Journal Français d Ophtalmologie, Journal Year: 2025, Volume and Issue: 48(5), P. 104509 - 104509
Published: April 6, 2025
Language: Английский
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Aug. 20, 2024
ABSTRACT Nanopore sequencing, a third-generation sequencing technology, has revolutionized the gene industry with its advantages of long reads, fast speed, real-time and analysis, potential in detecting base modifications. This technology allows researchers to sequence longer DNA fragments single read, providing more comprehensive genomic information compared previous methods. operates on electrical signals generated by nanopore embedded membrane separating two electrolyte-filled chambers. When single-stranded (ssDNA) passes through nanopore, it creates variations current that correspond different bases. By analyzing these fluctuations machine learning algorithms, can be determined. In this study, we introduced several improvements including local chemistry novel motor pore proteins, chip design, basecalling algorithms. Our new platform, CycloneSEQ, demonstrated long-duration (107 hours) high yield (>50 Gb). human CycloneSEQ was able produce reads N50 33.6 kb modal identity 97.0%. Preliminary findings whole-genome de novo assembly, variant calling, metagenomics single-cell RNA have further highlighted CycloneSEQ’s across areas genomics.
Language: Английский
Citations
6
The American Journal of Human Genetics, Journal Year: 2023, Volume and Issue: 110(11), P. 1832 - 1840
Published: Nov. 1, 2023
Language: Английский
Citations
13
JCO Precision Oncology, Journal Year: 2024, Volume and Issue: 8
Published: Jan. 11, 2024
Greater collaboration needed to realize potential of molecular profiling initiatives for pediatric cancers.
Language: Английский
Citations
5
Metabarcoding and Metagenomics, Journal Year: 2024, Volume and Issue: 8
Published: May 29, 2024
Oxford Nanopore Technologies has recently launched a duplex sequencing strategy and announced an improved error rate which is in similar order of magnitude as Illumina sequencing. We therefore conducted pilot study to assess whether potential be used technology eDNA-based marine biomonitoring. Specifically, we investigated bacterial communities sediment samples collected from Atlantic salmon ( Salmo salar ) aquaculture installations compared the ecological trends obtained short (V3-V4 region 16S rRNA gene) long (full length sequence reads. The amplicon reads with Phred score ≥ 30 was 36%, notably higher previous reports genome When inferring alpha- beta-diversity ASVs OTUs, found highly congruent patterns. Only when collating OTUs across taxonomic ranks, analyses Illumina-data slightly changed, due difficulties assign taxonomy While on family rank, both datasets had good agreement, genus-assignments data were critical, resulting disagreement between two protocols. Our provide evidence that monitoring aquaculture-related environmental impacts could equally well discuss what extent biomonitoring benefit long-read information.
Language: Английский
Citations
5
FEBS Open Bio, Journal Year: 2024, Volume and Issue: 14(11), P. 1779 - 1787
Published: Aug. 7, 2024
Amplicon sequencing has long served as a robust method for characterising microbial communities, and despite inherent resolution limitations, it remains preferred technique, offering cost‐ time‐effective insights into bacterial compositions. Here, we introduce ONT‐AmpSeq, user‐friendly pipeline designed processing amplicon data generated from Oxford Nanopore Technology (ONT) devices. Our enables efficient creation of taxonomically annotated operational taxonomic unit (OTU) tables ONT data, with the flexibility to multiplex amplicons on same barcode. The encompasses six main steps—statistics, quality filtering, alignment, clustering, polishing, classification—integrating various state‐of‐the‐art software tools. We provide detailed description each step, along performance tests robustness evaluations using both test ZymoBIOMICS ® Microbial Community Standard mock community dataset. results demonstrate ability ONT‐AmpSeq effectively process valuable composition. Additionally, discuss influence polishing tools insight impact annotation methods derived Overall, represents comprehensive solution analysing facilitating streamlined reliable analysis. pipeline, is freely available public use.
Language: Английский
Citations
4
Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15
Published: Aug. 13, 2024
Accurate and timely diagnosis of plant viral infections plays a key role in effective disease control maintaining agricultural productivity. Recent advances the viruses have significantly expanded our ability to detect monitor pathogens crops. This review discusses latest diagnostic technologies, including both traditional methods innovations. Conventional such as enzyme-linked immunosorbent assay DNA amplification-based assays remain widely used due their reliability accuracy. However, diagnostics next-generation sequencing CRISPR-based detection offer faster, more sensitive specific virus detection. The highlights main advantages limitations systems conventional methods, biosensor technologies advanced sequence-based techniques. In addition, it also effectiveness commercially available tools challenges facing modern techniques well future directions for improving informed management strategies. Understanding features methodologies would enable stakeholders choose optimal strategies against threats ensure global food security.
Language: Английский
Citations
4
Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 2, 2025
Nanopores are promising sensors for glycan analysis with the accurate identification of complex glycans laying foundation nanopore-based sequencing. However, their applicability toward continuous sequencing has not yet been demonstrated. Here, we present a proof-of-concept by combining nanopore technology glycosidase-hydrolyzing reactions. By continuously monitoring changes in characteristic current generated translocation hydrolysis products through nanopore, sequence can be accurately identified based on specificity glycosidases. With machine learning, improved accuracy to over 98%, allowing reliable determination consecutive building blocks and glycosidic linkages chains while reducing need operator expertise. This approach was validated real samples, calibrated using hydrophilic interaction chromatography-high-performance liquid chromatography (HILIC-HPLC) mass spectrometry (MS). We achieved ten units natural chains, which provided first evidence feasibility nanopore-glycosidase-compatible system Compared traditional methods, this strategy enhances efficiency 5-fold. Additionally, introduced concept 'inverse sequencing', focuses electrical signal rather than monosaccharide identification. eliminates reliance fingerprint libraries typically required putative 'forward hydrolysis' strategies. When challenges both inverse strategies' addressed, will pave way establishing at single-molecule level.
Language: Английский
Citations
0
Computational and Structural Biotechnology Journal, Journal Year: 2025, Volume and Issue: 27, P. 440 - 450
Published: Jan. 1, 2025
Biological information is encoded in a sequence of biochemical molecules such as nucleic acids and amino acids, nanopore sequencing long-read technology capable directly decoding these into human-readable signals. The long reads from offer the advantage obtaining contiguous information, which particularly beneficial for complex or repetitive regions genome. In this study, we investigated efficacy biological distinctive genomes metagenomic samples, pose significant challenges traditional short-read technologies. Specifically, sequenced blood fecal samples mice infected with Trypanosoma brucei, unicellular protozoan known its hypervariable dynamic that help it evade host immunity. Such characteristics are also prevalent other host-dependent parasites, bacteriophages. taxonomic classification results showed high proportion identified T. brucei no identification control samples. Furthermore, de novo assembly yielded contigs mapped to reference genome over 96 % accuracy. This exploratory work demonstrates potential challenging task classifying assembling
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 15, 2025
ABSTRACT The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had a profound global impact since its emergence in late 2019. Characterized wide spectrum of clinical manifestations, ranging from asymptomatic infection to distress and death, necessitated extensive research into host-pathogen interactions that drive disease progression. Understanding molecular mechanisms underlying host response SARS-CoV-2 is crucial for development effective therapeutic interventions preventative strategies. This study employed multi-omic approach combined direct RNA sequencing (DRS) Illumina cDNA investigate whole blood transcriptomic profiles patients. By leveraging unique capabilities Nanopore DRS, which provides long-read data, we were able capture not only gene expression levels but also modifications, including poly(A) tail length, non-adenine residue (non-A), pseudouridylation (psU), 5-methylcytosine (m5C) methylation. comprehensive analysis allowed us identify differentially expressed genes (DEGs) explore these modifications on function within context COVID-19. Our findings reveal significant alterations patterns, lengths, non-A prevalence psU m5C patients compared healthy controls. These results provide valuable insights complex interplay between viral infection, immune response, processing, contributing deeper understanding pathogenesis.
Language: Английский
Citations
0
Published: Jan. 1, 2025
Language: Английский
Citations
0