Unveiling microbial diversity: harnessing long-read sequencing technology

Nature Methods, Journal Year: 2024, Volume and Issue: 21(6), P. 954 - 966

Published: April 30, 2024

Language: Английский

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Nanopore sequencing: flourishing in its teenage years

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

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A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(7), P. 1366 - 1370

Published: June 27, 2024

Language: Английский

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The landscape of genomic structural variation in Indigenous Australians

Nature, Journal Year: 2023, Volume and Issue: 624(7992), P. 602 - 610

Published: Dec. 13, 2023

Abstract Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal Torres Strait Islander ancestries are historically under-represented in genomics research almost completely missing from reference datasets 1–3 . Addressing this representation gap is critical, both to advance our understanding of global human diversity as a prerequisite for ensuring equitable outcomes medicine. Here we apply population-scale whole-genome long-read sequencing 4 profile structural variation across four remote communities. We uncover an abundance large insertion–deletion variants (20–49 bp; n = 136,797), (50 b–50 kb; 159,912) regions variable copy number (>50 156). The majority composed tandem repeat or interspersed mobile element sequences (up 90%) have not been previously annotated 62%). A fraction appear be exclusive (12% lower-bound estimate) most these found only single community, underscoring the need broad deep sampling achieve comprehensive catalogue Australian continent. Finally, explore short repeats throughout genome characterize allelic at 50 known disease loci 5 , hundreds novel expansion sites within protein-coding genes, identify patterns constraint among sequences. Our study sheds new light on dimensions dynamics beyond Australia.

Language: Английский

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Simulation of nanopore sequencing signal data with tunable parameters

Genome Research, Journal Year: 2024, Volume and Issue: 34(5), P. 778 - 783

Published: May 1, 2024

In silico simulation of high-throughput sequencing data is a technique used widely in the genomics field. However, there currently lack effective tools for creating simulated from nanopore devices, which measure DNA or RNA molecules form time-series current signal data. Here, we introduce Squigulator, fast and simple tool realistic Squigulator takes reference genome, transcriptome, read sequences, generates corresponding raw This compatible with basecalling software Oxford Nanopore Technologies (ONT) other third-party tools, thereby providing useful substrate development, testing, debugging, validation, optimization at every stage analysis workflow. The user may generate preset parameters emulating specific ONT protocols noise-free “ideal” data, they deterministically modify range experimental variables and/or noise to shape their needs. We present brief example Squigulator's use, model degree different impact accuracy downstream variant detection. reveals new insights into nature algorithms. provide as an open-source community.

Language: Английский

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Targeted Long‐Read Sequencing as a Single Assay Improves the Diagnosis of Spastic‐Ataxia Disorders

Annals of Clinical and Translational Neurology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

ABSTRACT Objective The hereditary spastic‐ataxia spectrum disorders are a group of disabling neurological diseases. traditional genetic testing pathway is complex, multistep and leaves many cases unsolved. We aim to streamline improve this process using long‐read sequencing. Methods developed targeted sequencing strategy with the capacity characterise variation all types sizes within 469 disease‐associated genes, in single assay. applied cohort 34 individuals unsolved spastic‐ataxia. An additional five known diagnosis were included as positive controls. Results identified causative pathogenic variants that would be sufficient for 14/34 (41%) participants. success rate was 5/11 (45%) those who naïve 9/23 (39%) undiagnosed after prior testing, completed on clinical basis. Short tandem repeat expansions FGF14 most common (7/34, 21%). Two (2/34, 6%) had biallelic RFC1 one individual monoallelic expansion ATXN8OS / ATXN8 . Causative sequence other than short found four individuals, including VCP , STUB1 ANO10 SPG7 Furthermore, controls identified. Interpretation Our results demonstrate utility evaluation patients disorders, highlighting both increase overall diagnostic yield by capturing causes

Language: Английский

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Flexible and efficient handling of nanopore sequencing signal data with slow5tools

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 6, 2023

Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools , an intuitive toolkit handling SLOW5 format. Slow5tools enables lossless conversion range tools interacting files. uses multi-threading, multi-processing, other engineering strategies to achieve fast manipulation, including live FAST5-to-SLOW5 during sequencing. provide examples benchmarking experiments illustrate usage, describe the principles underpinning its performance.

Language: Английский

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LINE-1 retrotransposons contribute to mouse PV interneuron development

Nature Neuroscience, Journal Year: 2024, Volume and Issue: 27(7), P. 1274 - 1284

Published: May 21, 2024

Abstract Retrotransposons are mobile DNA sequences duplicated via transcription and reverse of an RNA intermediate. Cis -regulatory elements encoded by retrotransposons can also promote the adjacent genes. Somatic LINE-1 (L1) retrotransposon insertions have been detected in mammalian neurons. It is, however, unclear whether L1 only some neuronal lineages or therein neurodevelopmental gene expression. Here we report programmed activation SOX6, a factor critical for parvalbumin (PV) interneuron development. Mouse PV interneurons permit mobilization vitro vivo, harbor unmethylated promoters express full-length mRNAs proteins. Using nanopore long-read sequencing, identify L1s proximal to genes, including novel promoter-driven Caps2 transcript isoform that enhances neuron morphological complexity vitro. These data highlight contribution made cis development transcriptome diversity, uncovered due mobility this milieu.

Language: Английский

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Nanopore Sequencing Technology as an Emerging Tool for Diversity Studies of Plant Organellar Genomes

Diversity, Journal Year: 2024, Volume and Issue: 16(3), P. 173 - 173

Published: March 7, 2024

In this comprehensive review, we explore the significant role that nanopore sequencing technology plays in study of plant organellar genomes, particularly mitochondrial and chloroplast DNA. To date, application has led to successful over 100 genomes around 80 genomes. These figures not only demonstrate technology’s robustness but also mark a substantial advancement field, highlighting its efficacy decoding complex dynamic nature these Nanopore sequencing, known for long-read capabilities, significantly surpasses traditional techniques, especially addressing challenges like structural complexity sequence repetitiveness This review delves into nuances elaborating on benefits compared conventional methods groundbreaking applications it fostered genomics. While transformative impact is clear, limitations, including error rates computational requirements, are discussed, alongside potential solutions prospects technological refinement.

Language: Английский

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Trends and characteristics of multidrug-resistant MRSA in Norway 2008-2020

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: May 9, 2025

Infections caused by multidrug-resistant (MDR) bacteria are recognized as a critical One Health concern which poses significant threat to public health, leading increased morbidity and mortality across both high- low-income countries. In this study, we investigated the epidemiology molecular mechanisms of methicillin-resistant Staphylococcus aureus (MDR-MRSA) strains identified in Norway from 2008 2020, order gain better understanding evolution dissemination multidrug resistance S. . A total 452 MDR-MRSA isolated 429 individuals were analyzed dataset 23,412 MRSA strains. Methods included epidemiological characterization, antimicrobial susceptibility testing (AST), genetic analysis selection using nanopore sequencing identify (AMR) genes mutations, well their location on plasmids, SCC mec other mobile elements (MGEs). The study revealed an overall increasing trend strains, with healthcare-associated being more prevalent among compared population. Significant heterogeneity spa -types clonal complexes exhibiting was observed, high rates against multiple antibiotic groups, particularly erythromycin, ciprofloxacin/norfloxacin, tetracycline, gentamicin, clindamycin addition cefoxitin. predominant clones t1476/CC8, t127/CC1, t189/CC188, t030, t037/CC239. Among these, t1476/CC8 showed upward toward conclusion period, indicating emergence clone. broad range AMR mutations detected, linked wide variety MGEs, highlighting complex development within This highlights rising challenge posed reveals multifactorial nature , thus emphasizing importance continued surveillance, stewardship infection control measures, global cooperation, combat spread these pathogens.

Language: Английский

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