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Xu X, Deng Y, Ding J, Tang Q, Lin Y, Zheng X, Zhang T. High-resolution and real-time wastewater viral surveillance by Nanopore sequencing. WATER RESEARCH 2024; 256:121623. [PMID: 38657304 DOI: 10.1016/j.watres.2024.121623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Wastewater genomic sequencing stands as a pivotal complementary tool for viral surveillance in populations. While long-read Nanopore sequencing is a promising platform to provide real-time genomic data, concerns over the sequencing accuracy of the earlier Nanopore versions have somewhat restrained its widespread application in wastewater analysis. Here, we evaluate the latest improved version of Nanopore sequencing (R10.4.1), using SARS-CoV-2 as the model infectious virus, to demonstrate its effectiveness in wastewater viral monitoring. By comparing amplicon lengths of 400 bp and 1200 bp, we revealed that shorter PCR amplification is more suitable for wastewater samples due to viral genome fragmentation. Utilizing mock wastewater samples, we validated the reliability of Nanopore sequencing for variant identification by comparing it with Illumina sequencing results. The strength of Nanopore sequencing in generating real-time genomic data for providing early warning signals was also showcased, indicating that as little as 0.001 Gb of data can provide accurate results for variant prevalence. Our evaluation also identified optimal alteration frequency cutoffs (>50 %) for precise mutation profiling, achieving >99 % precision in detecting single nucleotide variants (SNVs) and insertions/deletions (indels). Monitoring two major wastewater treatment plants in Hong Kong from September 2022 to April 2023, covering over 4.5 million population, we observed a transition in dominant variants from BA.5 to XBB lineages, with XBB.1.5 being the most prevalent variants. Mutation detection also highlighted the potential of wastewater Nanopore sequencing in uncovering novel mutations and revealed links between signature mutations and specific variants. This study not only reveals the environmental implications of Nanopore sequencing in SARS-CoV-2 surveillance but also underscores its potential in broader applications including environmental health monitoring of other epidemic viruses, which could significantly enhance the field of wastewater-based epidemiology.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Qinling Tang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yunqi Lin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region; School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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2
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Kumari P, Kaur M, Dindhoria K, Ashford B, Amarasinghe SL, Thind AS. Advances in long-read single-cell transcriptomics. Hum Genet 2024:10.1007/s00439-024-02678-x. [PMID: 38787419 DOI: 10.1007/s00439-024-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited in their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The scRNA-Seq protocols developed for long-read sequencing platforms overcome these limitations by enabling the characterization of full-length transcripts. Long-read scRNA-Seq techniques initially suffered from comparatively poor accuracy compared to short read scRNA-Seq. However, with improvements in accuracy, accessibility, and cost efficiency, long-reads are gaining popularity in the field of scRNA-Seq. This review details the advances in long-read scRNA-Seq, with an emphasis on library preparation protocols and downstream bioinformatics analysis tools.
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Affiliation(s)
- Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Manmeet Kaur
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Bruce Ashford
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia
| | - Shanika L Amarasinghe
- Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G, Royal Parade, Parkville, VIC, 3025, Australia
| | - Amarinder Singh Thind
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia.
- The School of Chemistry and Molecular Bioscience (SCMB), University of Wollongong, Loftus St, Wollongong, NSW, 2500, Australia.
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3
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Yao G, Tian Y, Ke W, Fang J, Ma S, Li T, Cheng X, Xia B, Wen L, Gao Z. Direct Identification of Complex Glycans via a Highly Sensitive Engineered Nanopore. J Am Chem Soc 2024; 146:13356-13366. [PMID: 38602480 DOI: 10.1021/jacs.4c02081] [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: 04/12/2024]
Abstract
The crucial roles that glycans play in biological systems are determined by their structures. However, the analysis of glycan structures still has numerous bottlenecks due to their inherent complexities. The nanopore technology has emerged as a powerful sensor for DNA sequencing and peptide detection. This has a significant impact on the development of a related research area. Currently, nanopores are beginning to be applied for the detection of simple glycans, but the analysis of complex glycans by this technology is still challenging. Here, we designed an engineered α-hemolysin nanopore M113R/T115A to achieve the sensing of complex glycans at micromolar concentrations and under label-free conditions. By extracting characteristic features to depict a three-dimensional (3D) scatter plot, glycans with different numbers of functional groups, various chain lengths ranging from disaccharide to decasaccharide, and distinct glycosidic linkages could be distinguished. Molecular dynamics (MD) simulations show different behaviors of glycans with β1,3- or β1,4-glycosidic bonds in nanopores. More importantly, the designed nanopore system permitted the discrimination of each glycan isomer with different lengths in a mixture with a separation ratio of over 0.9. This work represents a proof-of-concept demonstration that complex glycans can be analyzed using nanopore sequencing technology.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Yinping Tian
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shengzhou Ma
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tiehai Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 330106, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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4
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Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
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5
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Cheng HP, Yang TH, Wang JC, Chuang HS. Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection. SENSORS (BASEL, SWITZERLAND) 2024; 24:2904. [PMID: 38733011 PMCID: PMC11086254 DOI: 10.3390/s24092904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Demand is strong for sensitive, reliable, and cost-effective diagnostic tools for cancer detection. Accordingly, bead-based biosensors have emerged in recent years as promising diagnostic platforms based on wide-ranging cancer biomarkers owing to the versatility, high sensitivity, and flexibility to perform the multiplexing of beads. This comprehensive review highlights recent trends and innovations in the development of bead-based biosensors for cancer-biomarker detection. We introduce various types of bead-based biosensors such as optical, electrochemical, and magnetic biosensors, along with their respective advantages and limitations. Moreover, the review summarizes the latest advancements, including fabrication techniques, signal-amplification strategies, and integration with microfluidics and nanotechnology. Additionally, the challenges and future perspectives in the field of bead-based biosensors for cancer-biomarker detection are discussed. Understanding these innovations in bead-based biosensors can greatly contribute to improvements in cancer diagnostics, thereby facilitating early detection and personalized treatments.
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Affiliation(s)
- Hui-Pin Cheng
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
| | - Tai-Hua Yang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
- Department of Orthopedic Surgery, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Jhih-Cheng Wang
- Department of Urology, Chimei Medical Center, Tainan 710, Taiwan
- Department of Electrical Engineering, Southern Taiwan University of Science and Technology, Tainan 710, Taiwan
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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6
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Tran DH, Do HDK, Tran HT, Pham TNM, Nguyen HD, Linh HT, Cuong HQ, Vu MT, Phung HTT. Rapid identification of SARS-CoV-2 strains via isothermal enzymatic recombinase amplification and nanopore sequencing. Arch Virol 2024; 169:87. [PMID: 38565796 DOI: 10.1007/s00705-024-06012-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/28/2024] [Indexed: 04/04/2024]
Abstract
Surveillance of the SARS-CoV-2 genome has become a crucial technique in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole-genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent need to develop rapid and cost-effective tools for precise on-site detection and identification of SARS-CoV-2 strains. In this study, we demonstrate the rapid diagnosis of COVID-19 and identification of SARS-CoV-2 variants by amplification and sequencing of the entire SARS-CoV-2 S gene using isothermal enzymatic recombinase amplification combined with the advanced Oxford nanopore sequencing technique. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing the effect of mutations on diagnostic approaches, antiviral treatments, and vaccines.
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Affiliation(s)
- Diem Hong Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hau Thi Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | | | - Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Thuy Linh
- Medical Device Testing Center, Pasteur Institute, Ho Chi Minh City, Vietnam
- University Medical Center, Ho Chi Minh City, Vietnam
| | - Hoang Quoc Cuong
- Directorial Board, Pasteur Institute, Ho Chi Minh City, Vietnam
- Department of Health, Can Tho City, Vietnam
| | - Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.
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7
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Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
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Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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8
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McCabe MG, Geoerger B, Chesler L, Hargrave D, Parsons DW, van Tilburg CM, Schleiermacher G, Hickman JA, George SL. Precision Medicine for Childhood Cancer: Current Limitations and Future Perspectives. JCO Precis Oncol 2024; 8:e2300117. [PMID: 38207228 DOI: 10.1200/po.23.00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/19/2023] [Accepted: 10/19/2023] [Indexed: 01/13/2024] Open
Abstract
Greater collaboration needed to realize potential of molecular profiling initiatives for pediatric cancers.
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Affiliation(s)
- Martin G McCabe
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Birgit Geoerger
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Louis Chesler
- Paediatric Oncology Experimental Medicine Centre, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Darren Hargrave
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - D Williams Parsons
- Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology & Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Gudrun Schleiermacher
- SiRIC RTOP (Recherche Translationelle en Oncologie Pédiatrique), Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Parbe the only one citing a postcodeis, France
| | - John A Hickman
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Sally L George
- Paediatric Oncology Experimental Medicine Centre, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, The Royal Marsden Hospital, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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Miga KH, Eichler EE. Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes. Am J Hum Genet 2023; 110:1832-1840. [PMID: 37922882 PMCID: PMC10645551 DOI: 10.1016/j.ajhg.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
Advances in long-read sequencing and assembly now mean that individual labs can generate phased genomes that are more accurate and more contiguous than the original human reference genome. With declining costs and increasing democratization of technology, we suggest that complete genome assemblies, where both parental haplotypes are phased telomere to telomere, will become standard in human genetics. Soon, even in clinical settings where rigorous sample-handling standards must be met, affected individuals could have reference-grade genomes fully sequenced and assembled in just a few hours given advances in technology, computational processing, and annotation. Complete genetic variant discovery will transform how we map, catalog, and associate variation with human disease and fundamentally change our understanding of the genetic diversity of all humans.
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Affiliation(s)
- Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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10
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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: 2] [Impact Index Per Article: 2.0] [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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11
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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