
| | - Simone Romagnoli
- CRIMM, Center of Research and Innovation of Myeloproliferative Neoplasms, Careggi University Hospital and Department of Experimental and Clinical Medicine, University of Florence, DENOTHE Excellence Center, Florence, Italy
| | - Alessandro Maria Vannucchi
- CRIMM, Center of Research and Innovation of Myeloproliferative Neoplasms, Careggi University Hospital and Department of Experimental and Clinical Medicine, University of Florence, DENOTHE Excellence Center, Florence, Italy.
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15
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Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing. Sci Rep 2021; 11:22372. [PMID: 34785703 PMCID: PMC8595663 DOI: 10.1038/s41598-021-01749-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 01/31/2023] Open
Abstract
More than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.
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16
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Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 470] [Impact Index Per Article: 156.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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17
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Takashima T, Brisset S, Furukawa A, Taniguchi H, Takeyasu R, Kawamura A, Tamura Y. Case Report: BMPR2-Targeted MinION Sequencing as a Tool for Genetic Analysis in Patients With Pulmonary Arterial Hypertension. Front Cardiovasc Med 2021; 8:711694. [PMID: 34589526 PMCID: PMC8473694 DOI: 10.3389/fcvm.2021.711694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/11/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Mutations in the bone morphogenetic protein receptor type 2 gene (BMPR2) represent a major genetic cause of pulmonary arterial hypertension (PAH). Identification of BMPR2 mutations is crucial for the genetic diagnosis of PAH. MinION nanopore sequencer is a portable third-generation technology that enables long-read sequencing at a low-cost. This nanopore technology-based device has not been used previously for PAH diagnosis. This study aimed to determine the feasibility of using MinION nanopore sequencing for the genetic analysis of PAH patients, focused on BMPR2. Methods: We developed a protocol for the custom bioinformatics pipeline analysis of long reads generated by long-PCR. To evaluate the potential of using MinION sequencing in PAH, we analyzed five samples, including those of two idiopathic PAH patients and a family of three members with one affected patient. Sanger sequencing analysis was performed to validate the variants. Results: The median read length was around 3.4 kb and a good mean quality score of approximately 19 was obtained. The total number of reads generated was uniform among the cases and ranged from 2,268,263 to 3,126,719. The coverage was consistent across flow cells in which the average number of reads per base ranged from 80,375 to 135,603. We identified two polymorphic variants and three mutations in four out of five patients. Certain indel variant calling-related errors were observed, mostly outside coding sequences. Conclusion: We have shown the ability of this portable nanopore sequencer to detect BMPR2 mutations in patients with PAH. The MinION nanopore sequencer is a promising tool for screening BMPR2 mutations, especially in small laboratories and research groups.
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Affiliation(s)
- Tomoya Takashima
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Sophie Brisset
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan.,Faculty of Medicine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Service d'Histologie, Embryologie et Cytogénétique, Assistance Publique Hôpitaux de Paris (AP-HP), Hôpital Antoine Béclère, Clamart, France
| | - Asuka Furukawa
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Hirohisa Taniguchi
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan.,Department of Cardiology, International University of Health and Welfare School of Medicine, Narita, Japan
| | - Rika Takeyasu
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Akio Kawamura
- Department of Cardiology, International University of Health and Welfare School of Medicine, Narita, Japan
| | - Yuichi Tamura
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan.,Department of Cardiology, International University of Health and Welfare School of Medicine, Narita, Japan
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18
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Nanopore sequencing approach for immunoglobulin gene analysis in chronic lymphocytic leukemia. Sci Rep 2021; 11:17668. [PMID: 34480068 PMCID: PMC8417258 DOI: 10.1038/s41598-021-97198-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022] Open
Abstract
The evaluation of the somatic hypermutation of the clonotypic immunoglobulin heavy variable gene has become essential in the therapeutic management in chronic lymphocytic leukemia patients. European Research Initiative on Chronic Lymphocytic Leukemia promotes good practices and standardized approaches to this assay but often they are labor-intensive, technically complex, with limited in scalability. The use of next-generation sequencing in this analysis has been widely tested, showing comparable accuracy and distinct advantages. However, the adoption of the next generation sequencing requires a high sample number (run batching) to be economically convenient, which could lead to a longer turnaround time. Here we present data from nanopore sequencing for the somatic hypermutation evaluation compared to the standard method. Our results show that nanopore sequencing is suitable for immunoglobulin heavy variable gene mutational analysis in terms of sensitivity, accuracy, simplicity of analysis and is less time-consuming. Moreover, our work showed that the development of an appropriate data analysis pipeline could lower the nanopore sequencing error rate attitude.
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19
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Rodriguez PD, Mariani M, Gay J, Hogan TC, Amiel E, Deming PB, Frietze S. A guided-inquiry investigation of genetic variants using Oxford nanopore sequencing for an undergraduate molecular biology laboratory course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:588-597. [PMID: 33939256 PMCID: PMC8356555 DOI: 10.1002/bmb.21514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/24/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Next Generation Sequencing (NGS) has become an important tool in the biological sciences and has a growing number of applications across medical fields. Currently, few undergraduate programs provide training in the design and implementation of NGS applications. Here, we describe an inquiry-based laboratory exercise for a college-level molecular biology laboratory course that uses real-time MinION deep sequencing and bioinformatics to investigate characteristic genetic variants found in cancer cell-lines. The overall goal for students was to identify non-small cell lung cancer (NSCLC) cell-lines based on their unique genomic profiles. The units described in this laboratory highlight core principles in multiplex PCR primer design, real-time deep sequencing, and bioinformatics analysis for genetic variants. We found that the MinION device is an appropriate, feasible tool that provides a comprehensive, hands-on NGS experience for undergraduates. Student evaluations demonstrated increased confidence in using molecular techniques and enhanced understanding of NGS concepts. Overall, this exercise provides a pedagogical tool for incorporating NGS approaches in the teaching laboratory as way of enhancing students' comprehension of genomic sequence analysis. Further, this NGS lab module can easily be added to a variety of lab-based courses to help undergraduate students learn current DNA sequencing methods with limited effort and cost.
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Affiliation(s)
- Princess D. Rodriguez
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
- Cellular Molecular Biomedical Sciences ProgramUniversity of VermontBurlingtonVermontUSA
| | - Michael Mariani
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
- Cellular Molecular Biomedical Sciences ProgramUniversity of VermontBurlingtonVermontUSA
| | - Jamie Gay
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Tyler C. Hogan
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Eyal Amiel
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
- Cellular Molecular Biomedical Sciences ProgramUniversity of VermontBurlingtonVermontUSA
| | - Paula B. Deming
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
- Cellular Molecular Biomedical Sciences ProgramUniversity of VermontBurlingtonVermontUSA
- The University of Vermont Cancer CenterBurlingtonVermontUSA
| | - Seth Frietze
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
- Cellular Molecular Biomedical Sciences ProgramUniversity of VermontBurlingtonVermontUSA
- The University of Vermont Cancer CenterBurlingtonVermontUSA
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20
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Stefaniuk P, Onyszczuk J, Szymczyk A, Podhorecka M. Therapeutic Options for Patients with TP53 Deficient Chronic Lymphocytic Leukemia: Narrative Review. Cancer Manag Res 2021; 13:1459-1476. [PMID: 33603488 PMCID: PMC7886107 DOI: 10.2147/cmar.s283903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/20/2020] [Indexed: 01/03/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL), which is the most common type of leukemia in western countries in adults, is characterized by heterogeneity in clinical course, prognosis and response to the treatment. Although, in recent years a number of factors with probable prognostic value in CLL have been identified (eg NOTCH1, SF3B1 and BIRC-3 mutations, or evaluation of microRNA expression), TP53 aberrations are still the most important single factors of poor prognosis. It was found that approximately 30% of all TP53 defects are mutations lacking 17p13 deletion, whereas sole 17p13 deletion with the absence of TP53 mutation consists of 10% of all TP53 defects. The detection of del(17)(p13) and/or TP53 mutation is not a criterion itself for starting antileukemic therapy, but it is associated with an aggressive course of the disease and poor response to the standard chemoimmunotherapy. Treatment of patients with CLL harbouring TP53-deficiency requires drugs that promote cell death independently of TP53. Novel and smarter therapies revolutionize the treatment of del(17p) and/or aberrant TP53 CLL, but development of alternative therapeutic approaches still remains an issue of critical importance.
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Affiliation(s)
- Paulina Stefaniuk
- Department of Haematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Julia Onyszczuk
- Students Scientific Association, Department of Haematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Agnieszka Szymczyk
- Department of Clinical Transplantology, Medical University of Lublin, Lublin, Poland
| | - Monika Podhorecka
- Department of Haematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
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21
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Cumbo C, Orsini P, Anelli L, Zagaria A, Minervini CF, Coccaro N, Tota G, Impera L, Parciante E, Conserva MR, Redavid I, Carluccio P, Tarantini F, Specchia G, Musto P, Albano F. Nanopore sequencing sheds a light on the FLT3 gene mutations complexity in acute promyelocytic leukemia. Leuk Lymphoma 2020; 62:1219-1225. [PMID: 33289421 DOI: 10.1080/10428194.2020.1856838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Acute promyelocytic leukemia (APL) patients carry in 27% of cases an activating mutation of the fms-like tyrosine kinase-3 (FLT3) gene: internal tandem duplication (ITD) or tyrosine kinase domain (TKD) point mutation. The simultaneous presence of both types of mutations, so-called FLT3 dual mutations, has been reported in 2% of APL, but this circumstance has never been studied. We studied a cohort of 74 APL cases, performing an in-depth analysis of three FLT3 dual mutant cases. Nanopore sequencing (NS) allowed us to characterize their complex mutational profile, showing the occurrence of multiple activating FLT3 mutations on different alleles in the leukemic promyelocytes and suggesting a cumulative impact of these events on the constitutive activation of the FLT3 pathway in APL cells. NS approach not only sheds light on the FLT3 mutational complexity in APL, but may also be useful to better clarify the FLT3 mutations landscape in acute myeloid leukemia.
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Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Paola Orsini
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Crescenzio Francesco Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Maria Rosa Conserva
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Immacolata Redavid
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Paola Carluccio
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Francesco Tarantini
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | | | - Pellegrino Musto
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit, University of Bari 'Aldo Moro', Bari, Italy
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22
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Chan WS, Au CH, Chung Y, Leung HCM, Ho DN, Wong EYL, Lam TW, Chan TL, Ma ESK, Tang BSF. Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis. BMC Res Notes 2020; 13:444. [PMID: 32948225 PMCID: PMC7501614 DOI: 10.1186/s13104-020-05287-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 09/11/2020] [Indexed: 01/30/2023] Open
Abstract
Objective We designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden. Results At least 8 loci were successfully amplified from the majority for predicting first- and second-line drug resistance (14/23, 60.87%), and the 12 specimens yielding all 10 targets were sequenced with Nanopore MinION and Illumina MiSeq. MinION sequencing data was corrected by Nanopolish and recurrent variants were filtered. A total of 67,082 bases across all consensus sequences were analyzed, with 67,019 bases called by both MinION and MiSeq as wildtype. For the 41 single nucleotide variants (SNVs) called by MiSeq with 100% variant allelic frequency (VAF), 39 (95.1%) were called by MinION. For the 22 mixed bases called by MiSeq, a SNV with the highest VAF (70%) was called by MinION. With short assay time, reasonable reagent cost as well as continuously improving sequencing chemistry and signal correction pipelines, this Nanopore method can be a viable option for direct tuberculosis drug resistance profiling in the near future.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Yvonne Chung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Henry Chi Ming Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.,L3 Bioinformatics Limited, Hong Kong, China
| | - Dona N Ho
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Tak Wah Lam
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.,L3 Bioinformatics Limited, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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23
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Epitranscriptomics in Normal and Malignant Hematopoiesis. Int J Mol Sci 2020; 21:ijms21186578. [PMID: 32916783 PMCID: PMC7555315 DOI: 10.3390/ijms21186578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Epitranscriptomics analyze the biochemical modifications borne by RNA and their downstream influence. From this point of view, epitranscriptomics represent a new layer for the control of genetic information and can affect a variety of molecular processes including the cell cycle and the differentiation. In physiological conditions, hematopoiesis is a tightly regulated process that produces differentiated blood cells starting from hematopoietic stem cells. Alteration of this process can occur at different levels in the pathway that leads from the genetic information to the phenotypic manifestation producing malignant hematopoiesis. This review focuses on the role of epitranscriptomic events that are known to be implicated in normal and malignant hematopoiesis, opening a new pathophysiological and therapeutic scenario. Moreover, an evolutionary vision of this mechanism will be provided.
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24
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Hobeika C, Rached G, Chebly A, Chouery E, Kourie HR. Whole-exome and whole-genome sequencing in chronic lymphocytic leukemia: new biomarkers to target. Pharmacogenomics 2020; 21:957-962. [PMID: 32799640 DOI: 10.2217/pgs-2020-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Many biomarkers indicate prognosis in chronic lymphocytic leukemia; such as fluorescence in situ hybridization testing: 17p or 11q deletions have a worse prognosis than trisomy 12, 13q deletion or normal result, or the mutational status of the immunoglobulin heavy chain (IGHV): unmutated IGHV have a worse prognosis than mutated IGHV. Recently, many gene mutations (TP53, NOTCH1 etc.,) have been linked to a worse prognosis. With the new era of high-throughput sequencing, it has become easier to study gene mutations and their implication in predicting prognosis. In this review, we aim to review all the studies that performed whole-exome sequencing or whole-genome sequencing on chronic lymphocytic leukemia cells and explore the implication of various genes in disease prognosis.
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Affiliation(s)
- Charbel Hobeika
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Gaelle Rached
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Alain Chebly
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Eliane Chouery
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Hampig Raphael Kourie
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon.,Department of Hematology-Oncology, Hotel Dieu de France University Hospital, Faculty of Medicine, Saint Joseph University, Beirut, BP-17 5208, Lebanon
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25
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Slusher AL, Kim JJJ, Ludlow AT. The Role of Alternative RNA Splicing in the Regulation of hTERT, Telomerase, and Telomeres: Implications for Cancer Therapeutics. Cancers (Basel) 2020; 12:E1514. [PMID: 32531916 PMCID: PMC7352778 DOI: 10.3390/cancers12061514] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative RNA splicing impacts the majority (>90%) of eukaryotic multi-exon genes, expanding the coding capacity and regulating the abundance of gene isoforms. Telomerase (hTERT) is a key example of a gene that is alternatively spliced during human fetal development and becomes dysregulated in nearly all cancers. Approximately 90% of human tumors use telomerase to synthesize de novo telomere repeats and obtain telomere-dependent cellular immortality. Paradigm shifting data indicates that hTERT alternative splicing, in addition to transcription, plays an important role in the regulation of active telomerase in cells. Our group and others are pursuing the basic science studies to progress this emerging area of telomerase biology. Recent evidence demonstrates that switching splicing of hTERT from the telomerase activity producing full-length hTERT isoform to alternatively spliced, non-coding isoforms may be a novel telomerase inhibition strategy to prevent cancer growth and survival. Thus, the goals of this review are to detail the general roles of telomerase in cancer development, explore the emerging regulatory mechanisms of alternative RNA splicing of the hTERT gene in various somatic and cancer cell types, define the known and potential roles of hTERT splice isoforms in cancer cell biology, and provide insight into new treatment strategies targeting hTERT in telomerase-positive cancers.
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Affiliation(s)
| | | | - Andrew T. Ludlow
- School of Kinesiology, University of Michigan, Ann Arbor, MI 48109, USA; (A.L.S.); (J.J.K.)
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Minervini A, Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. HMGA Proteins in Hematological Malignancies. Cancers (Basel) 2020; 12:E1456. [PMID: 32503270 PMCID: PMC7353061 DOI: 10.3390/cancers12061456] [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: 04/22/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023] Open
Abstract
The high mobility group AT-Hook (HMGA) proteins are a family of nonhistone chromatin remodeling proteins known as "architectural transcriptional factors". By binding the minor groove of AT-rich DNA sequences, they interact with the transcription apparatus, altering the chromatin modeling and regulating gene expression by either enhancing or suppressing the binding of the more usual transcriptional activators and repressors, although they do not themselves have any transcriptional activity. Their involvement in both benign and malignant neoplasias is well-known and supported by a large volume of studies. In this review, we focus on the role of the HMGA proteins in hematological malignancies, exploring the mechanisms through which they enhance neoplastic transformation and how this knowledge could be exploited to devise tailored therapeutic strategies.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy; (A.M.); (N.C.); (L.A.); (A.Z.); (G.S.)
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Cumbo C, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. TP53 in Myelodysplastic Syndromes: Recent Biological and Clinical Findings. Int J Mol Sci 2020; 21:E3432. [PMID: 32414002 PMCID: PMC7279310 DOI: 10.3390/ijms21103432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
TP53 dysregulation plays a pivotal role in the molecular pathogenesis of myelodysplastic syndromes (MDS), identifying a subgroup of patients with peculiar features. In this review we report the recent biological and clinical findings of TP53-mutated MDS, focusing on the molecular pathways activation and on its impact on the cellular physiology. In MDS, TP53 mutational status is deeply associated with del(5q) syndrome and its dysregulation impacts on cell cycle, DNA repair and apoptosis inducing chromosomal instability and the clonal evolution of disease. TP53 defects influence adversely the MDS clinical outcome and the treatment response rate, thus new therapeutic approaches are being developed for these patients. TP53 allelic state characterization and the mutational burden evaluation can therefore predict prognosis and identify the subgroup of patients eligible for targeted therapy. For these reasons, in the era of precision medicine, the MDS diagnostic workup cannot do without the complete assessment of TP53 mutational profile.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy; (C.C.); (G.T.); (L.A.); (A.Z.); (G.S.)
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Cumbo C, Anelli L, Specchia G, Albano F. Monitoring of Minimal Residual Disease (MRD) in Chronic Myeloid Leukemia: Recent Advances. Cancer Manag Res 2020; 12:3175-3189. [PMID: 32440215 PMCID: PMC7211966 DOI: 10.2147/cmar.s232752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm caused by the BCR-ABL1 fusion gene generation as a consequence of the t(9;22)(q34;q11) rearrangement. The identification of the BCR-ABL1 transcript was of critical importance for both CML diagnosis and minimal residual disease (MRD) monitoring. In this review, we report the recent advances in the CML MRD monitoring based on RNA, DNA and protein analysis. The detection of the BCR-ABL1 transcript by the quantitative reverse-transcriptase polymerase chain reaction is the gold standard method, but other systems based on digital PCR or on GeneXpert technology have been developed. In the last years, DNA-based assays showed high sensitivity and specificity, and flow cytometric approaches for the detection of the BCR-ABL1 fusion protein have also been tested. Recently, new MRD monitoring systems based on the detection of molecular markers other than the BCR-ABL1 fusion were proposed. These approaches, such as the identification of CD26+ leukemic stem cells, microRNAs and mitochondrial DNA mutations, just remain preliminary and need to be implemented. In the precision medicine era, the constant improvement of the CML MRD monitoring practice could allow clinicians to choose the best therapeutic algorithm and a more accurate selection of CML patients eligible for the tyrosine kinase inhibitors discontinuation.
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Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
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Wei S, Levy B, Hoffman N, Cujar C, Rodney-Sandy R, Wapner R, D'Alton M, Williams Z. A rapid and simple bead-bashing-based method for genomic DNA extraction from mammalian tissue. Biotechniques 2020; 68:240-244. [PMID: 32054310 PMCID: PMC7252492 DOI: 10.2144/btn-2019-0172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022] Open
Abstract
Conventional genomic DNA (gDNA) extraction methods can take hours to complete, may require fume hoods and represent the most time-consuming step in many gDNA-based molecular assays. We systematically optimized a bead bashing-based (BBB) approach for rapid gDNA extraction without the need for a fume hood. Human tissue specimens (n = 34) subjected to the 12-min BBB method yielded 0.40 ± 0.17 (mean ± SD) μg of gDNA per milligram of tissue, sufficient for many downstream applications, and 3- and 6-min extensions resulted in an additional 0.43 ± 0.23 μg and 0.48 ± 0.43 μg per milligram of tissue, respectively. The BBB method provides a simple and rapid method for gDNA extraction from mammalian tissue that is applicable to time-sensitive clinical applications.
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Affiliation(s)
- Shan Wei
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Clinical Cytogenetics Laboratory, Columbia University Medical Center & the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Nataly Hoffman
- Clinical Cytogenetics Laboratory, Columbia University Medical Center & the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Claudia Cujar
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Reunet Rodney-Sandy
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ronald Wapner
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Mary D'Alton
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zev Williams
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
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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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31
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Abstract
The current therapies against cancer showed limited success. Nanotechnology is a promising strategy for cancer tracking, diagnosis, and therapy. The hybrid nanotechnology assembled several materials in a multimodal system to develop multifunctional approaches to cancer treatment. The quantum dot and polymer are some of these hybrid nanoparticle platforms. The quantum dot hybrid system possesses photonic and magnetic properties, allowing photothermal therapy and live multimodal imaging of cancer. These quantum dots were used to convey medicines to cancer cells. Hybrid polymer nanoparticles were utilized for the systemic delivery of small interfering RNA to malignant tumors and metastasis. They allowed non-invasive imaging to track in real-time the biodistribution of small interfering RNA in the whole body. They offer an opportunity to treat cancers by specifically silencing target genes. This review highlights the major nanotechnology approaches to effectively treat cancer and metastasis.
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32
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Minervini CF, Cumbo C, Orsini P, Anelli L, Zagaria A, Specchia G, Albano F. Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities. Front Genet 2020; 11:76. [PMID: 32140171 PMCID: PMC7043087 DOI: 10.3389/fgene.2020.00076] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/23/2020] [Indexed: 12/20/2022] Open
Abstract
The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disorders becoming ever more widespread in clinical practice. In 2012 Oxford Nanopore Technologies (ONT) released the MinION, the first long-read nanopore-based sequencer, overcoming the main limits of short-reads sequences generation. In the last years, several nanopore sequencing approaches have been performed in various "-omic" sciences; this review focuses on the challenge to introduce ONT devices in the hematological field, showing advantages, disadvantages and future perspectives of this technology in the precision medicine era.
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Affiliation(s)
| | | | | | | | | | | | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari, Italy
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33
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Blakemore SJ, Clifford R, Parker H, Antoniou P, Stec-Dziedzic E, Larrayoz M, Davis Z, Kadalyayil L, Colins A, Robbe P, Vavoulis D, Forster J, Carr L, Morilla R, Else M, Bryant D, McCarthy H, Walewska RJ, Steele AJ, Chan J, Speight G, Stankovic T, Cragg MS, Catovsky D, Oscier DG, Rose-Zerilli MJJ, Schuh A, Strefford JC. Clinical significance of TP53, BIRC3, ATM and MAPK-ERK genes in chronic lymphocytic leukaemia: data from the randomised UK LRF CLL4 trial. Leukemia 2020; 34:1760-1774. [PMID: 32015491 PMCID: PMC7326706 DOI: 10.1038/s41375-020-0723-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/06/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022]
Abstract
Despite advances in chronic lymphocytic leukaemia (CLL) treatment, globally chemotherapy remains a central treatment modality, with chemotherapy trials representing an invaluable resource to explore disease-related/genetic features contributing to long-term outcomes. In 499 LRF CLL4 cases, a trial with >12 years follow-up, we employed targeted resequencing of 22 genes, identifying 623 mutations. After background mutation rate correction, 11/22 genes were recurrently mutated at frequencies between 3.6% (NFKBIE) and 24% (SF3B1). Mutations beyond Sanger resolution (<12% VAF) were observed in all genes, with KRAS mutations principally composed of these low VAF variants. Firstly, employing orthogonal approaches to confirm <12% VAF TP53 mutations, we assessed the clinical impact of TP53 clonal architecture. Whilst ≥ 12% VAF TP53mut cases were associated with reduced PFS and OS, we could not demonstrate a difference between <12% VAF TP53 mutations and either wild type or ≥12% VAF TP53mut cases. Secondly, we identified biallelic BIRC3 lesions (mutation and deletion) as an independent marker of inferior PFS and OS. Finally, we observed that mutated MAPK-ERK genes were independent markers of poor OS in multivariate survival analysis. In conclusion, our study supports using targeted resequencing of expanded gene panels to elucidate the prognostic impact of gene mutations.
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Affiliation(s)
- Stuart J Blakemore
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Department I of Internal Medicine, Centre of Excellence in Aging Research, University of Cologne, Cologne, Germany
| | - Ruth Clifford
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Helen Parker
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Pavlos Antoniou
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Ewa Stec-Dziedzic
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Marta Larrayoz
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zadie Davis
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Latha Kadalyayil
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Colins
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Pauline Robbe
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Dimitris Vavoulis
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Jade Forster
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Louise Carr
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ricardo Morilla
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Monica Else
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Dean Bryant
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Helen McCarthy
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Renata J Walewska
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Andrew J Steele
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jacqueline Chan
- Oxford Gene Technology, Begbroke Science Park, Begbroke, Oxfordshire, UK
| | - Graham Speight
- Oxford Gene Technology, Begbroke Science Park, Begbroke, Oxfordshire, UK
| | - Tanja Stankovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Services, IBR West, University of Birmingham, Birmingham, UK
| | - Mark S Cragg
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Antibody & Vaccine Group, Centre for Cancer Immunology, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - David G Oscier
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Matthew J J Rose-Zerilli
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Anna Schuh
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Jonathan C Strefford
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
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Sakamoto Y, Sereewattanawoot S, Suzuki A. A new era of long-read sequencing for cancer genomics. J Hum Genet 2020; 65:3-10. [PMID: 31474751 PMCID: PMC6892365 DOI: 10.1038/s10038-019-0658-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 02/08/2023]
Abstract
Cancer is a disease largely caused by genomic aberrations. Utilizing many rapidly emerging sequencing technologies, researchers have studied cancer genomes to understand the molecular statuses of cancer cells and to reveal their vulnerabilities, such as driver mutations or gene expression. Long-read technologies enable us to identify and characterize novel types of cancerous mutations, including complicated structural variants in haplotype resolution. In this review, we introduce three representative platforms for long-read sequencing and research trends of cancer genomics with long-read data. Further, we describe that aberrant transcriptome and epigenome statuses, namely, fusion transcripts, as well as aberrant transcript isoforms and the phase information of DNA methylation, are able to be elucidated by long-read sequencers. Long-read sequencing may shed light on novel types of aberrations in cancer genomics that are being missed by conventional short-read sequencing analyses.
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Affiliation(s)
- Yoshitaka Sakamoto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Sarun Sereewattanawoot
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
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35
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Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia. Genes (Basel) 2019; 10:genes10121026. [PMID: 31835432 PMCID: PMC6947272 DOI: 10.3390/genes10121026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but these methods remain expensive and time consuming. In this context, we present a nanopore-based assay for rapid (24 h) sequencing of six genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2) that are recurrently mutated in AML. The study included 22 AML patients at diagnosis; all data were compared with the results of S5 sequencing, and discordant variants were validated by Sanger sequencing. Nanopore approach showed substantial advantages in terms of speed and low cost. Furthermore, the ability to generate long reads allows a more accurate detection of longer FLT3 internal tandem duplications and phasing double CEBPA mutations. In conclusion, we propose a cheap, rapid workflow that can potentially enable all basic molecular biology laboratories to perform detailed targeted gene sequencing analysis in AML patients, in order to define their prognosis and the appropriate treatment.
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Magi A, Semeraro R, Mingrino A, Giusti B, D'Aurizio R. Nanopore sequencing data analysis: state of the art, applications and challenges. Brief Bioinform 2019. [PMID: 28637243 DOI: 10.1093/bib/bbx062] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data. Despite the short period of time from the release of the MinION, a large number of algorithms and tools have been developed for base calling, data handling, read mapping, de novo assembly and variant discovery. Here, we face the main computational challenges related to the analysis of nanopore data, and we carry out a comprehensive and up-to-date survey of the algorithmic solutions adopted by the bioinformatic community comparing performance and reporting limits and advantages of using this new generation of sequences for genomic analyses. Our analyses demonstrate that the use of nanopore data dramatically improves the de novo assembly of genomes and allows for the exploration of structural variants with an unprecedented accuracy and resolution. However, despite the impressive improvements reached by ONT in the past 2 years, the use of these data for small-variant calling is still challenging, and at present, it needs to be coupled with complementary short sequences for mitigating the intrinsic biases of nanopore sequencing technology.
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Affiliation(s)
- Alberto Magi
- Department of Statistics, National Cheng Kung University in Taiwan
| | - Roberto Semeraro
- Department of Molecular Physiology and Biophysics, Vanderbilt University, USA
| | | | - Betti Giusti
- Department of Biostatistics, Vanderbilt University, USA
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37
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Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. Next-Generation Sequencing in Acute Lymphoblastic Leukemia. Int J Mol Sci 2019; 20:ijms20122929. [PMID: 31208040 PMCID: PMC6627957 DOI: 10.3390/ijms20122929] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.
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Affiliation(s)
- Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
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38
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Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, Parkes D, Freeman C, Dhalla F, Patel SY, Popitsch N, Ip CLC, Roberts HE, Salatino S, Lockstone H, Lunter G, Taylor JC, Buck D, Simpson MA, Donnelly P. Sequencing of human genomes with nanopore technology. Nat Commun 2019; 10:1869. [PMID: 31015479 PMCID: PMC6478738 DOI: 10.1038/s41467-019-09637-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/19/2019] [Indexed: 12/17/2022] Open
Abstract
Whole-genome sequencing (WGS) is becoming widely used in clinical medicine in diagnostic contexts and to inform treatment choice. Here we evaluate the potential of the Oxford Nanopore Technologies (ONT) MinION long-read sequencer for routine WGS by sequencing the reference sample NA12878 and the genome of an individual with ataxia-pancytopenia syndrome and severe immune dysregulation. We develop and apply a novel reference panel-free analytical method to infer and then exploit phase information which improves single-nucleotide variant (SNV) calling performance from otherwise modest levels. In the clinical sample, we identify and directly phase two non-synonymous de novo variants in SAMD9L, (OMIM #159550) inferring that they lie on the same paternal haplotype. Whilst consensus SNV-calling error rates from ONT data remain substantially higher than those from short-read methods, we demonstrate the substantial benefits of analytical innovation. Ongoing improvements to base-calling and SNV-calling methodology must continue for nanopore sequencing to establish itself as a primary method for clinical WGS.
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Affiliation(s)
- Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Robert W Davies
- Genomics plc, Oxford, OX1 1JD, UK
- Program in Genetics and Genomic Biology and The Centre for Applied Genomics, Hospital for Sick Children, Toronto, M5G 0A4, Canada
| | | | - Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | | | - Laura E Oikkonen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Duncan Parkes
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Colin Freeman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Fatima Dhalla
- Department of Clinical Immunology, Oxford University Hospitals, Oxford, OX3 9DU, UK
- Developmental Immunology Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Smita Y Patel
- Department of Clinical Immunology, Oxford University Hospitals, Oxford, OX3 9DU, UK
- Clinical Immunology Group, National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Niko Popitsch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Camilla L C Ip
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hannah E Roberts
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Silvia Salatino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Helen Lockstone
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Gerton Lunter
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Genomics plc, Oxford, OX1 1JD, UK
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - David Buck
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | | | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Genomics plc, Oxford, OX1 1JD, UK.
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK.
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Leija‐Salazar M, Sedlazeck FJ, Toffoli M, Mullin S, Mokretar K, Athanasopoulou M, Donald A, Sharma R, Hughes D, Schapira AH, Proukakis C. Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION. Mol Genet Genomic Med 2019; 7:e564. [PMID: 30637984 PMCID: PMC6418358 DOI: 10.1002/mgg3.564] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/23/2018] [Accepted: 12/13/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Mutations in GBA cause Gaucher disease when biallelic and are strong risk factors for Parkinson's disease when heterozygous. GBA analysis is complicated by the nearby pseudogene. We aimed to design and validate a method for sequencing GBA using long reads. METHODS We sequenced GBA on the Oxford Nanopore MinION as an 8.9 kb amplicon from 102 individuals, including patients with Parkinson's and Gaucher diseases. We used NanoOK for quality metrics, NGMLR to align data (after comparing with GraphMap), Nanopolish and Sniffles to call variants, and WhatsHap for phasing. RESULTS We detected all known missense mutations in these samples, including the common p.N409S (N370S) and p.L483P (L444P) in multiple samples, and nine rarer ones, as well as a splicing and a truncating mutation, and intronic SNPs. We demonstrated the ability to phase mutations, confirm compound heterozygosity, and assign haplotypes. We also detected two known risk variants in some Parkinson's patients. Rare false positives were easily identified and filtered, with the Nanopolish quality score adjusted for the number of reads a very robust discriminator. In two individuals carrying a recombinant allele, we were able to detect and fully define it in one carrier, where it included a 55-base pair deletion, but not in another one, suggesting a limitation of the PCR enrichment method. Missense mutations were detected at the correct zygosity, except for the case where the RecNciI one was missed. CONCLUSION The Oxford Nanopore MinION can detect missense mutations and an exonic deletion in this difficult gene, with the added advantages of phasing and intronic analysis. It can be used as an efficient research tool, but additional work is required to exclude all recombinants.
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Affiliation(s)
- Melissa Leija‐Salazar
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | | | - Marco Toffoli
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | - Stephen Mullin
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
- Institute of Translational and Stratified MedicinePlymouth University Peninsula School of MedicinePlymouthUK
| | - Katya Mokretar
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | - Maria Athanasopoulou
- Department of Molecular Neuroscience, Institute of NeurologyUniversity College LondonLondonUK
| | - Aimee Donald
- Department of PaediatricsRoyal Manchester Children’s HospitalManchesterUK
| | - Reena Sharma
- The Mark Holland Metabolic Unit, Salford Royal Foundation NHS TrustSalfordUK
| | - Derralynn Hughes
- Institute of Immunity and TransplantationLysosomal Storage Disorders Unit, Royal Free HospitalLondonUK
| | - Anthony H.V. Schapira
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
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40
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Zascavage RR, Thorson K, Planz JV. Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing. Electrophoresis 2019; 40:272-280. [PMID: 30511783 PMCID: PMC6590251 DOI: 10.1002/elps.201800083] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 10/25/2018] [Accepted: 11/03/2018] [Indexed: 12/31/2022]
Abstract
Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps. A comparison is made between libraries sequenced directly from native DNA and the same samples sequenced from libraries generated with nine overlapping mtDNA amplicons on the Oxford Nanopore MinION™ device. The native and amplicon library preparation methods and alternative base calling strategies were assessed to establish error rates and identify trends of discordance between the two library preparation approaches. For the complete mtGenome, 16 569 nucleotides, an overall error rate of approximately 1.00% was observed. As expected with mtDNA, the majority of error was detected in homopolymeric regions. The use of a modified basecaller that corrects for ambiguous signal in homopolymeric stretches reduced the error rate for both library preparation methods to approximately 0.30%. Our study indicates that direct mtDNA sequencing from native DNA on the MinION™ device provides comparable results to those obtained from common mtDNA sequencing methods and is a reliable alternative to approaches using PCR-enriched libraries.
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Affiliation(s)
- Roxanne R. Zascavage
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
- Department of Criminology and Criminal JusticeUniversity of Texas at ArlingtonArlingtonTXUSA
| | - Kelcie Thorson
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
- Zoetis Inc.ParsippanyNJUSA
| | - John V. Planz
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
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41
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Campo E, Cymbalista F, Ghia P, Jäger U, Pospisilova S, Rosenquist R, Schuh A, Stilgenbauer S. TP53 aberrations in chronic lymphocytic leukemia: an overview of the clinical implications of improved diagnostics. Haematologica 2018; 103:1956-1968. [PMID: 30442727 PMCID: PMC6269313 DOI: 10.3324/haematol.2018.187583] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/26/2018] [Indexed: 12/19/2022] Open
Abstract
Chronic lymphocytic leukemia is associated with a highly heterogeneous disease course in terms of clinical outcomes and responses to chemoimmunotherapy. This heterogeneity is partly due to genetic aberrations identified in chronic lymphocytic leukemia cells such as mutations of TP53 and/or deletions in chromosome 17p [del(17p)], resulting in loss of one TP53 allele. These aberrations are associated with markedly decreased survival and predict impaired response to chemoimmunotherapy thus being among the strongest predictive markers guiding treatment decisions in chronic lymphocytic leukemia. Clinical trials demonstrate the importance of accurately testing for TP53 aberrations [both del(17p) and TP53 mutations] before each line of treatment to allow for appropriate treatment decisions that can optimize patients' outcomes. The current report reviews the diagnostic methods to detect TP53 disruption better, the role of TP53 aberrations in treatment decisions and current therapies available for patients with chronic lymphocytic leukemia carrying these abnormalities. The standardization in sequencing technologies for accurate identification of TP53 mutations and the importance of continued evaluation of TP53 aberrations throughout initial and subsequent lines of therapy remain unmet clinical needs as new therapeutic alternatives become available.
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Affiliation(s)
- Elias Campo
- Hospital Clinic of Barcelona, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, and CIBERONC, Spain
| | - Florence Cymbalista
- Hôpital Avicenne, AP-HP, UMR INSERMU978/Paris 13 University, Bobigny, France
| | - Paolo Ghia
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Stephan Stilgenbauer
- Internal Medicine III, Ulm University, Germany and Innere Medizin I, Universitätsklinikum des Saarlandes, Homburg, Germany
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42
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Suzuki A, Suzuki M, Mizushima-Sugano J, Frith MC, Makalowski W, Kohno T, Sugano S, Tsuchihara K, Suzuki Y. Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer. DNA Res 2018; 24:585-596. [PMID: 29117310 PMCID: PMC5726485 DOI: 10.1093/dnares/dsx027] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/29/2017] [Indexed: 01/18/2023] Open
Abstract
Here, we employed cDNA amplicon sequencing using a long-read portable sequencer, MinION, to characterize various types of mutations in cancer-related genes, namely, EGFR, KRAS, NRAS and NF1. For homozygous SNVs, the precision and recall rates were 87.5% and 91.3%, respectively. For previously reported hotspot mutations, the precision and recall rates reached 100%. The precise junctions of EML4-ALK, CCDC6-RET and five other gene fusions were also detected. Taking advantages of long-read sequencing, we conducted phasing of EGFR mutations and elucidated the mutational allelic backgrounds of anti-tumor drug-sensitive and resistant mutations, which could provide useful information for selecting therapeutic approaches. In the H1975 cells, 72% of the reads harbored both L858R and T790M mutations, and 22% of the reads harbored neither mutation. To ensure that the clinical requirements can be met in potentially low cancer cell populations, we further conducted a serial dilution analysis of the template for EGFR mutations. Several percent of the mutant alleles could be detected depending on the yield and quality of the sequencing data. Finally, we characterized the mutation genotypes in eight clinical samples. This method could be a convenient long-read sequencing-based analytical approach and thus may change the current approaches used for cancer genome sequencing.
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Affiliation(s)
- Ayako Suzuki
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Mizuto Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Junko Mizushima-Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Department of Chemistry and Life Science, Kogakuin University, Nishi-Shinjuku, Shinjuku-Ku, Tokyo, Japan
| | - Martin C Frith
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Computational Biology Research Center, The National Institute for Advanced Industrial Science and Technology, Aomi, Koto-Ku, Tokyo, Japan
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Munster, Germany
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tsukiji, Chuo-Ku, Tokyo, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Katsuya Tsuchihara
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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43
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Patel A, Belykh E, Miller EJ, George LL, Martirosyan NL, Byvaltsev VA, Preul MC. MinION rapid sequencing: Review of potential applications in neurosurgery. Surg Neurol Int 2018; 9:157. [PMID: 30159201 PMCID: PMC6094492 DOI: 10.4103/sni.sni_55_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/22/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Gene sequencing has played an integral role in the advancement and understanding of disease pathology and treatment. Although historically expensive and time consuming, new sequencing technologies improve our capability to obtain the genetic information in an accurate and timely manner. Within neurosurgery, gene sequencing is routinely used in the diagnosis and treatment of neurosurgical diseases, primarily for brain tumors. This paper reviews nanopore sequencing, an innovation utilized by MinION and outlines its potential use for neurosurgery. METHODS A literature search was conducted for publications containing the keywords of Oxford MinION, nanopore sequencing, brain tumor, glioma, whole genome sequencing (WGS), epigenomics, molecular neuropathology, and next-generation sequencing (NGS). In total, 64 articles were selected and used for this review. RESULTS The Oxford MinION nanopore sequencing technology has had successful applications within clinical microbiology, human genome sequencing, and cancer genotyping across multiple specialties. Technical details, methodology, and current use of MinION sequencing are discussed through the prism of potential applications to solve neurosurgery-related scientific and diagnostic questions. The MinION device has proven to provide rapid and accurate reads with longer read lengths when compared with NGS. For applications within neurosurgery, the MinION device is capable of providing critical diagnostic information for central nervous system (CNS) tumors within a single day. CONCLUSIONS MinION provides rapid and accurate gene sequencing with better affordability and convenience compared with current NGS methods. Widespread success of the MinION nanopore sequencing technology in providing accurate, rapid, and convenient gene sequencing suggests a promising future within research laboratories and to improve care for neurosurgical patients.
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Affiliation(s)
- Arpan Patel
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Evgenii Belykh
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- Department of Neurosurgery, Irkutsk State Medical University, Irkutsk, Russia
| | - Eric J. Miller
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Laeth L. George
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Nikolay L. Martirosyan
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
| | - Vadim A. Byvaltsev
- Department of Neurosurgery, Irkutsk State Medical University, Irkutsk, Russia
| | - Mark C. Preul
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
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44
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Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia. Sci Rep 2018; 8:11798. [PMID: 30087429 PMCID: PMC6081477 DOI: 10.1038/s41598-018-30330-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/27/2018] [Indexed: 12/12/2022] Open
Abstract
We report a customized gene panel assay based on multiplex long-PCR followed by third generation sequencing on nanopore technology (MinION), designed to analyze five frequently mutated genes in chronic lymphocytic leukemia (CLL): TP53, NOTCH1, BIRC3, SF3B1 and MYD88. For this purpose, 12 patients were selected according to specific cytogenetic and molecular features significantly associated with their mutational status. In addition, simultaneous analysis of the targets genes was performed by molecular assays or Sanger Sequencing. Data analysis included mapping to the GRCh37 human reference genome, variant calling and annotation, and average sequencing depth/error rate analysis. The sequencing depth resulted on average higher for smaller amplicons, and the final breadth of coverage of the panel was 94.1%. The error rate was about 6% and 2% for insertions/deletions and single nucleotide variants, respectively. Our gene panel allows analysis of the prognostically relevant genes in CLL, with two PCRs per patient. This strategy offers an easy and affordable workflow, although further advances are required to improve the accuracy of the technology and its use in the clinical field. Nevertheless, the rapid and constant development of nanopore technology, in terms of chemistry advances, more accurate basecallers and analysis software, offers promise for a wide use of MinION in the future.
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45
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Fraiture MA, Saltykova A, Hoffman S, Winand R, Deforce D, Vanneste K, De Keersmaecker SCJ, Roosens NHC. Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO. Sci Rep 2018; 8:7903. [PMID: 29785005 PMCID: PMC5962636 DOI: 10.1038/s41598-018-26259-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region. This DNA walking is performed on transgenic elements, commonly found in GMO, that were earlier detected by real-time PCR (qPCR) screening. Previously, we have demonstrated the ability of this approach to detect unauthorized GMO via the identification of unique transgene flanking regions and the unnatural associations of elements from the transgenic cassette. In the present study, we investigate the feasibility to integrate the described workflow with the MinION Next-Generation-Sequencing (NGS). The MinION sequencing platform can provide long read-lengths and deal with heterogenic DNA libraries, allowing for rapid and efficient delivery of sequences of interest. In addition, the ability of this NGS platform to characterize unauthorized and unknown GMO without any a priori knowledge has been assessed.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Assia Saltykova
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Ghent University (UGent), Department of Information Technology, IMEC, Internet Technology and Data Science Lab (IDLab), Technologiepark-Zwijnaarde 15, 9052, Ghent, Belgium
| | - Stefan Hoffman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Raf Winand
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Kevin Vanneste
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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46
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Audebert C, Hot D, Caboche S. [Prospects for applications in human health of nanopore-based sequencing]. Med Sci (Paris) 2018; 34:319-325. [PMID: 29658474 DOI: 10.1051/medsci/20183404012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High throughput sequencing has opened up new clinical opportunities moving towards a medicine of precision. Oncology, infectious diseases or human genomics, many applications have been developed in recent years. The introduction of a third generation of nanopore-based sequencing technology, addressing some of the weaknesses of the previous generation, heralds a new revolution. Portability, real time, long reads and marginal investment costs, these promising new technologies point to a new shift of paradigm. What are the perspectives opened up by nanopores for clinical applications?
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Affiliation(s)
- Christophe Audebert
- Gènes Diffusion, 3595, route de Tournai, 59501 Douai, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France
| | - David Hot
- Univ Lille, CNRS, Inserm, CHU de Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, 1, rue du professeur Calmette, F-59000 Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France
| | - Ségolène Caboche
- Univ Lille, CNRS, Inserm, CHU de Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, 1, rue du professeur Calmette, F-59000 Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France
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47
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Cumbo C, Impera L, Minervini CF, Orsini P, Anelli L, Zagaria A, Coccaro N, Tota G, Minervini A, Casieri P, Brunetti C, Rossi AR, Parciante E, Specchia G, Albano F. Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for "personalized monitoring" of residual disease in chronic myeloid leukemia patients. Oncotarget 2018. [PMID: 29541390 PMCID: PMC5834283 DOI: 10.18632/oncotarget.23971] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology. Finally, after defining the BCR-ABL1 genomic junction, we performed the target CML patient–specific quantification, using droplet digital PCR (ddPCR). FISH and MinION steps, respectively, together with ddPCR analysis, greatly reduce the complexity that has impeded the use of “personalized monitoring” of CML in clinical practice. Our report suggests a feasible pipeline, in terms of costs and reproducibility, aimed at characterizing and quantifying the genomic BCR-ABL1 rearrangement during MRD monitoring in CML patients.
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Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | | | - Paola Orsini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Nicoletta Coccaro
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Angela Minervini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Paola Casieri
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Claudia Brunetti
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Russo Rossi
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
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48
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Minervini CF, Cumbo C, Orsini P, Anelli L, Zagaria A, Impera L, Coccaro N, Brunetti C, Minervini A, Casieri P, Tota G, Russo Rossi A, Specchia G, Albano F. Mutational analysis in BCR - ABL1 positive leukemia by deep sequencing based on nanopore MinION technology. Exp Mol Pathol 2017; 103:33-37. [DOI: 10.1016/j.yexmp.2017.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/22/2017] [Accepted: 06/25/2017] [Indexed: 01/11/2023]
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