Relevant bibliographies by topics / Oxford Nanopore sequencing

Academic literature on the topic 'Oxford Nanopore sequencing'

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Published: 14 March 2023

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Journal articles on the topic "Oxford Nanopore sequencing"

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Heikema, Astrid P., Deborah Horst-Kreft, Stefan A. Boers, Rick Jansen, Saskia D. Hiltemann, Willem de Koning, Robert Kraaij, et al. "Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota." Genes 11, no. 9 (September 21, 2020): 1105. http://dx.doi.org/10.3390/genes11091105.

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Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable.
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Lin, Bo, Jianan Hui, and Hongju Mao. "Nanopore Technology and Its Applications in Gene Sequencing." Biosensors 11, no. 7 (June 30, 2021): 214. http://dx.doi.org/10.3390/bios11070214.

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In recent years, nanopore technology has become increasingly important in the field of life science and biomedical research. By embedding a nano-scale hole in a thin membrane and measuring the electrochemical signal, nanopore technology can be used to investigate the nucleic acids and other biomacromolecules. One of the most successful applications of nanopore technology, the Oxford Nanopore Technology, marks the beginning of the fourth generation of gene sequencing technology. In this review, the operational principle and the technology for signal processing of the nanopore gene sequencing are documented. Moreover, this review focuses on the applications using nanopore gene sequencing technology, including the diagnosis of cancer, detection of viruses and other microbes, and the assembly of genomes. These applications show that nanopore technology is promising in the field of biological and biomedical sensing.
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Lu, Hengyun, Francesca Giordano, and Zemin Ning. "Oxford Nanopore MinION Sequencing and Genome Assembly." Genomics, Proteomics & Bioinformatics 14, no. 5 (October 2016): 265–79. http://dx.doi.org/10.1016/j.gpb.2016.05.004.

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Eisenstein, Michael. "Oxford Nanopore announcement sets sequencing sector abuzz." Nature Biotechnology 30, no. 4 (April 2012): 295–96. http://dx.doi.org/10.1038/nbt0412-295.

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Sereika, Mantas, Rasmus Hansen Kirkegaard, Søren Michael Karst, Thomas Yssing Michaelsen, Emil Aarre Sørensen, Rasmus Dam Wollenberg, and Mads Albertsen. "Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing." Nature Methods 19, no. 7 (July 2022): 823–26. http://dx.doi.org/10.1038/s41592-022-01539-7.

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AbstractLong-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.
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MacKenzie, Morgan, and Christos Argyropoulos. "An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations." Micromachines 14, no. 2 (February 16, 2023): 459. http://dx.doi.org/10.3390/mi14020459.

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There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
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Салахов, Р. Р., М. В. Голубенко, Е. Н. Павлюкова, А. В. Марков, Н. П. Бабушкина, А. Ф. Канев, Н. Р. Валиахметов, and М. С. Назаренко. "Application of monomolecular sequencing technology to the diagnostics of hypertrophic cardiomyopathy." Nauchno-prakticheskii zhurnal «Medicinskaia genetika», no. 5(214) (May 29, 2020): 9–10. http://dx.doi.org/10.25557/2073-7998.2020.05.9-10.

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В работе представлены результаты секвенирования пяти генов, ассоциированных с гипертрофической кардиомиопатией, с использованием технологии мономолекулярного секвенирования компании Oxford Nanopore Technologies. В результате анализа данных с помощью различных алгоритмов были выявлены миссенс-варианты в исследованных генах, которые могут являться причиной заболевания у пациентов. The paper presents the results of sequencing of five genes associated with hypertrophic cardiomyopathy, using monomolecular sequencing (Oxford Nanopore Technologies). As a result of data analysis with various algorithms, missense variants were identified in the studied genes that may be the cause of the disease in the patients.
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Burns, Adam, David Robert Bruce, Pauline Robbe, Adele Timbs, Basile Stamatopoulos, Ruth Clifford, Maria Lopopolo, Duncan Parkes, Kate E. Ridout, and Anna Schuh. "Detection of Clinically Relevant Molecular Alterations in Chronic Lymphocytic Leukemia (CLL) By Nanopore Sequencing." Blood 132, Supplement 1 (November 29, 2018): 1847. http://dx.doi.org/10.1182/blood-2018-99-110948.

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Abstract Introduction Chronic Lymphocytic Leukaemia (CLL) is the most prevalent leukaemia in the Western world and characterised by clinical heterogeneity. IgHV mutation status, mutations in the TP53 gene and deletions of the p-arm of chromosome 17 are currently used to predict an individual patient's response to therapy and give an indication as to their long-term prognosis. Current clinical guidelines recommend screening patients prior to initial, and any subsequent, treatment. Routine clinical laboratory practices for CLL involve three separate assays, each of which are time-consuming and require significant investment in equipment. Nanopore sequencing offers a rapid, low-cost alternative, generating a full prognostic dataset on a single platform. In addition, Nanopore sequencing also promises low failure rates on degraded material such as FFPE and excellent detection of structural variants due to long read length of sequencing. Importantly, Nanopore technology does not require expensive equipment, is low-maintenance and ideal for patient-near testing, making it an attractive DNA sequencing device for low-to-middle-income countries. Methods Eleven untreated CLL samples were selected for the analysis, harbouring both mutated (n=5) and unmutated (n=6) IgHV genes, seven TP53 mutations (five missense, one stop gain and one frameshift) and two del(17p) events. Primers were designed to amplify all exons of TP53, along with the IgHV locus, and each primer included universal tails for individual sample barcoding. The resulting PCR amplicons were prepared for sequencing using a ligation sequencing kit (SQK-LSK108, Oxford Nanopore Technologies, Oxford, UK). All IgHV libraries were pooled and sequenced on one R9.4 flowcell, with the TP53 libraries pooled and sequenced on a second R9.4 flowcell. Whole genome libraries were prepared from 400ng genomic DNA for each sample using a rapid sequencing kit (SQK-RAD004, Oxford Nanopore Technologies, Oxford, UK), and each sample sequenced on individual flowcells on a MinION mk1b instrument (Oxford Nanopore Technologies, Oxford, UK). We developed a bespoke bioinformatics pipeline to detect copy-number changes, TP53 mutations and IgHV mutation status from the Nanopore sequencing data. Results were compared to short-read sequencing data obtained earlier by targeted deep sequencing (MiSeq, Illumina Inc, San Diego, CA, USA) and whole genome sequencing (HiSeq 2500, Illumina Inc, San Diego CA, USA). Results Following basecalling and adaptor trimming, the raw data were submitted to the IMGT database. In the absence of error correction, it was possible to identify the correct VH family for each sample; however the germline homology was not sufficient to differentiate between IgHVmut and IgHVunmut CLL cases. Following bio-informatic error correction and consensus building, the percentage to germline homology was the same as that obtained from short-read sequencing and nanopore sequencing also called the same productive rearrangements in all cases. A total of 77 TP53 variants were identified, including 68 in non-coding regions, and three synonymous SNVs. The remaining 6 were predicted to be functional variants (eight missense and two stop-gains) and had all been identified in early MiSeq targeted sequencing. However, the frameshift mutation was not called by the analysis pipeline, although it is present in the aligned reads. Using the low-coverage WGS data, we were able to identify del(17p) events, of 19Mb and 20Mb length, in both patients with high confidence. Conclusions Here we demonstrate that characterization of the IgHV locus in CLL cases is possible using the MinION platform, provided sufficient downstream analysis, including error correction, is applied. Furthermore, somatic SNVs in TP53 can be identified, although similar to second generation sequencing, variant calling of small insertions and deletions is more problematic. Identification of del(17p) is possible from low-coverage WGS on the MinION and is inexpensive. Our data demonstrates that Nanopore sequencing can be a viable, patient-near, low-cost alternative to established screening methods, with the potential of diagnostic implementation in resource-poor regions of the world. Disclosures Schuh: Giles, Roche, Janssen, AbbVie: Honoraria.
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Dumschott, Kathryn, Maximilian H.-W. Schmidt, Harmeet Singh Chawla, Rod Snowdon, and Björn Usadel. "Oxford Nanopore sequencing: new opportunities for plant genomics?" Journal of Experimental Botany 71, no. 18 (May 27, 2020): 5313–22. http://dx.doi.org/10.1093/jxb/eraa263.

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Abstract DNA sequencing was dominated by Sanger’s chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.
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Leger, Adrien, and Tommaso Leonardi. "pycoQC, interactive quality control for Oxford Nanopore Sequencing." Journal of Open Source Software 4, no. 34 (February 28, 2019): 1236. http://dx.doi.org/10.21105/joss.01236.

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Dissertations / Theses on the topic "Oxford Nanopore sequencing"

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Shikh, Khaled Saad. "Sequencing the genomic DNA of Anodonta anatina using Oxford nanopore technology." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-18874.

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Freshwater mussels are members of phylum Mollusca, which live in freshwater habitats such as lakes and rivers. Freshwater mussels are essential ecologically in the aquatic ecosystems, they have a high capacity for water purification and play a significant role in calcium recycling. The genomic DNA of many freshwater mussels' species has not yet been sequenced. Knowledge of such a sequence can be useful in the development of a multi-biomarker panel to identify water pollution, and it also helps to develop a method to identify freshwater mussels' species according to their genomic DNA. This study aims to use nanopore sequencing technology to sequence the genomic DNA of Anodonta anatina, a species of freshwater mussel common in Europe. The DNA used in this experiment was extracted from the foot tissues, and two tissue homogenization methods were tested in this experiment to determine the best approach. The genomic DNA was sequenced by using Oxford nanopore MinION device, and the reads were assembled and polished using multiple software tools. The reads obtained from sequencing the DNA cover 3.5x of the estimated genome size of Anodonta anatina. 20x coverage is required for a complete genome assembly, and due to the low coverage, only a partial sequence of the genomic DNA was obtained during this experiment. This indicates that nanopore sequencing could be used to sequence the genome of freshwater mussels, but further sequencing runs are required to get enough coverage to assemble the whole genomic DNA.
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PINZAUTI, DAVID. "Implementation of a flexible Oxford Nanopore sequencing platform for microbial genomics." Doctoral thesis, Università di Siena, 2021. http://hdl.handle.net/11365/1138520.

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Oxford Nanopore sequencing technology is slowly revolutionising the entire microbiology field. Its ease of use and cost effective approaches coupled with long reads sequencing represent an essential and powerful tool. In the present thesis I have implemented a sequencing platform based on the Oxford Nanopore technology, a flexible system suitable for both research and diagnostic fields. The first part of my work was dedicated to the optimization of a DNA extraction protocol capable of isolating high molecular weight (HMW) genomic DNA. In fact, Nanopore sequencing readouts are highly influenced by both the quality and the integrity of the genomic DNA. An enzymatic lysis based extraction protocol was optimized, recovering HMW DNA from two strains of Streptococcus mitis and generating multiple ultra long reads (i.e. >100 Kb in length), making it possible to achieve complete genome assemblies. As the extraction protocol was mainly optimized for Gram-positive bacteria, it is also suitable to lyse the thinner cell wall of Gram-negatives. Oxford Nanopore Whole Genome Sequencing (WGS) approaches have enabled the complete genome sequencing and assembly of 16 Enterococcus faecalis isolates from clinical dental samples. Sequencing data provided enough information enabling i) population studies, defining genomic clusters based on isolates homologies; ii) bacterial profiling, assessing antimicrobial resistance genes and virulence traits; iii) comparative analysis, identifying genomic rearrangements and homologies based on synteny blocks. Finally, the platform was used for the monitoring of the ongoing SARS-CoV-2 pandemic. We have proposed a 900 bp amplicon sequencing protocol, adapted from the ARTIC sequencing protocol (https://artic.network/), enabling a near-complete genome assembly of SARS-CoV-2 strains, helping in the detection of nucleotide changes and monitoring the circulating viral lineages. In conclusion, the Oxford Nanopore sequencing platform can bring several improvements in the microbiology field, allowing i) complete genome assembly, ii) rapid microbial profiling, and iii) helping in the monitoring of local or global outbreaks.
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Murphy, Trevor. "Expanding the Knowledgebase of Earth’s Microbiome Using Culture Dependent and Independent Methods." OpenSIUC, 2021. https://opensiuc.lib.siu.edu/theses/2837.

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Microorganisms exist ubiquitously on Earth, yet their functions and ecological roles remain elusive. Investigating these microbes is accomplished by using culture-dependent and culture-independent methodologies. This study employs both methodologies to characterize: 1) the genomic potential of the novel deep-subsurface bacterial isolate Thermanaerosceptrum fracticalcis strain DRI-13T by combining next-generation and nanopore sequencing technologies and 2) the microbiome of the artificial marine environment for the Hawaiian Bobtail Squid in aquaculture using next-generation sequencing of 16S rRNA gene. Microbial ecology of the deep-subsurface remains understudied in terms of microbial diversity and function. The genomic information of DRI-13T revealed a potential for syntrophic relationships, diverse metabolic potential including prophages/antiviral defenses, and novel methylation motifs. Artificial marine environments housing marine the Hawaiian Bobtail Squid (Euprymna scolopes) contain microorganisms that can directly influence animal and aquaculture health. No studies presently show if bacterial communities of the tank environment correlate with the health and productivity of E. scolopes. This study sought to address this by sampling from a year of unproductive aquaculture yield and comparing the bacterial communities from productive cohorts. Bacterial communities from unproductive samples show less bacterial diversity and abundance coupled with shifts in bacterial composition. Nitrate and pH levels between the tanks were found to be strong influences on determining the bacterial populations of productive and unproductive cohorts.
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Lebó, Marko. "Přímá klasifikace metagenomických signálů ze sekvenace nanopórem." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2019. http://www.nusl.cz/ntk/nusl-400964.

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This diploma thesis deals with taxonomy independent methods for classification of metagenomic signals, aquired by a MinION sequencer. It describes the formation and character of metagenomic data and already existing methods of metagenomic data classification and their development. This thesis also evaluates an impact of the third generation sequencing techniques in the world of metagenomics and further specialises on the function of the Oxford Nanopore MinION sequencing device. Lastly, a custom method for metagenomic data classification, based on data obtained from a MinION sequencer, is proposed and compared with an already existing method of classification.
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Hunt, Spencer Philip. "Whole-Genome Assembly of Atriplex hortensis L. Using OxfordNanopore Technology with Chromatin-Contact Mapping." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/8580.

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Atriplex hortensis (2n = 2x = 18, 1C genome size ~1.1 gigabases), also known as garden orach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae family that has spread from its native Eurasia to other temperate and subtropical environments worldwide. Atriplex is a highly complex and polyphyletic genus of generally halophytic and/or xerophytic plants, some of which have been used as food sources for humans and animals alike. Although there is some literature describing the taxonomy and ecology of orach, there is a lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic position, and future potential of this species. Here, we report the assembly of the first highquality, chromosome-scale reference genome for orach cv. ‘Golden’. Sequence data was produced using Oxford Nanopore’s MinION sequencing technology in conjunction with Illumina short-reads and chromatin-contact mapping. Genome assembly was accomplished using the high-noise, single-molecule sequencing assembler, Canu. The genome is enriched for highly repetitive DNA (68%). The Canu assembly combined with the Hi-C chromatin-proximity data yielded a final assembly containing 1,325 scaffolds with a contig N50 of 98.9 Mb and with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-eight percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy and Copia-like LTRs. The annotation was completed using MAKER which identified 31,010 gene models and 2,555 tRNA genes. Completeness of the genome was assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) platform, which quantifies functional gene content using a large core set of highly conserved orthologous genes (COGs). Of the 1,375 plant-specific COGs in the Embryophyta database, 1,330 (96.7%) were identified in the Atriplex assembly. We also report the results of a resequencing panel consisting of 21 accessions which illustrates a high degree of genetic similarity among cultivars and wild material from various locations in North America and Europe. These genome resources provide vital information to better understand orach and facilitate future study and comparison.
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Cain, Elizabeth. "Targeted STR and SNP in-field sequencing by Oxford Nanopore MinION™ for the identification of an individual in a military scenario." Thesis, Cain, Elizabeth (2019) Targeted STR and SNP in-field sequencing by Oxford Nanopore MinION™ for the identification of an individual in a military scenario. Masters by Coursework thesis, Murdoch University, 2019. https://researchrepository.murdoch.edu.au/id/eprint/49630/.

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The requirement for DNA evidence in forensics has increased, meaning the demand for DNA typing has also increased. Current analytical processes for DNA evidence are known to be costly and time-consuming and traditionally occur at a centralised laboratory which can impact on the amount of time from sample collection to DNA profile generation. Therefore, research has focused on creating technologies that are capable of in-field analysis. Oxford Nanopore Technologies developed MinION™, a portable, cost-effective nanopore sequencer that is capable of in-field analysis. The development of in-field sequencing technologies is favourable for isolated and remote communities where traditional laboratory environments are not feasible. Furthermore, the development of these processes is favourable as backlogs and costs with traditional methods can be reduced. In-field sequencing also has the potential to be used in a range of disciplines including personal healthcare, pathogen identification and disaster victim identification. With the advancement of sequencing technologies research has also focused on how to increase the discriminatory power of DNA typing with the selection of alternative markers specific for human identification. This review will investigate current sequencing technologies and techniques as well as evaluating current targets for DNA analysis.
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Hu, Yue. "Microbial DNA Sequencing in Environmental Studies." Doctoral thesis, KTH, Skolan för bioteknologi (BIO), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-204897.

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The field of microbial ecology has just entered a new era of rapid technological development and generation of big data. The high-throughput sequencing techniques presently available provide an opportunity to extensively inventorize the blueprints of life. Now, millions of microbes of natural microbial communities can be studied simultaneously without prior cultivation. New species and new functions (genes) can be discovered just by mining sequencing data. However, there is still a tremendous number of microorganisms not yet examined, nor are the ecosystem functions these carry out. The modern genomic technologies can contribute to solve environmental problems and help us understand ecosystems, but to most efficiently do so, methods need to be continuously optimised.   During my Ph. D. studies, I developed a method to survey eukaryotic microbial diversity with a higher accuracy, and applied various sequencing-based approaches in an attempt to answer questions of importance in environmental research and ecology. In PAPER-I, we developed a set of 18S rRNA gene PCR primers with high taxonomic coverage, meeting the requirements of currently popular sequencing technologies and matching the richness of 18S rRNA reference sequences accumulated so far. In PAPER-II, we conducted the first sequencing-based spatial survey on the combined eukaryotic and bacterial planktonic community in the Baltic Sea to uncover the relationship of microbial diversity and environmental conditions. Here, the 18S primers designed in PAPER-I and a pair of broad-coverage 16S primers were employed to target the rRNA genes of protists and bacterioplankton for amplicon sequencing. In PAPER-III, we integrated metagenomic, metabarcoding, and metatranscriptomic data in an effort to scrutinise the protein synthesis potential (i.e., activity) of microbes in the sediment at a depth of 460 m in the Baltic Sea and, thus, disclosing microbial diversity and their possible ecological functions within such an extreme environment. Lastly, in PAPER-IV, we compared the performance of E. coli culturing, high-throughput sequencing, and portable real-time sequencing in tracking wastewater contamination in an urban stormwater system. From the aspects of cost, mobility and accuracy, we evaluated the usage of sequencing-based approaches in civil engineering, and for the first time, validated the real-time sequencing device in use within water quality monitoring.   In summary, these studies demonstrate how DNA sequencing of microbial communities can be applied in environmental monitoring and ecological research.

Yue Hu was supported by a scholarship from the China Scholarship Council (CSC #201206950024)

Yue Hu has been publishing papers under the name "Yue O. O. Hu".

QC 20170403

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Tu, Siang-Jyun, and 塗翔鈞. "Allele sequence reconstruction via Oxford Nanopore Technologies and Next Generation Sequencing." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/439rx7.

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碩士
國立交通大學
生物資訊及系統生物研究所
107
Pharmacogenomics is the research of genetic variants and drug response. It aims to reduce side-effect and increase treatment effect by modifying prescription according to genetic variants of the patient. The developments of polymerase chain reaction, PCR, and next-generation sequencing, NGS, improve researchers understanding about the relation in genetic variants and drug response. Moreover, the long read-length oxford nanopore technologies, ONT, facilitates the reconstruction of an allele of patients and makes identifying haplotype more efficiently. To develop precision medicine in Taiwan, the construction of a Taiwan population-based alleles database (HapTW) is important. The build processes including gene selection, primers design, well experiment practice, storage of sequencing data, full-length allele analysis system, database management system, external resources annotation system, and user-friendly interface. In this study, we implemented and designed a full-length allele reconstruction pipeline: HLA_ONTu, a type annotation system with IPD-IMGT/HLA database, a simulation tool: SimulationTOOLKIT and the database schema of HapTW. We choose three HLA Class I genes as examples to demonstrate this study.
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Dippenaar, A., S. N. Goossens, M. Grobbelaar, S. Oostvogels, B. Cuypers, K. Laukens, Conor J. Meehan, R. M. Warren, and Rie A. van. "Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities." 2021. http://hdl.handle.net/10454/18521.

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yes
The next-generation short-read sequencing technologies that generate comprehensive, whole-genome data with single-nucleotide resolution have already advanced tuberculosis diagnosis, treatment, surveillance and source investigation. Their high costs, tedious and lengthy processes, and large equipment remain major hurdles for research use in high tuberculosis burden countries and implementation into routine care. The portable next-generation sequencing devices developed by Oxford Nanopore Technologies (ONT) are attractive alternatives due to their long-read sequence capability, compact low-cost hardware, and continued improvements in accuracy and throughput. A systematic review of the published literature demonstrated limited uptake of ONT sequencing in tuberculosis research and clinical care. Of the 12 eligible articles presenting ONT sequencing data on at least one Mycobacterium tuberculosis sample, four addressed software development for long read ONT sequencing data with potential applications for M. tuberculosis. Only eight studies presented results of ONT sequencing of M. tuberculosis, of which five performed whole-genome and three did targeted sequencing. Based on these findings, we summarize the standard processes, reflect on the current limitations of ONT sequencing technology, and the research needed to overcome the main hurdles. Summary: The low capital cost, portable nature and continued improvement in the performance of ONT sequencing make it an attractive option for sequencing for research and clinical care, but limited data is available on its application in the tuberculosis field. Important research investment is needed to unleash the full potential of ONT sequencing for tuberculosis research and care.
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Book chapters on the topic "Oxford Nanopore sequencing"

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He, Ming, Xu Chi, and Jie Ren. "Applications of Oxford Nanopore Sequencing in Schizosaccharomyces pombe." In Methods in Molecular Biology, 97–116. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0868-5_9.

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Karamitros, Timokratis, and Gkikas Magiorkinis. "Multiplexed Targeted Sequencing for Oxford Nanopore MinION: A Detailed Library Preparation Procedure." In Methods in Molecular Biology, 43–51. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7514-3_4.

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Liu, Huanle, Oguzhan Begik, and Eva Maria Novoa. "EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing." In Methods in Molecular Biology, 31–52. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1374-0_3.

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Al Kadi, Mohamad, and Daisuke Okuzaki. "Unfolding the Bacterial Transcriptome Landscape Using Oxford Nanopore Technology Direct RNA Sequencing." In Methods in Molecular Biology, 269–79. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2996-3_19.

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Conference papers on the topic "Oxford Nanopore sequencing"

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Huang, Neng, Fan Nie, Peng Ni, Feng Luo, and Jianxin Wang. "An attention-based neural network basecaller for Oxford Nanopore sequencing data." In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8983231.

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Gribchenko, E. S. "The study of transcriptomes of symbiotic tissue of pea using the third-generation sequencing technology Oxford Nanopore." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.093.

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The transcriptome profiles the cv. Frisson mycorrhizal roots and inoculated nitrogen-fixing nodules were investigated using the Oxford Nanopore sequencing technology. A database of gene isoforms and their expression has been created.
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Кечин, А. А., М. А. Корюков, В. С. Боробова, and М. Л. Филипенко. "FEATURES OF MUTATION DETECTION IN LONG-READ WHOLE GENOME SEQUENCING DATA." In Сборник трудов XVIII Российской конференции "РАСПРЕДЕЛЕННЫЕ ИНФОРМАЦИОННО-ВЫЧИСЛИТЕЛЬНЫЕ РЕСУРСЫ". Crossref, 2023. http://dx.doi.org/10.25743/dir.2022.16.63.019.

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Технологии секвенирования третьего поколения позволяют идентифицировать не только точечные и короткие мутации, но и протяженные перестройки. В результате генерируется огромное количество данных, которое анализируется при помощи различных методов, в том числе машинного обучения. Целью работы стала отработка подходов к выявлению различных мутаций в данных полногеномного секвенирования технологией Oxford Nanopore. В результате были подобраны оптимальные параметры для BWA и minimap2 (картирование), Pisces (точечные мутации), Sniffles и Nanovar (крупные перестройки), а также сконструированы праймеры для валидации некоторых крупных перестроек. Third-generation sequencing technologies make it possible to identify not only point and short mutations, but also large rearrangements. Therefore, a huge amount of data is generated, which is analyzed using various methods, including machine learning. The aim of the study was to develop approaches to identifying various mutations in Oxford Nanopore sequencing data. As a result, optimal parameters were selected for BWA and minimap2 (mapping), Pisces (point mutations), Sniffles and Nanovar (large rearrangements), and primers were designed to validate some large rearrangements.
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Amin, Mohammad Ruhul, Steven Skiena, and Michael C. Schatz. "NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads." In 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2016. http://dx.doi.org/10.1109/iccabs.2016.7802776.

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Boughattas, Sonia, Dana Al Batesh, Bruno Giraldes, Asmaa Al-Thani, and Fatiha Benslimane. "Optimized DNA Extracting Method for Oxford Nanopore- Long reads Sequencing from Marine samples." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0136.

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Sustaining social and economic growth is impossible without a holistic environmental vision that places environmental preservation for Qatar’s future generations at the forefront. According to the Ministry of Development and Planning and Statistics, the Qatar National Vision (QNV) 2030 aims to direct Qatar towards a balance between developmental needs and the protection of its natural environment, whether land, sea or air. As such, the QNV 2030 includes an emphasis on establishing environmental institutions that can serve as the guardians of Qatar’s environmental heritage. The QNV 2030 also emphasizes the importance of increasing citizens’ awareness of their role in protecting the country’s environment for their children and the nation’s future generations. The State of Qatar has chosen to pursue the path of sustainable development, making it the focus of the Qatar National Development Strategy. Given the large-scale industrialization and the limited land availability, the urban environment will be crucial in maintaining native species. The presence of heavy petrochemical firms in Qatar necessitates stressing on researches related to biomonitoring of environmental ecosystem with the aim to understand and provide impactful solution for different environmental challenges affecting Qatari health, and damages to local ecosystem. Due to the extreme temperatures and salinities in the Gulf region, the national biodiversity has adapted to survive under extreme conditions. Furthermore, the barriers that isolate the Arabian Gulf have created an environment that is rich with endemic species that are specific to the region. As such, this project aimed to cover the gap in the genomic analysis of Qatar’s rich environment. The goal was to decipher the genetic background of different animal species, marine and environmental species specific to the Qatari environmental landscape that has been previously described by Qatar University’s environmental science center. The study also deciphered the microflora in marine environment that is an important building block of the environment and an indicator of its richness. The outcome from this study is to help in preservation of important species in Qatar and will guide the establishment of a national genomic habitat platform in Qatar
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"Whole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-037.

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"Applicability of the Oxford Nanopore sequencing technology to the analysis of DNA modifications." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-118.

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Hess, A., A. Caulton, R. Clarke, R. Brauning, K. McRae, and S. Clarke. "253. Expanding the genomic toolkit: what does Oxford Nanopore sequencing have to offer?" In World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_253.

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9

Benslimane, Fatiha M., Hebah Al Khatib, Dana Albatesh, Ola Al-Jamal, Sonia Boughattas, Asmaa A. Althani, and Hadi M. Yassine. "Nanopore Sequencing SARS-CoV-2 Genome in Qatar." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0289.

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Background: The current pandemic, COVID-19, is cause by an RNA Coronavirus that was recently identified as SARS-CoV-2. RNA viruses tend to have a high mutation rate; the rate is around a million times greater than that of their hosts. The mutagenic potential of the virus depends on many factors, including the fidelity of nucleic acid-replicating viral enzymes, such as SARSCoV-2 RNA dependent RNA polymerase (RdRp). The rate of mutation drives viral evolution and genome variability, consequently allowing viruses to escape the immunity of the host and develop resistance to drugs. Therefore, the characterization of SARS-CoV-2 variants might lead to implement better therapeutics treatments, vaccines design and identify new diagnostics approaches. Aim: The aim of this study was to establish a fast sequencing method to identify SARS-CoV-2 mutations in Qatar. This will help to assess if there are new viral variants that are spreading in country. Methods: RNA was isolated from samples collected from Qatar COVID-19 positive patients. The Artic Network V3 primer scheme and Oxford Nanopore ligation sequencing kit were used to prepare the sequencing libraries. Libraries were loaded on to R9.4.1 flow cells and ran on a GridION. Bioinformatics analysis was done following the Artic Network SARA-CoV-2 bioinformatics tools. Results: Genome coverage of sequenced samples was >80% and the depth was average at 200x. The coverage was highly dependable on sample viral load; samples of CT value lower than 30 resulted in better sequence coverage. The sequenced genomes were deposited in GISAID and were mainly clustering with genomes deposited from the UK. Sequences were compared to Illumina and sanger sequences and they showed compatible results. Conclusion: The use of ONT to sequence SARA-CoV-2 is a quick, affordable, and reliable technique to determine viral mutation. Using this technique, the first sequences from Qatar were deposited in to GISAID. Up to date, 700 genomes have been sequenced from Qatari samples.
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De Block, T., I. De Baetselier, S. Abdellati, J. Laumen, S. Manoharan-Basil, C. Kenyon, and D. Van den Bossche. "P207 Evaluation of Oxford Nanopore MinION sequencing to predict antimicrobial resistance profiles in clinical N. gonorrhoeae strains." In Abstracts for the STI & HIV World Congress, July 14–17 2021. BMJ Publishing Group Ltd, 2021. http://dx.doi.org/10.1136/sextrans-2021-sti.296.

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