Sekwencjonowanie Nanoporowe I Jego Zastosowanie W Biologii

Żmieńko, Agnieszka; Satyr, Anastasiia

doi:10.18388/pb.2020_328

Cited by 6 publications

(8 citation statements)

References 57 publications

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“…Electrodes are set at both ends of the nanopore sequencer to form a stable electric field. Nucleic acids (including DNA and RNA) will move to the nanopores under the action of an electric field in the nanopore sequencer 31–34 . The process of nucleic acid molecules passing through the nanopores is pulled by motor proteins, which can control the speed of nucleic acid passing through the nanopore 2 .…”

Section: Molecular Mechanisms Of Nanopore Sequencingmentioning

confidence: 99%

Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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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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Section: Molecular Mechanisms Of Nanopore Sequencingmentioning

confidence: 99%

Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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“…Third-generation sequencing (TGS) is proved to be a newly and improved sequencing technology, which can access in-depth the splicing regulation, enhance the RNA isoforms' characterisation and predict more comprehensive gene expression diversity. 178,179 In addition, traditional methods determine the DEGs owing to the analyses of whole-tissue samples, but the contribution of individual cell populations are unknown. Single-cell RNA sequencing (scRNA-seq) including genomics, transcriptomics, proteomics, epigenomics and metabolomics sequencing, can successfully resolve this problem and directly measure molecular signatures in thousands to millions of individual cells, which provides us an opportunity to uncover the mysteries underlying cellular populations.…”

Section: Future Perspectivesmentioning

confidence: 99%

“…Third, the revolution of genome‐wide analyses of gene expression alternations and AS events is continuing after the successful applications of microarrays and NGS technology. Third‐generation sequencing (TGS) is proved to be a newly and improved sequencing technology, which can access in‐depth the splicing regulation, enhance the RNA isoforms’ characterisation and predict more comprehensive gene expression diversity 178,179 . In addition, traditional methods determine the DEGs owing to the analyses of whole‐tissue samples, but the contribution of individual cell populations are unknown.…”

Section: Future Perspectivesmentioning

confidence: 99%

Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives

Zou,

Zan,

Jia

et al. 2023

Clinical & Translational Med

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BackgroundAlternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD).MethodsOur review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next‐generation sequencing (NGS) for AS events in IBD have been also discussed.ResultsAvailable evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis‐associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro‐fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third‐generation sequencing (TGS), single‐cell RNA sequencing (scRNA‐seq) and spatial transcriptomics (ST), will be desired with great expectations.ConclusionsTo our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.

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“…A nanopore sequencer is with an array containing thousands of sequencing units, which is composed of a reader, motor and tether protein; it determines the sequence of a target molecule (DNA, RNA or peptide) by analyzing the changes in electronic current (squiggle) when the molecule passes through the unit [ 1–3 ]. Oxford nanopore sequencers, such as MinION or PromethION, have recently been applied in biomedical research, especially clinical microbiological studies [ 4–6 ].…”

Section: Introductionmentioning

confidence: 99%

NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing

Lin,

Zhang,

Sun

et al. 2023

Briefings in Bioinformatics

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Nanopore sequencers can enrich or deplete the targeted DNA molecules in a library by reversing the voltage across individual nanopores. However, it requires substantial computational resources to achieve rapid operations in parallel at read-time sequencing. We present a deep learning framework, NanoDeep, to overcome these limitations by incorporating convolutional neural network and squeeze and excitation. We first showed that the raw squiggle derived from native DNA sequences determines the origin of microbial and human genomes. Then, we demonstrated that NanoDeep successfully classified bacterial reads from the pooled library with human sequence and showed enrichment for bacterial sequence compared with routine nanopore sequencing setting. Further, we showed that NanoDeep improves the sequencing efficiency and preserves the fidelity of bacterial genomes in the mock sample. In addition, NanoDeep performs well in the enrichment of metagenome sequences of gut samples, showing its potential applications in the enrichment of unknown microbiota. Our toolkit is available at https://github.com/lysovosyl/NanoDeep.

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Sekwencjonowanie Nanoporowe I Jego Zastosowanie W Biologii

Cited by 6 publications

References 57 publications

Nanopore sequencing technology and its applications

Nanopore sequencing technology and its applications

Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives

NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing

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