1
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Gómez-Peregrina D, Cicala CM, Serrano C. Monitoring advanced gastrointestinal stromal tumor with circulating tumor DNA. Curr Opin Oncol 2024; 36:282-290. [PMID: 38726808 DOI: 10.1097/cco.0000000000001040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
PURPOSE OF REVIEW This review explores the role of circulating tumor (ct)DNA as a biomarker for clinical decision-making and monitoring purposes in metastatic gastrointestinal stromal tumor (GIST) patients. We discuss key insights from recent clinical trials and anticipate the future perspectives of ctDNA profiling within the clinical landscape of GIST. RECENT FINDINGS The identification and molecular characterization of KIT/platelet-derived growth factor receptor alpha (PDGFRA) mutations from ctDNA in metastatic GIST is feasible and reliable. Such identification through ctDNA serves as a predictor of clinical outcomes to tyrosine-kinase inhibitors (TKIs) in metastatic patients. Additionally, conjoined ctDNA analysis from clinical trials reveal the evolving mutational landscapes and increase in intratumoral heterogeneity across treatment lines. Together, this data positions ctDNA determination as a valuable tool for monitoring disease progression and guiding therapy in metastatic patients. These collective efforts culminated in the initiation of a ctDNA-based randomized clinical trial in GIST, marking a significant milestone in integrating ctDNA testing into the clinical care of GIST patients. SUMMARY The dynamic field of ctDNA technologies is rapidly evolving and holds significant promise for research. Several trials have successfully validated the clinical utility of ctDNA in metastatic GIST, laying the foundations for its prospective integration into the routine clinical management of GIST patients.
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Affiliation(s)
- David Gómez-Peregrina
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO)
| | - Carlo Maria Cicala
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO)
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - César Serrano
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO)
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
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2
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Ermini L, Driguez P. The Application of Long-Read Sequencing to Cancer. Cancers (Basel) 2024; 16:1275. [PMID: 38610953 PMCID: PMC11011098 DOI: 10.3390/cancers16071275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation sequencing (TGS), led by the Pacific Biosciences and Oxford Nanopore Technologies platforms, employs long-read sequences, which have marked a paradigm shift in cancer research. Cancer genomes often harbour complex events, and TGS, with its ability to span large genomic regions, has facilitated their characterisation, providing a better understanding of how complex rearrangements affect cancer initiation and progression. TGS has also characterised the entire transcriptome of various cancers, revealing cancer-associated isoforms that could serve as biomarkers or therapeutic targets. Furthermore, TGS has advanced cancer research by improving genome assemblies, detecting complex variants, and providing a more complete picture of transcriptomes and epigenomes. This review focuses on TGS and its growing role in cancer research. We investigate its advantages and limitations, providing a rigorous scientific analysis of its use in detecting previously hidden aberrations missed by NGS. This promising technology holds immense potential for both research and clinical applications, with far-reaching implications for cancer diagnosis and treatment.
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Affiliation(s)
- Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
| | - Patrick Driguez
- Bioscience Core Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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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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van der Pol Y, Tantyo NA, Evander N, Hentschel AE, Wever BM, Ramaker J, Bootsma S, Fransen MF, Lenos KJ, Vermeulen L, Schneiders FL, Bahce I, Nieuwenhuijzen JA, Steenbergen RD, Pegtel DM, Moldovan N, Mouliere F. Real-time analysis of the cancer genome and fragmentome from plasma and urine cell-free DNA using nanopore sequencing. EMBO Mol Med 2023; 15:e17282. [PMID: 37942753 DOI: 10.15252/emmm.202217282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Cell-free DNA (cfDNA) can be isolated and sequenced from blood and/or urine of cancer patients. Conventional short-read sequencing lacks deployability and speed and can be biased for short cfDNA fragments. Here, we demonstrate that with Oxford Nanopore Technologies (ONT) sequencing we can achieve delivery of genomic and fragmentomic data from liquid biopsies. Copy number aberrations and cfDNA fragmentation patterns can be determined in less than 24 h from sample collection. The tumor-derived cfDNA fraction calculated from plasma of lung cancer patients and urine of bladder cancer patients was highly correlated (R = 0.98) with the tumor fraction calculated from short-read sequencing of the same samples. cfDNA size profile, fragmentation patterns, fragment-end composition, and nucleosome profiling near transcription start sites in plasma and urine exhibited the typical cfDNA features. Additionally, a high proportion of long tumor-derived cfDNA fragments (> 300 bp) are recovered in plasma and urine using ONT sequencing. ONT sequencing is a cost-effective, fast, and deployable approach for obtaining genomic and fragmentomic results from liquid biopsies, allowing the analysis of previously understudied cfDNA populations.
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Affiliation(s)
- Ymke van der Pol
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Normastuti Adhini Tantyo
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Nils Evander
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Anouk E Hentschel
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Urology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Birgit Mm Wever
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jip Ramaker
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sanne Bootsma
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Marieke F Fransen
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Famke L Schneiders
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Idris Bahce
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jakko A Nieuwenhuijzen
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Urology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Renske Dm Steenbergen
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Norbert Moldovan
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Florent Mouliere
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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5
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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6
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Huang X, Duijf PHG, Sriram S, Perera G, Vasani S, Kenny L, Leo P, Punyadeera C. Circulating tumour DNA alterations: emerging biomarker in head and neck squamous cell carcinoma. J Biomed Sci 2023; 30:65. [PMID: 37559138 PMCID: PMC10413618 DOI: 10.1186/s12929-023-00953-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023] Open
Abstract
Head and Neck cancers (HNC) are a heterogeneous group of upper aero-digestive tract cancer and account for 931,922 new cases and 467,125 deaths worldwide. About 90% of these cancers are of squamous cell origin (HNSCC). HNSCC is associated with excessive tobacco and alcohol consumption and infection with oncogenic viruses. Genotyping tumour tissue to guide clinical decision-making is becoming common practice in modern oncology, but in the management of patients with HNSCC, cytopathology or histopathology of tumour tissue remains the mainstream for diagnosis and treatment planning. Due to tumour heterogeneity and the lack of access to tumour due to its anatomical location, alternative methods to evaluate tumour activities are urgently needed. Liquid biopsy approaches can overcome issues such as tumour heterogeneity, which is associated with the analysis of small tissue biopsy. In addition, liquid biopsy offers repeat biopsy sampling, even for patients with tumours with access limitations. Liquid biopsy refers to biomarkers found in body fluids, traditionally blood, that can be sampled to provide clinically valuable information on both the patient and their underlying malignancy. To date, the majority of liquid biopsy research has focused on blood-based biomarkers, such as circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), and circulating microRNA. In this review, we will focus on ctDNA as a biomarker in HNSCC because of its robustness, its presence in many body fluids, adaptability to existing clinical laboratory-based technology platforms, and ease of collection and transportation. We will discuss mechanisms of ctDNA release into circulation, technological advances in the analysis of ctDNA, ctDNA as a biomarker in HNSCC management, and some of the challenges associated with translating ctDNA into clinical and future perspectives. ctDNA provides a minimally invasive method for HNSCC prognosis and disease surveillance and will pave the way in the future for personalized medicine, thereby significantly improving outcomes and reducing healthcare costs.
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Affiliation(s)
- Xiaomin Huang
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia
| | - Pascal H G Duijf
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- University Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Sharath Sriram
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Ganganath Perera
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Sarju Vasani
- Department of Otolaryngology, Royal Brisbane Women's Hospital, Brisbane, QLD, Australia
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Lizbeth Kenny
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Paul Leo
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Translational Genomics Centre, Brisbane, QLD, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia.
- Menzies Health Institute Queensland (MIHQ), Griffith University, Gold coast, QLD, Australia.
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7
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Wang W, He Y, Yang F, Chen K. Current and emerging applications of liquid biopsy in pan-cancer. Transl Oncol 2023; 34:101720. [PMID: 37315508 DOI: 10.1016/j.tranon.2023.101720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023] Open
Abstract
Cancer morbidity and mortality are growing rapidly worldwide and it is urgent to develop a convenient and effective method that can identify cancer patients at an early stage and predict treatment outcomes. As a minimally invasive and reproducible tool, liquid biopsy (LB) offers the opportunity to detect, analyze and monitor cancer in any body fluids including blood, complementing the limitations of tissue biopsy. In liquid biopsy, circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are the two most common biomarkers, displaying great potential in the clinical application of pan-cancer. In this review, we expound the samples, targets, and newest techniques in liquid biopsy and summarize current clinical applications in several specific cancers. Besides, we put forward a bright prospect for further exploring the emerging application of liquid biopsy in the field of pan-cancer precision medicine.
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Affiliation(s)
- Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute, Beijing 100044, China
| | - Yue He
- Department of Thoracic Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute, Beijing 100044, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute, Beijing 100044, China
| | - Kezhong Chen
- Department of Thoracic Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute, Beijing 100044, China.
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8
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Soni N, Chandra Verma N, Talor N, Meller A. Over 30-Fold Enhancement in DNA Translocation Dynamics through Nanoscale Pores Coated with an Anionic Surfactant. NANO LETTERS 2023; 23:4609-4616. [PMID: 37149783 DOI: 10.1021/acs.nanolett.3c01096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Solid-state nanopores (ssNPs) are single-molecule sensors capable of label-free quantification of different biomolecules, which have become highly versatile with the introduction of different surface treatments. By modulating the surface charges of the ssNP, the electro-osmotic flow (EOF) can be controlled in turn affecting the in-pore hydrodynamic forces. Herein, we demonstrate that negative charge surfactant coating to ssNPs generates EOF that slows-down DNA translocation speed by >30-fold, without deterioration of the NP noise, hence significantly improving its performances. Consequently, surfactant-coated ssNPs can be used to reliably sense short DNA fragments at high voltage bias. To shed light on the EOF phenomena inside planar ssNPs, we introduce visualization of the electrically neutral fluorescent molecule's flow, hence decoupling the electrophoretic from EOF forces. Finite elements simulations are then used to show that EOF is likely responsible for in-pore drag and size-selective capture rate. This study broadens ssNPs use for multianalyte sensing in a single device.
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Affiliation(s)
- Neeraj Soni
- Russell Berrie Nanotechnology Institute, Technion IIT, Haifa 3200003, Israel
- Department of Biomedical Engineering, Technion IIT, Haifa 3200003, Israel
| | | | - Noam Talor
- Department of Biomedical Engineering, Technion IIT, Haifa 3200003, Israel
| | - Amit Meller
- Russell Berrie Nanotechnology Institute, Technion IIT, Haifa 3200003, Israel
- Department of Biomedical Engineering, Technion IIT, Haifa 3200003, Israel
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9
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Nakamichi K, Stacey A, Mustafi D. Targeted long-read sequencing allows for rapid identification of pathogenic disease-causing variants in retinoblastoma. Ophthalmic Genet 2022; 43:762-770. [PMID: 36325802 DOI: 10.1080/13816810.2022.2141797] [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: 11/06/2022]
Abstract
BACKGROUND Identification of disease-causing variants of the retinoblastoma gene (RB1), the predominant cause of retinoblastoma, is challenging. Targeted long-read genome sequencing offers a novel approach to resolve the diverse range of pathogenic variants in RB1 and provides haplotype information rapidly. MATERIALS AND METHODS Genomic DNA was isolated from a venipuncture blood draw of a retinoblastoma patient. Whole genome sequencing (WGS) was carried out using the short-read Ilumina platform. WGS and targeted sequencing of RB1 was accomplished using the long-read Oxford Nanopore Technologies (ONT) platform. Deep-learning frameworks allowed haplotagging, variant calling, and variant annotation of both short- and long-read data. RESULTS Targeted long-read sequencing of the RB1 gene allowed for enhanced depth of read coverage for discovery of rare variants and haplotype analysis. A duplication leading to a frameshift and early termination in RB1 was identified as the most deleterious variant by all sequencing methods, with long-read technology providing additional information of methylation signal and haplotype information. More importantly, there was greater than 98% concordance of RB1 variants identified between short-read and targeted long-read sequencing modalities. CONCLUSIONS Targeted long-read technology allows for focused sequencing effort for variant discovery. Application of this for the first time in a retinoblastoma patient allowed haplotagged variant identification and demonstrated excellent concordance with benchmark short-read sequencing. The added benefit of targeted long-read sequencing to resolve disease-causing genomic variation in RB1 rapidly from a blood draw will provide a more definitive diagnosis of heritable RB and guide management decisions for patients and their families.
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Affiliation(s)
- Kenji Nakamichi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA
| | - Andrew Stacey
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA.,Department of Ophthalmology, Seattle Children's Hospital, Seattlees, WA, USA
| | - Debarshi Mustafi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA.,Department of Ophthalmology, Seattle Children's Hospital, Seattlees, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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10
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Wadden J, Newell BS, Bugbee J, John V, Bruzek AK, Dickson RP, Koschmann C, Blaauw D, Narayanasamy S, Das R. Ultra-rapid somatic variant detection via real-time targeted amplicon sequencing. Commun Biol 2022; 5:708. [PMID: 35840782 PMCID: PMC9284968 DOI: 10.1038/s42003-022-03657-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
Molecular markers are essential for cancer diagnosis, clinical trial enrollment, and some surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform due to time-consuming DNA extraction, targeted amplification, and library preparation times. In this work, we present a proof-of-principle approach for sub-1 hour targeted variant detection using real-time DNA sequencers. By modifying existing protocols, optimizing for diagnostic time-to-result, we demonstrate confirmation of a hot-spot mutation from tumor tissue in ~52 minutes. To further reduce time, we explore rapid, targeted Loop-mediated Isothermal Amplification (LAMP) and design a bioinformatics tool-LAMPrey-to process sequenced LAMP product. LAMPrey's concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Using LAMPrey, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes.
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Affiliation(s)
- Jack Wadden
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA.
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA.
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA.
| | - Brandon S Newell
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joshua Bugbee
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vishal John
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Amy K Bruzek
- Department of Neurosurgery, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Carl Koschmann
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - David Blaauw
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Satish Narayanasamy
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Reetuparna Das
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA.
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11
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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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Wadden J, Ravi K, John V, Babila CM, Koschmann C. Cell-Free Tumor DNA (cf-tDNA) Liquid Biopsy: Current Methods and Use in Brain Tumor Immunotherapy. Front Immunol 2022; 13:882452. [PMID: 35464472 PMCID: PMC9018987 DOI: 10.3389/fimmu.2022.882452] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022] Open
Abstract
Gliomas are tumors derived from mutations in glial brain cells. Gliomas cause significant morbidity and mortality and development of precision diagnostics and novel targeted immunotherapies are critically important. Radiographic imaging is the most common technique to diagnose and track response to treatment, but is an imperfect tool. Imaging does not provide molecular information, which is becoming critically important for identifying targeted immunotherapies and monitoring tumor evolution. Furthermore, immunotherapy induced inflammation can masquerade as tumor progression in images (pseudoprogression) and confound clinical decision making. More recently, circulating cell free tumor DNA (cf-tDNA) has been investigated as a promising biomarker for minimally invasive glioma diagnosis and disease monitoring. cf-tDNA is shed by gliomas into surrounding biofluids (e.g. cerebrospinal fluid and plasma) and, if precisely quantified, might provide a quantitative measure of tumor burden to help resolve pseudoprogression. cf-tDNA can also identify tumor genetic mutations to help guide targeted therapies. However, due to low concentrations of cf-tDNA, recovery and analysis remains challenging. Plasma cf-tDNA typically represents <1% of total cf-DNA due to the blood-brain barrier, limiting their usefulness in practice and motivating the development and use of highly sensitive and specific detection methods. This mini review summarizes the current and future trends of various approaches for cf-tDNA detection and analysis, including new methods that promise more rapid, lower-cost, and accessible diagnostics. We also review the most recent clinical case studies for longitudinal disease monitoring and highlight focus areas, such as novel accurate detection methodologies, as critical research priorities to enable translation to clinic.
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Affiliation(s)
- Jack Wadden
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
| | | | | | | | - Carl Koschmann
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
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Bhatti H, Lu Z, Liu Q. Nanopore Detection of Cancer Biomarkers: A Challenge to Science. Technol Cancer Res Treat 2022; 21:15330338221076669. [PMID: 35229683 PMCID: PMC8891933 DOI: 10.1177/15330338221076669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Cancer is the most complex and leading cause of fatality worldwide. Despite meritorious research in the field of cancer, it is still a substantial threat to human life. In this article, we address a question on the present strategies and manifest the importance of critical biomarkers for cancer screening and early diagnosis before the symptoms appear. However, this goal can only be achieved if scientists will focus on ultra-sensitive detection techniques such as “Nanopore.” Nanopore sensing is a simple and rapid single-molecule detection technique that can detect multiple cancer biomarkers in femto-Molar concentrations in real time. Last but not least, we propose a systematic policy to win the war against cancer that is a big challenge to science.
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Affiliation(s)
- Huma Bhatti
- Southeast University, Nanjing, People's Republic of China
| | - Zuhong Lu
- Southeast University, Nanjing, People's Republic of China
| | - Quanjun Liu
- Southeast University, Nanjing, People's Republic of China
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