An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations

MacKenzie, Morgan; Argyropoulos, Christos

doi:10.20944/preprints202301.0323.v1

Cited by 9 publications

(1 citation statement)

References 92 publications

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“…Nanopores are nanoscale pores that allow the passage of biomolecules through them. By functionalizing beads with capture molecules and introducing them into a nanopore system, the binding events between the target biomarker and the capture molecule can be detected based on changes in ionic current or impedance [66]. An electrical biosensing method is established using synthetic nanopores and nanochannels integrated into fluidic devices for versatile analyte detection through size calibrations.…”

Section: Integration With Microfluidics and Nanotechnologymentioning

confidence: 99%

Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection

Cheng,

Yang,

Wang

et al. 2024

Sensors

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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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Section: Integration With Microfluidics and Nanotechnologymentioning

confidence: 99%

Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection

Cheng,

Yang,

Wang

et al. 2024

Sensors

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Deciphering the Cell-Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish

Lin,

Wang,

Liu

et al. 2024

Preprint

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Cell fate determination during early embryonic development is a complex process modulated by gene expression. The intricate interplay of transcriptional and post-transcriptional regulation is integral to the developmental trajectory of embryogenesis, yet how RNA processing may contribute to early development programming is largely elusive. Leveraging recent technological advances in single-molecule nanopore sequencing, we developed a single-cell long-read transcriptome sequencing technology, allowing a clear view of transcript diversity during zebrafish embryogenesis during pre- and post-zygotic genome activation (ZGA). A closer examination of the dynamic transcript usage and potential alternative splicing revealed that abundant stage-specific transcripts with differential coding potentials are involved in distinct biological functions. Specifically, we identified two cell populations at the onset of ZGA based on isoform diversity instead of gene profiling, which followed divergent developmental trajectories toward the ectoderm and the presumptive ectoderm. These two populations of cells were characterized by divergent splicing regulations linked to differential RNA-binding proteins, including SNRPA and SFPQ. Altogether, using the single-cell long-read transcriptome sequencing strategy, we work has revealed the cell-specific transcriptome dynamics contributing to the cell fate determination during embryogenesis.

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Sequencing, Fast and Slow: Profiling Microbiomes in Human Samples with Nanopore Sequencing

Park,

Lee,

Shim

2023

Applied Biosciences

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Rapid and accurate pathogen identification is crucial in effectively combating infectious diseases. However, the current diagnostic tools for bacterial infections predominantly rely on century-old culture-based methods. Furthermore, recent research highlights the significance of host–microbe interactions within the host microbiota in influencing the outcome of infection episodes. As our understanding of science and medicine advances, there is a pressing need for innovative diagnostic methods that can identify pathogens and also rapidly and accurately profile the microbiome landscape in human samples. In clinical settings, such diagnostic tools will become a powerful predictive instrument in directing the diagnosis and prognosis of infectious diseases by providing comprehensive insights into the patient’s microbiota. Here, we explore the potential of long-read sequencing in profiling the microbiome landscape from various human samples in terms of speed and accuracy. Using nanopore sequencers, we generate native DNA sequences from saliva and stool samples rapidly, from which each long-read is basecalled in real-time to provide downstream analyses such as taxonomic classification and antimicrobial resistance through the built-in software (<12 h). Subsequently, we utilize the nanopore sequence data for in-depth analysis of each microbial species in terms of host–microbe interaction types and deep learning-based classification of unidentified reads. We find that the nanopore sequence data encompass complex information regarding the microbiome composition of the host and its microbial communities, and also shed light on the unexplored human mobilome including bacteriophages. In this study, we use two different systems of long-read sequencing to give insights into human microbiome samples in the ‘slow’ and ‘fast’ modes, which raises additional inquiries regarding the precision of this novel technology and the feasibility of extracting native DNA sequences from other human microbiomes.

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An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations

Cited by 9 publications

References 92 publications

Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection

Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection

Deciphering the Cell-Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish

Sequencing, Fast and Slow: Profiling Microbiomes in Human Samples with Nanopore Sequencing

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