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Nakamura W, Hirata M, Oda S, Chiba K, Okada A, Mateos RN, Sugawa M, Iida N, Ushiama M, Tanabe N, Sakamoto H, Sekine S, Hirasawa A, Kawai Y, Tokunaga K, Tsujimoto SI, Shiba N, Ito S, Yoshida T, Shiraishi Y. Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes. NPJ Genom Med 2024; 9:11. [PMID: 38368425 PMCID: PMC10874402 DOI: 10.1038/s41525-024-00394-z] [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: 05/28/2023] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read sequencing. In addition, Oxford Nanopore Technologies (ONT) offers adaptive sampling and computationally driven target enrichment technology. This enables more affordable intensive analysis of target gene regions compared to standard non-selective long-read sequencing. In this study, we developed an efficient computational workflow for target adaptive sampling long-read sequencing (TAS-LRS) and evaluated it through application to 33 genomes collected from suspected hereditary cancer patients. Our workflow can identify single nucleotide variants with nearly the same accuracy as the short-read platform and elucidate complex forms of structural variations. We also newly identified several SINE-R/VNTR/Alu (SVA) elements affecting the APC gene in two patients with familial adenomatous polyposis, as well as their sites of origin. In addition, we demonstrated that off-target reads from adaptive sampling, which is typically discarded, can be effectively used to accurately genotype common single-nucleotide polymorphisms (SNPs) across the entire genome, enabling the calculation of a polygenic risk score. Furthermore, we identified allele-specific MLH1 promoter hypermethylation in a Lynch syndrome patient. In summary, our workflow with TAS-LRS can simultaneously capture monogenic risk variants including complex structural variations, polygenic background as well as epigenetic alterations, and will be an efficient platform for genetic disease research and diagnosis.
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Affiliation(s)
- Wataru Nakamura
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Makoto Hirata
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoyo Oda
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Division of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Raúl Nicolás Mateos
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Sugawa
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Mineko Ushiama
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Noriko Tanabe
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigeki Sekine
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Hirasawa
- Department of Clinical Genetics and Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Central Biobank, National Center Biobank Network, Tokyo, Japan
| | - Shin-Ichi Tsujimoto
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Norio Shiba
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Shuichi Ito
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Teruhiko Yoshida
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
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Frascarelli C, Zanetti N, Nasca A, Izzo R, Lamperti C, Lamantea E, Legati A, Ghezzi D. Nanopore long-read next-generation sequencing for detection of mitochondrial DNA large-scale deletions. Front Genet 2023; 14:1089956. [PMID: 37456669 PMCID: PMC10344361 DOI: 10.3389/fgene.2023.1089956] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Primary mitochondrial diseases are progressive genetic disorders affecting multiple organs and characterized by mitochondrial dysfunction. These disorders can be caused by mutations in nuclear genes coding proteins with mitochondrial localization or by genetic defects in the mitochondrial genome (mtDNA). The latter include point pathogenic variants and large-scale deletions/rearrangements. MtDNA molecules with the wild type or a variant sequence can exist together in a single cell, a condition known as mtDNA heteroplasmy. MtDNA single point mutations are typically detected by means of Next-Generation Sequencing (NGS) based on short reads which, however, are limited for the identification of structural mtDNA alterations. Recently, new NGS technologies based on long reads have been released, allowing to obtain sequences of several kilobases in length; this approach is suitable for detection of structural alterations affecting the mitochondrial genome. In the present work we illustrate the optimization of two sequencing protocols based on long-read Oxford Nanopore Technology to detect mtDNA structural alterations. This approach presents strong advantages in the analysis of mtDNA compared to both short-read NGS and traditional techniques, potentially becoming the method of choice for genetic studies on mtDNA.
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Affiliation(s)
- Chiara Frascarelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Nadia Zanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Rossella Izzo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
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3
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Spealman P, De T, Chuong JN, Gresham D. Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution. J Mol Evol 2023; 91:356-368. [PMID: 37012421 PMCID: PMC10275804 DOI: 10.1007/s00239-023-10102-7] [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: 09/28/2022] [Accepted: 02/21/2023] [Indexed: 04/05/2023]
Abstract
Copy number variants (CNVs), comprising gene amplifications and deletions, are a pervasive class of heritable variation. CNVs play a key role in rapid adaptation in both natural, and experimental, evolution. However, despite the advent of new DNA sequencing technologies, detection and quantification of CNVs in heterogeneous populations has remained challenging. Here, we summarize recent advances in the use of CNV reporters that provide a facile means of quantifying de novo CNVs at a specific locus in the genome, and nanopore sequencing, for resolving the often complex structures of CNVs. We provide guidance for the engineering and analysis of CNV reporters and practical guidelines for single-cell analysis of CNVs using flow cytometry. We summarize recent advances in nanopore sequencing, discuss the utility of this technology, and provide guidance for the bioinformatic analysis of these data to define the molecular structure of CNVs. The combination of reporter systems for tracking and isolating CNV lineages and long-read DNA sequencing for characterizing CNV structures enables unprecedented resolution of the mechanisms by which CNVs are generated and their evolutionary dynamics.
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Affiliation(s)
- Pieter Spealman
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Titir De
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Julie N Chuong
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, 10003, USA.
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
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Senanayake A, Gamaarachchi H, Herath D, Ragel R. DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing. BMC Bioinformatics 2023; 24:31. [PMID: 36709261 PMCID: PMC9883605 DOI: 10.1186/s12859-023-05151-0] [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: 10/24/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Nanopore sequencing allows selective sequencing, the ability to programmatically reject unwanted reads in a sample. Selective sequencing has many present and future applications in genomics research and the classification of species from a pool of species is an example. Existing methods for selective sequencing for species classification are still immature and the accuracy highly varies depending on the datasets. For the five datasets we tested, the accuracy of existing methods varied in the range of [Formula: see text] 77 to 97% (average accuracy < 89%). Here we present DeepSelectNet, an accurate deep-learning-based method that can directly classify nanopore current signals belonging to a particular species. DeepSelectNet utilizes novel data preprocessing techniques and improved neural network architecture for regularization. RESULTS For the five datasets tested, DeepSelectNet's accuracy varied between [Formula: see text] 91 and 99% (average accuracy [Formula: see text] 95%). At its best performance, DeepSelectNet achieved a nearly 12% accuracy increase compared to its deep learning-based predecessor SquiggleNet. Furthermore, precision and recall evaluated for DeepSelectNet on average were always > 89% (average [Formula: see text] 95%). In terms of execution performance, DeepSelectNet outperformed SquiggleNet by [Formula: see text] 13% on average. Thus, DeepSelectNet is a practically viable method to improve the effectiveness of selective sequencing. CONCLUSIONS Compared to base alignment and deep learning predecessors, DeepSelectNet can significantly improve the accuracy to enable real-time species classification using selective sequencing. The source code of DeepSelectNet is available at https://github.com/AnjanaSenanayake/DeepSelectNet .
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Affiliation(s)
- Anjana Senanayake
- grid.11139.3b0000 0000 9816 8637Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - Hasindu Gamaarachchi
- grid.415306.50000 0000 9983 6924Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia ,grid.1005.40000 0004 4902 0432School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
| | - Damayanthi Herath
- grid.11139.3b0000 0000 9816 8637Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - Roshan Ragel
- grid.11139.3b0000 0000 9816 8637Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka
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5
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Lin Y, Dai Y, Zhang S, Guo H, Yang L, Li J, Wang K, Ni M, Hu Z, Jia L, Liu H, Li P, Song H. Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection. Front Cell Infect Microbiol 2023; 13:1064317. [PMID: 36756615 PMCID: PMC9900021 DOI: 10.3389/fcimb.2023.1064317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/11/2023] [Indexed: 01/24/2023] Open
Abstract
Introduction Nanopore sequencing has been widely used in clinical metagenomic sequencing for pathogen detection with high portability and real-time sequencing. Oxford Nanopore Technologies has recently launched an adaptive sequencing function, which can enrich on-target reads through real-time alignment and eject uninteresting reads by reversing the voltage across the nanopore. Here we evaluated the utility of adaptive sequencing in clinical pathogen detection. Methods Nanopore adaptive sequencing and standard sequencing was performed on a same flow cell with a bronchoalveolar lavage fluid sample from a patient with Chlamydia psittacosis infection, and was compared with the previous mNGS results. Results Nanopore adaptive sequencing identified 648 on-target stop receiving reads with the longest median read length(688bp), which account for 72.4% of all Chlamydia psittaci reads and 0.03% of total reads in enriched group. The read proportion matched to C. psittaci in the stop receiving group was 99.85%, which was much higher than that of the unblock (<0.01%) and fail to adapt (0.02%) groups. Nanopore adaptive sequencing generated similar data yield of C. psittaci compared with standard nanopore sequencing. The proportion of C. psittaci reads in adaptive sequencing is close to that of standard nanopore sequencing and mNGS, but generated lower genome coverage than mNGS. Discussion Nanopore adaptive sequencing can effectively identify target C. psittaci reads in real-time, but how to increase the targeted data of pathogens still needs to be further evaluated.
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Affiliation(s)
- Yanfeng Lin
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yan Dai
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Shuang Zhang
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China,Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ming Ni
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China,Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Zongqian Hu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China,Beijing Institute of Radiation Medicine, Beijing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Huiying Liu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China,*Correspondence: Huiying Liu, ; Peng Li, ; Hongbin Song,
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China,*Correspondence: Huiying Liu, ; Peng Li, ; Hongbin Song,
| | - Hongbin Song
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China,Chinese PLA Center for Disease Control and Prevention, Beijing, China,*Correspondence: Huiying Liu, ; Peng Li, ; Hongbin Song,
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6
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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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7
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Li P, Dupont B, Hu Q, Crimi M, Shen Y, Lebedev I, Liehr T. The past, present, and future for constitutional ring chromosomes: A report of the international consortium for human ring chromosomes. HGG ADVANCES 2022; 3:100139. [PMID: 36187226 PMCID: PMC9519620 DOI: 10.1016/j.xhgg.2022.100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Human ring chromosomes (RCs) are rare diseases with an estimated newborn incidence of 1/50,000 and an annual occurrence of 2,800 patients globally. Over the past 60 years, banding cytogenetics, fluorescence in situ hybridization (FISH), chromosome microarray analysis (CMA), and whole-genome sequencing (WGS) has been used to detect an RC and further characterize its genomic alterations. Ring syndrome featuring sever growth retardation and variable intellectual disability has been considered as general clinical presentations for all RCs due to the cellular losses from the dynamic mosaicism of RC instability through mitosis. Cytogenomic heterogeneity ranging from simple complete RCs to complex rearranged RCs and variable RC intolerance with different relative frequencies have been observed. Clinical heterogeneity, including chromosome-specific deletion and duplication syndromes, gene-related organ and tissue defects, cancer predisposition to different types of tumors, and reproductive failure, has been reported in the literature. However, the patients with RCs reported in the literature accounted for less than 1% of its occurrence. Current diagnostic practice lacks laboratory standards for analyzing cellular behavior and genomic imbalances of RCs to evaluate the compound effects on patients. Under-representation of clinical cases and lack of comprehensive diagnostic analysis make it a challenge for evidence-based interpretation of clinico-cytogenomic correlations and recommendation of follow-up clinical management. Given recent advancements in genomic technologies and organized efforts by international collaborations and patient advocacy organizations, the prospective of standardized cytogenomic diagnosis and evidence-based clinical management for all patients with RCs could be achieved at an unprecedented global scale.
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Affiliation(s)
- Peining Li
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Corresponding author
| | - Barbara Dupont
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, SC, USA
- Corresponding author
| | - Qiping Hu
- Department of Cell Biology and Genetics, Institute of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Marco Crimi
- Ring 14 International, Via Santa Maria Alla Porta 2, 20123 Milano, Italy
- Kaleidos SCS, Scientific Office, Via Moretti Andrea 20, 24121 Bergamo, Italy
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children’s Hospital, Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Igor Lebedev
- Laboratory of Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk 634050, Russia
- Corresponding author
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747 Jena, Germany
- Corresponding author
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8
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Lin Y, Dai Y, Liu Y, Ren Z, Guo H, Li Z, Li J, Wang K, Yang L, Zhang S, Liu H, Jia L, Ni M, Li P, Song H. Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance. Front Microbiol 2022; 13:929241. [PMID: 35783376 PMCID: PMC9244360 DOI: 10.3389/fmicb.2022.929241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Nanopore sequencing has been widely used for the real-time detection and surveillance of pathogens with portable MinION. Nanopore adaptive sequencing can enrich on-target sequences without additional pretreatment. In this study, the performance of adaptive sequencing was evaluated for viral genome enrichment of clinical respiratory samples. Ligation-based nanopore adaptive sequencing (LNAS) and rapid PCR-based nanopore adaptive sequencing (RPNAS) workflows were performed to assess the effects of enrichment on nasopharyngeal swab samples from human adenovirus (HAdV) outbreaks. RPNAS was further applied for the enrichment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasopharyngeal swab samples to evaluate sensitivity and timeliness. The RPNAS increased both the relative abundance (7.87–12.86-fold) and data yield (1.27–2.15-fold) of HAdV samples, whereas the LNAS increased only the relative abundance but had no obvious enrichment on the data yield. Compared with standard nanopore sequencing, RPNAS detected the SARS-CoV-2 reads from two low-abundance samples, increased the coverage of SARS-CoV-2 by 36.68–98.92%, and reduced the time to achieve the same coverage. Our study highlights the utility of RPNAS for virus enrichment directly from clinical samples, with more on-target data and a shorter sequencing time to recover viral genomes. These findings promise to improve the sensitivity and timeliness of rapid identification and genomic surveillance of infectious diseases.
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Affiliation(s)
- Yanfeng Lin
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yan Dai
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Yuqi Liu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Zhuli Ren
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Zhenzhong Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shuang Zhang
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ming Ni
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Institute of Health Service and Transfusion Medicine, Beijing, China
- *Correspondence: Ming Ni,
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Peng Li,
| | - Hongbin Song
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Hongbin Song,
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