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Clinical research

Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment

A pentanucleotide TTTCA repeat insertion into a polymorphic TTTTA repeat element in SAMD12 causes benign adult familial myoclonic epilepsy.

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ECNano: a cost-effective workflow for target enrichment sequencing and accurate variant calling on 4,800 clinically significant genes using a single MinION flowcell

Background: The application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field.

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The GGC repeat expansion in NOTCH2NLC is associated with oculopharyngodistal myopathy type 3

Oculopharyngodistal myopathy (OPDM) is an adult-onset neuromuscular disease characterized by progressive ocular, facial, pharyngeal and distal limb muscle involvement.

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Alpha satellite insertions and the evolutionary landscape of centromeres

Human centromeres are composed of alpha satellite DNA hierarchically organized as higher-order repeats and epigenetically specified by CENP-A binding. Current evolutionary models assert that new centromeres are first epigenetically established and subsequently acquire an alphoid array.

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Long-read sequencing improves the detection of structural variations impacting complex non-coding elements of the genome

The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases.

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Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole genome sequencing

Background

During the SARS-CoV-2 pandemic, healthcare workers (HCWs) are exposed to infection both at work and in their communities. Determining where HCWs might have been infected is challenging based on epidemiological data alone.

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Emergence of a hypervirulent carbapenem-resistant Klebsiella pneumoniae co-harbouring a blaNDM-1-carrying virulent plasmid and a blaKPC-2-carrying plasmid in an Egyptian Hospital

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Egyptian hospitals has been reported. However, the genetic basis and the analysis of the plasmids associated with CR-hypervirulent-KP (CR-HvKP) in Egypt are not presented.

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First report of an extensively drug-resistant ST23 Klebsiella pneumoniae of capsular serotype K1 co-producing CTX-M-15, OXA-48 and ArmA in Spain

An extensively drug-resistant (XDR) Klebsiella pneumoniae isolate MS3802 from a tracheostomy exudate was whole-genome sequenced using MiSeq and Oxford Nanopore MinION platforms in order to identify the antimicrobial resistance and virulence determinates and their genomic context.

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How the replication and transcription complex of SARS-CoV-2 functions in leader-to-body fusion

Background Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

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IsoTV: processing and visualizing functional features of translated transcript isoforms

Despite the continuous discovery of new transcript isoforms, fueled by the recent increase in accessibility and accuracy of long-read RNA sequencing data, functional differences between isoforms originating from the same gene often remain obscure.

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A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

Metagenomic next-generation sequencing (mNGS) holds promise as a diagnostic tool for unbiased pathogen identification and precision medicine. However, its medical utility depends largely on assay simplicity and reproducibility.

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Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis

Background

Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative.

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High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells

Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years.

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Nanopore Flongle sequencing as a rapid, single specimen clinical test for fusion detection

The identification of gene fusions is a cornerstone of diagnosis and treatment decision making for tumors of many forms and primary sites.

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Genomic characterisation of a multidrug-resistant Escherichia coli strain carrying the mcr-1 gene recovered from a paediatric patient in China

Objectives

The global spread of carbapenem-resistant Enterobacterales is a leading public-health threat. Lack of effective treatment has resulted in use of colistin as a last-resort therapeutic option for multidrug-resistant (MDR) bacterial infections.

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Promoting axon regeneration by enhancing the non-coding function of the injury-responsive coding gene Gpr151

Gene expression profiling in response to nerve injury has been mainly focused on protein functions of coding genes to understand mechanisms of axon regeneration and to identify targets of potential therapeutics for nerve repair.

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Molecular characterization of vancomycin-resistant Enterococcus faecium isolates collected from the Dallas, Texas area

Molecular characterization was performed for 46 vancomycin-resistant E. faecium (VREfm) isolates and one vancomycin-sensitive comparator obtained during routine fecal surveillance of high-risk patients from a Dallas, Texas area hospital system.

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Ancient migrations - The first complete genome assembly, annotation and variants of the Zoroastrian-Parsi community of India

With the advent of Next Generation Sequencing, many population specific whole genome sequences published thus far, predominantly represent individuals of European ancestry.

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Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance.

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Rampant prophage movement among transient competitors drives rapid adaptation during infection

Interactions between bacteria, their close competitors, and viral parasites are common in infections but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes.

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MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution

Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolution given the read-length limitations of next-generation sequencing platforms.

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Molecular characterisation of the first New Delhi metallo-β-lactamase 1-producing Acinetobacter baumannii from Tanzania

Background

We aimed to characterise the genetic determinants and context of two meropenem-resistant clinical isolates of Acinetobacter baumannii isolated from children hospitalised with bloodstream infections in Dar es Salaam, Tanzania.

Methods

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Haploflow: Strain-resolved de novo assembly of viral genomes

In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm.

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Genomic diversity and antimicrobial resistance of Haemophilus colonising the airways of young children with cystic fibrosis

Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF, h

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Dissemination of NDM-producing Klebsiella pneumoniae and Escherichia coli high-risk clones in Catalan healthcare institutions

Objectives

To characterize the clonal spread of carbapenem-resistant Klebsiella pneumoniae and Escherichia coli isolates between different healthcare institutions in Catalonia, Spain.

Methods

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Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus

Background: In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications.

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Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy

Background Analysis of vector integration sites in gene-modified cells can provide critical information on clonality and potential biological impact on nearby genes.

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Oxford nanopore sequencing in clinical microbiology and infection diagnostics

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting.

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A novel blaCTX-M-65-harboring IncHI2 plasmid pE648CTX-M-65 isolated from a clinical extensively-drug-resistant Escherichia coli ST648

Background: An ESBL, carbapenemase- and MCR-1-producing Escherichia coli ST648 strain was isolated from the urine sample of a patient in a Chinese tertiary hospital in 2016.

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Template switching mechanism drives the tandem amplification of chromosome 20q11.21 in human pluripotent stem cells

Copy number variants (CNVs) are genomic rearrangements implicated in numerous congenital and acquired diseases, including cancer. In human pluripotent stem cells (PSC), the appearance of culture-acquired CNVs prompted concerns for their use in regenerative medicine applications.

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Complete genome of Lactobacillus iners KY using Flongle provides insight into the genetic background of optimal adaption to vaginal econiche

Despite the importance of Lactobacillus iners and its unique characteristics for the study of vaginal adaption, its genome and genomic researches for identifying molecular backgrounds of these specific phenotypes are still limited.

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The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study

Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect of other tobacco types on the oral microbiome.

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Two cases of vancomycin-resistant Enterococcus faecium bacteremia with development of daptomycin-resistant phenotype and its detection using Oxford Nanopore sequencing

In this work, we report 2 cases of vancomycin-resistant Enterococcus faecium bacteremia with development of daptomycin resistance in 2 patients with acute myeloid leukemia and myelodysplastic syndrome.

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Genomic characterization of MICA gene using multiple next generation sequencing platforms: a validation study

We have developed a protocol regarding the genomic characterization of the MICA gene by next generation sequencing (NGS). The amplicon includes the full length of the gene and is about 13 kb. A total of 156 samples were included in the study.

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Emergence of multidrug resistant hypervirulent ST23 Klebsiella pneumoniae: multidrug resistant plasmid acquisition drives evolution

Background: In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health.

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A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases.

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Preliminary assessment of nanopore-based metagenomic sequencing for the diagnosis of prosthetic joint infection

Objectives

Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection (PJI). Although culturing methods are the foundation of pathogen detection in PJI, false-negative results often occur.

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Long-read Nanopore sequencing validated for human leukocyte antigen class I typing in routine diagnostics

Matching of human leukocyte antigen (HLA) gene polymorphisms by high-resolution DNA sequence analysis is the gold standard for determining compatibility between patient and donor for hematopoietic stem cell transplantation.

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Molecular and functional analysis of the novel cfr(D) linezolid resistance gene identified in Enterococcus faecium

Objectives

To characterize the novel cfr(D) gene identified in an Enterococcus faecium clinical isolate (15-307.1) collected from France.

Methods

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De novo genome assembly of a Han Chinese male and genome-wide detection of structural variants using Oxford Nanopore sequencing

Advances in third-generation sequencing technologies provide an opportunity to investigate the complex organizational structure of the genome and unravel the genetic mechanisms of disease and physiological traits.

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Rapid diagnostics of orthopaedic-implant-associated infections using Nanopore shotgun metagenomic sequencing on tissue biopsies

Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous.

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MinION™, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting

It has been suggested that the local microbiota in the reproductive organs is relevant to women’s health and may also affect pregnancy outcomes.

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Sequencing of SARS CoV2 in local transmission cases through oxford nanopore MinION platform from Karachi Pakistan

The first case of severe acute respiratory syndrome 2 (SARS CoV2) was imported to Pakistan in February 2020 since then 10,258 deaths have been witnessed. The virus has been mutating and local transmission cases from different countries vary due to host dependent viral adaptation.

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Rapid and accurate species identification of mitis group Streptococci using the MinION Nanopore sequencer

Differentiation between mitis group streptococci (MGS) bacteria in routine laboratory tests has become important for obtaining accurate epidemiological information on the characteristics of MGS and understanding their clinical significance.

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Single-cell individual complete mtDNA sequencing uncovers hidden mitochondrial heterogeneity in human and mouse oocytes

The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods.

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Cytoplasmic polyadenylation by TENT5A is required for proper bone formation

Osteoblasts orchestrate bone formation by secreting dense, highly cross-linked type I collagen and other proteins involved in osteogenesis. Mutations in Col1α1, Col1α2, or collagen biogenesis factors lead to the human genetic disease, osteogenesis imperfecta (OI).

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Genetic identification and drug-resistance characterization of Mycobacterium tuberculosis using a portable sequencing device. A pilot study

Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture.

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In vivo genetic screen identifies a SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia

An enhanced requirement for extracellular nutrients is a hallmark property of cancer cells.

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Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections.

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Suberoyl bis-hydroxamic acid reactivates Kaposi’s sarcoma-associated herpesvirus through histone acetylation and induces apoptosis in lymphoma cells

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an etiologic agent of Kaposi’s sarcoma as well as primary effusion lymphoma (PEL), an aggressive B-cell neoplasm which mostly arises in immunocompromised individuals.

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Amyloid-β1–43 cerebrospinal fluid levels and the interpretation of APP, PSEN1 and PSEN2 mutations

Background

Alzheimer’s disease (AD) mutations in amyloid precursor protein (APP) and presenilins (PSENs) could potentially lead to the production of longer amyloidogenic Aβ peptides.

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Nicotinamide mononucleotide (NMN) deamidation by the gut microbiome and evidence for indirect upregulation of the NAD+ metabolome

Treatment with nicotinamide mononucleotide (NMN) is a prominent strategy to address the age-related decline in nicotinamide adenine dinucleotide (NAD+) levels for maintaining aspects of late-life health.

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Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient with e14a3 BCR‐ABL1 transcript using Nanopore sequencing

Background

The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations.

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Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS)

Middle East Respiratory Syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses.

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Lack of evidence of ACE2 expression and replicative infection by SARS-CoV-2 in human endothelial cells

A striking feature of severe COVID-19 is thrombosis in large as well as small vessels of multiple organs. This has led to the assumption that SARS-CoV-2 virus directly infects and damages the vascular endothelium.

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A fluoroquinolone-sensitive Shigella sonnei UKMCC1015 downregulates the expression of ribosomal proteins in response to sub-lethal concentration of norfloxacin

Shigella spp. commonly causes gastroenteritis known as shigellosis, and severe cases require antibiotic treatments. However, the increased presence of antibiotics in the environment in recent years can lead to antibiotic resistance.

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Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096 Klebsiella pneumoniae in India: The rise of a new superbug?

Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR).

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blaOXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands

Carbapenem-hydrolyzing enzymes belonging to the OXA-48-like group are encoded by blaOXA-48-like alleles and are abundant among Enterobacterales in the Netherlands.

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A novel blaCTX-M-6Harboring IncHI2 plasmid pE648CTX-M-65 isolated from a clinical extensively-drug-resistant Escherichia coli ST648

Background: An ESBL, carbapenemase- and MCR-1-producing Escherichia coli ST648 strain was isolated from the urine sample of a patient in a Chinese tertiary hospital in 2016.

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The furin cleavage site of SARS-CoV-2 spike protein is a key determinant for transmission due to enhanced replication in airway cells

SARS-CoV-2 enters cells via its spike glycoprotein which must be cleaved sequentially at the S1/S2, then the S2’ cleavage sites (CS) to mediate membrane fusion. SARS-CoV-2 has a unique polybasic insertion at the S1/S2 CS, which we demonstrate can be cleaved by furin.

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Transposon-insertion sequencing in a clinical isolate of Legionella pneumophila identifies essential genes and determinants of natural transformation

Legionella pneumophila is a Gram-negative bacterium ubiquitous in freshwater environments which, if inhaled, can cause a severe pneumonia in humans. The emergence of L.

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Two SARS-CoV-2 genome sequences of isolates from rural U.S. patients harboring the D614G mutation, obtained using Nanopore Sequencing

Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States.

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Immunological and pathological outcomes of SARS-CoV-2 challenge after formalin-inactivated vaccine immunisation of ferrets and rhesus macaques

There is an urgent requirement for safe and effective vaccines to prevent novel coronavirus disease (COVID-19) caused by SARS-CoV-2. A concern for the development of new viral vaccines is the potential to induce vaccine-enhanced disease (VED).

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The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping

I performed whole-genome sequencing on SARS-CoV-2 collected from COVID-19 samples at Mayo Clinic Rochester in mid-April, 2020, generated 85 consensus genome sequences and compared them to other genome sequences collected worldwide.

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High resolution copy number inference in cancer using short-molecule nanopore sequencing

Genome copy number is an important source of genetic variation in health and disease. In cancer, clinically actionable Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology.

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Single molecule, near full-length genome sequencing of dengue virus

Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome.

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Evolution and adaptation of Pseudomonas aeruginosa in the paranasal sinuses of people with cystic fibrosis

People with the genetic disorder cystic fibrosis (CF) harbor lifelong respiratory infections, with morbidity and mortality frequently linked to chronic lung infections dominated by the opportunistically pathogenic bacterium Pseudomonas aeruginosa.

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Addition of daptomycin to levofloxacin increased the efficacy of levofloxacin monotherapy against a methicillin-susceptible Staphylococcus aureus strain in experimental meningitis and prevented development of resistance

Daptomycin and levofloxacin were tested as monotherapies and in combination against the antibiotic-susceptible S. aureus strain MSSA 1112 in a rabbit meningitis model and the effect of the combination on induction of resistance was determined in vitro.

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Human genomics of the humoral immune response against polyomaviruses

Human polyomaviruses are widespread in human populations and are able to cause severe disease in immunocompromised individuals. There remains an incomplete understanding of the potential impact of human genetic variation on inter-individual responses to polyomaviruses.

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Human Chr18: “Stakhanovite” genes, missing and uPE1 proteins in liver tissue and HepG2 cells

Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of human Chr18 genes.

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Single gene targeted nanopore sequencing enables simultaneous identification and antimicrobial resistance detection of sexually transmitted infections

Objectives To develop a simple DNA sequencing test for simultaneous identification and antimicrobial resistance (AMR) detection of multiple sexually transmitted infections (STIs).

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Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing

Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens.

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Third-generation sequencing: any future opportunities for PGT?

Purpose

To investigate use of the third-generation sequencing (TGS) Oxford Nanopore system as a new approach for preimplantation genetic testing (PGT).

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Classification of changes in the fecal microbiota associated with colonic adenomatous polyps using a long-read sequencing platform

The microbiota is the community of microorganisms that colonizes the oral cavity, respiratory tract, and gut of multicellular organisms. The microbiota exerts manifold physiological and pathological impacts on the organism it inhabits.

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A long-read sequencing approach for direct haplotype phasing in clinical settings

The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings.

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Prevalence of hypervirulence-associated pathogenicity loci among Klebsiella pneumoniae bloodstream isolates at a United States Hospital

Klebsiella pneumoniae is a major threat to human health worldwide. “Classical” K. pneumoniae (cKp) strains commonly cause multidrug-resistant (MDR) infections in debilitated patients residing in hospitals and long-term care facilities.

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Assessment of viral targeted sequence capture using nanopore sequencing directly from clinical samples

Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis.

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Clinical and immunological benefits of convalescent plasma therapy in severe COVID-19: insights from a single center open label randomised control trial

Introduction A single center open label phase II randomised control trial was done to assess the pathogen and host-intrinsic factors influencing clinical and immunological benefits of passive immunization using convalescent plasma therapy (CPT), in addition to standard of care (S

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Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks

Many healthcare facilities report SARS-CoV-2 outbreaks but transmission analysis is complicated by the high prevalence of infection and limited viral genetic diversity.

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Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3,200 cases were reported between March and August 2020.

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Genomic epidemiology of COVID-19 in care homes in the East of England

COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people.

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Kinetics of viral load, immunological mediators and characterization of a SARS-CoV-2 isolate in mild COVID-19 patients during acute phase of infection

Over 95% of COVID-19 cases are mild-to-asymptomatic cases which contribute to disease transmission whereas most of the severe manifestations of the disease are observed in elderly and in patients with comorbidities and dysregulation of immune response has been implicated in severe clinical o

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Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis of KMT2A-rearranged leukemia

Infant ALL is a devastating malignancy caused by rearrangements of the KMT2A gene (KMT2A-r) in approximately 70% of patients. The outcome is dismal and younger age at diagnosis is associated with increased risk of relapse.

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Oncogene concatenated enriched amplicon nanopore sequencing for rapid, accurate, and affordable somatic mutation detection

Nanopore sequencing is more than 10-fold faster than sequencing-by-synthesis and provides reads that are roughly 100-fold longer.

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Epigenetic heterogeneity after de novo assembly of native full-length Hepatitis B Virus genomes

Methylation of Hepatitis B Virus (HBV) DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation.

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EcDNA hubs drive cooperative intermolecular oncogene expression

Extrachromosomal DNAs (ecDNAs) are prevalent in human cancers and mediate high oncogene expression through elevated copy number and altered gene regulation. Gene expression typically involves distal enhancer DNA elements that contact and activate genes on the same chromosome.

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Long-chain polyphosphates impair SARS-CoV-2 infection and replication: a route for therapy in man

Anti-viral activities of long-chain inorganic polyphosphates (PolyPs) against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection were investigated.

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Metagenomic next-generation sequencing of nasopharyngeal specimens collected from confirmed and suspect COVID-19 patients

Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens.

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Transcriptional silencing of ALDH2 in acute myeloid leukemia confers a dependency on Fanconi anemia proteins

Hundreds of genes become aberrantly silenced in acute myeloid leukemia (AML), with most of these epigenetic changes being of unknown functional consequence.

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The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

SARS-CoV-2 can mutate to evade immunity, with consequences for the efficacy of emerging vaccines and antibody therapeutics.

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Characterization of a COPD-Associated NPNT Functional Splicing Genetic Variant in Human Lung Tissue via Long-Read Sequencing

Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide. Genome-wide association studies (GWAS) have identified over 80 loci that are associated with COPD and emphysema, however for most of these loci the causal variant and gene are unknown.

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Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection

The SARS-CoV-2 pandemic is continuing to disrupt personal lives, global healthcare systems and economies. Hence, there is an urgent need for a vaccine that prevents viral infection, transmission and disease.

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Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia

The COVID-19 pandemic has brought with it the largest ever cohort of patients requiring mechanical ventilation.

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Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis

In the present work, two complete genome sequences of SARS-CoV-2 were obtained from nasal swab samples of Tunisian SARS-CoV-2 PCR-positive patients using nanopore sequencing.

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Assessing Nanopore sequencing for clinical diagnostics: A comparison of NGS methods for Mycobacterium tuberculosis

Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories.

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Chromosomal translocation disrupting the SMAD4 gene resulting in the combined phenotype of Juvenile polyposis syndrome and Hereditary Hemorrhagic Telangiectasia

Background

Patients with germline variants in SMAD4 can present symptoms of both juvenile polyposis syndrome (JPS) and Hereditary Hemorrhagic Telangiectasia (HHT): JP‐HHT syndrome.

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Sequential infection with influenza A virus followed by SARS-CoV-2 leads to more severe disease and encephalitis in a mouse model of COVID-19

COVID-19 is a spectrum of clinical symptoms in humans caused by infection with SARS-CoV-2, a recently emerged coronavirus that has rapidly caused a pandemic.

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BugSeq: a highly accurate cloud platform for long-read metagenomic analyses

As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification in a fast and accurate manner are needed. Existing tools were either designed for short-read data (eg.

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Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing

LamPORE is a novel diagnostic platform for the detection of SARS-CoV-2 RNA that combines loop-mediated isothermal amplification with nanopore sequencing, which could potentially be used to analyse thousands of samples per day on a single instrument.

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Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus

Bats are exceptional among mammals for harbouring diverse pathogens and for their robust immune systems. In addition, bats are unusually long-lived and show low rates of cancer.

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Strand-wise and bait-assisted assembly of nearly-full rrn operons applied to assess species engraftment after faecal microbiota transplantation

Background 
Effective methodologies to accurately identify members of the gut microbiota at the species and strain levels are necessary to unveiling more specific and detailed host-microbe interactions and associations with health and disease.

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Whole genome sequencing reveals virulence potentials of Helicobacter pylori strain KE21 isolated from a Kenyan patient with gastric signet ring cell carcinoma

Helicobacter pylori (H.pylori) infection is etiologically associated with severe diseases including gastric cancer; but its pathogenicity is deeply shaped by the exceptional genomic diversification and geographic variation of the species.

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Long-read sequencing resolves structural variants in SERPINC1 causing antithrombin deficiency and identifies a complex rearrangement and a retrotransposon insertion not characterized by routine diagnostic methods

The identification and characterization of structural variants (SVs) in clinical genetics have remained historically challenging as routine genetic diagnostic techniques have limited ability to evaluate repetitive regions and SVs.

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Whole-genome sequencing of human Enteroviruses from clinical samples by nanopore direct RNA sequencing

Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms.

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Landscape and function of multiple mutations within individual oncogenes

Sporadic reports have described cancer cases in which multiple driver mutations (MMs) occur in the same oncogene. However, the overall landscape and relevance of MMs remain elusive.

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Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

The importance of structural variants (SVs) on phenotypes and human diseases is now recognized.

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Genetic Variation, Comparative Genomics, and the Diagnosis of Disease

The discovery of mutations associated with human genetic disease is an exercise in comparative genomics (see Glossary).

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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized.

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Nanopore sequencing and its clinical applications

Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore).

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Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor.

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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide.

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A novel Cas9-targeted long-read assay for simultaneous detection of IDH1/2 mutations and clinically relevant MGMT methylation in fresh biopsies of diffuse glioma

Molecular biomarkers provide both diagnostic and prognostic results for patients with diffuse glioma, the most common primary brain tumor in adults.

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Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

Alterations in the genetic content, such as Copy Number Variations (CNVs) is one of the hallmarks of cancer and their detection is used to recognize tumoral DNA. Analysis of cell-free DNA from plasma is a powerful tool for non-invasive disease monitoring in cancer patients.

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Rapid and Point-of-Care Testing in Respiratory Tract Infections: An Antibiotic Guardian?

This is a narrative review on the potential of rapid and point-of-care microbiological testing in pneumonia patients, focusing particularly on hospital-acquired and ventilator-associated pneumonia, which have substantial mortality and diverse microbiology.

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Relationship between anti-spike protein antibody titers and SARS-CoV-2 in vitro virus neutralization in convalescent plasma

Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective.

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Rapid, highly accurate and cost‐effective open‐source simultaneous complete HLA typing & phasing of Class I & II alleles using nanopore sequencing

Introduction
Accurate rapid genotyping of the genes within the HLA region presents many difficulties due to the complexity of this region.

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Potential utility of targeted nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection

Background
Diversified etiology of lower respiratory tract infection renders diagnosis challenging. The mainstay microbial culture is time-consuming and constrained by variable growth requirements.

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A long road/read to rapid high-resolution HLA typing: The nanopore perspective

Next-generation sequencing (NGS) has been widely adopted for clinical HLA typing and advanced immunogenetics researches.

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Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived and wild-type polioviruses and ensure an appropriate response.

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Mechanisms generating cancer genome complexity from single cell division error

The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes alongside chromothripsis, another catastrophic mutational phenomenon.

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Rapid high resolution HLA genotyping by MinION Oxford Nanopore sequencing for deceased donor organ allocation

Recently, HLA epitopes on donor HLA molecules have been shown to be important in the success of solid organ transplantation. However, these epitopes can only be defined using high resolution typing results of which are often not available prior to deceased donor allocation.

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Limited SARS-CoV-2 diversity within hosts and following passage in cell culture

Since the first reports of pneumonia associated with a novel coronavirus (COVID-19) emerged in Wuhan, Hubei province, China, there have been considerable efforts to sequence the causative virus, SARS-CoV-2 (also referred to as hCoV-19) and to make viral genomic information available quic

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DNA thermo-protection facilitates whole genome sequencing of Mycobacteria direct from clinical samples by the Nanopore platform

Mycobacterium tuberculosis (MTB) is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole genome sequencing, are required.

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Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies (ONT) PromethION platform is a now a viable solution for genome sequencing.

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Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

Coronavirus disease 2019 (COVID-19) causes severe community and nosocomial outbreaks. Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available.

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Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

Adherent-invasive Escherichia coli (AIEC) are a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn’s disease, and colorectal cancer. AIEC have no known molecular or genomic markers, but instead are defined by in vitro functional attributes.

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Rapid next-generation sequencing–based diagnostics of bacteremia in septic patients

The increasing incidence of bloodstream infections including sepsis is a major challenge in intensive care units worldwide.

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Whole-genome sequencing of rare disease patients in a national healthcare system

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and mediating genes for more than half such disorders remain to be discovered.

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Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient

The etiologic agent of the outbreak of pneumonia in Wuhan China in January-2020, was identified as severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2).

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Nanopore metagenomic sequencing to investigate nosocomial transmission of human metapneumovirus from a unique genetic group among haematology patients in the United Kingdom

Background
Human metapneumovirus (HMPV) infection causes a spectrum of respiratory tract disease, and may be a significant pathogen in the context of immunocompromise.

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DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing

Identification of bacteria causing tissue infections can be comprehensive and, in the cases of non- or slow-growing bacteria, near impossible with conventional methods.

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Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks.

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Nanopore sequencing in blood diseases: a wide range of opportunities

The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disorders becoming ever more widespread in clinical practice.

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Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs

Accurately quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems.

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Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes.

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Rapid and real-time identification of fungi up to the species level with long amplicon nanopore sequencing from clinical samples

The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-28S) and to improve the taxonomy assignment of the communities up to species level

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A novel Coronavirus from patients with pneumonia in China, 2019

In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia.

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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health.

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Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital

Background
Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety.

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Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing

The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception.

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Enhancer hijacking determines intra- and extrachromosomal circular MYCN amplicon architecture in neuroblastoma

MYCN amplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA.

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Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population

Tandem repeats are highly mutable and contribute to the development of human disease by a variety of mechanisms. However, it is difficult to predict which tandem repeats may cause a disease.

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Cerebrospinal fluid MinION sequencing of 16S rRNA gene for rapid and accurate diagnosis of bacterial meningitis

Bacterial meningitis causes substantial morbidity and mortality worldwide. Rapid identification of the microorganisms is essential for early initiation of appropriate antimicrobial therapy, thereby improving clinical outcome.

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MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling

In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information.

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Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing

Human papillomavirus (HPV) is a major pathogen that causes cervical cancer and many other related diseases. The HPV infection-related cervical microbiome could be an inducing factor of cervical cancer.

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Generation of a transcriptional radiation exposure signature in human blood using long-read nanopore sequencing

In the event of a large-scale event leading to acute ionizing radiation exposure, high-throughput methods would be required to assess individual dose estimates for triage purposes.

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Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings.

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Nanopore targeted sequencing for rapid gene mutations detection in acute myeloid leukemia

Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy.

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Rapid, unbiased PRRSV strain detection using MinION direct RNA sequencing and bioinformatics tools

Prompt detection and effective control of porcine reproductive and respiratory syndrome virus (PRRSV) during outbreaks is important given its immense adverse impact on the swine industry.

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Mechanisms of colistin resistance in Escherichia strains isolated from bloodstream infections

Infections by multidrug resistant Gram negative bacteria are increasingly common, prompting the renewed interest in the use of colistin.

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Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics

The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing.

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Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression.

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Rapid identification of genomic structural variations with nanopore sequencing enables blood-based cancer monitoring

Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of circulating tumor DNA (ctDNA) in liquid biopsies.

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Effective downregulation of BCR-ABL tumorigenicity by RNA targeted CRISPR-Cas13a

CML is a clonal myeloproliferative disorder of pluripotent stem cells driven by a reciprocal translocation between chromosome 9 and 22, forming a BCR-ABL fusion gene.

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The WIPE assay for selection and elimination of HIV-1 provirus in vitro using latency-reversing agents

Persistence of HIV-1 latent reservoir cells during antiretroviral therapy (ART) is a major obstacle for curing HIV-1.

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Full-coverage native RNA sequencing of HIV-1 viruses

Objective: To evaluate native RNA sequencing for sequencing HIV-1 viral genomes.

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Comprehensive analysis of horizontal gene transfer among multidrug-resistant bacterial pathogens in a single hospital

Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings.

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Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing

Phage display methodologies offer a versatile platform for the isolation of single-chain Fv (scFv) molecules which may be rebuilt into monoclonal antibodies.

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Nanopore sequencing of African swine fever virus

African swine fever (ASF) is one of the most pathogenic viral diseases in pigs caused by African swine fever virus (ASFV). The fatality rate is almost 100%, which brings huge economic losses to the hog industry in countries with epidemics.

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Analysis of polyclonal vector integration sites using Nanopore sequencing as a scalable, cost-effective platform

Vector integration site analysis can be important in the follow-up of patients who received gene-modified cells, but current platforms based on next-generation sequencing are expensive and relatively inaccessible.

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Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids

Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen.

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Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

Every successful cancer therapy story has Exhibit B, comprised of patients who either did not respond to the initial treatment or acquired resistance after a seemingly curative intervention.

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Using nanopore RNA-Seq to HLA genotype and correlate donor HLA expression with flow cytometric crossmatch results

Transplant centers are increasingly using virtual crossmatching (VXM) to evaluate recipient and donor compatibility.

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Long‐read nanopore sequencing resolves a TMEM231 gene conversion event causing Meckel‐Gruber syndrome

The diagnostic deployment of massively parallel short‐read next generation sequencing (NGS) has greatly improved genetic test availability, speed and diagnostic yield, particularly for rare inherited disorders.

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Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify.

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Long reads, short time: feasibility of prenatal sample karyotyping by nanopore genome sequencing

Chromosomal abnormalities causing genomic imbalance are a major cause of congenital developmental defects and intellectual disability, constituting the leading cause of stillbirth and birth with malformations.

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An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: a pilot study of head and neck cancer patients

Gut metagenome profiling using the Oxford Nanopore Technology (ONT) sequencer was assessed in a pilot-sized study of 10 subjects. The taxonomic abundance of gut microbiota derived from ONT was comparable with Illumina Technology (IT) for the high-abundance species.

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Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment.

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Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing

Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, length of time to results, and need for technical and bioinformatics expertise.

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Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing

The human immune system relies on highly complex and diverse transcripts and the proteins they encode.

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Ciprofloxacin facilitates the transfer of XDR plasmids from commensal E. coli into epidemic fluoroquinolone-resistant Shigella sonnei

The global dissemination of a ciprofloxacin-resistant (cipR) S. sonnei clone outlines the mobility of this important agent of diarrheal disease, and threatens the utility of ciprofloxacin as a first-line antimicrobial for shigellosis. Here, we aimed to track the emergence of cipR S.

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Targeted sequencing workflows for comprehensive drug resistance profiling of Mycobacterium tuberculosis cultures using Illumina MiSeq and Nanopore MinION: comparison of analytical and diagnostic performance, turnaround time and cost

The emergence of Mycobacterium tuberculosis strains with complex drug resistance profiles necessitates a rapid and extensive drug susceptibility test for comprehensive guidance of patient treatment.

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Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: A pilot study

Early administration of antibiotics is crucial in the management of bacterial meningitis. Rapid pathogen identification helps to make a definite diagnosis of bacterial meningitis and enables tailored antibiotic treatment.

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Non-hierarchical, RhlR-regulated acyl-homoserine lactone quorum sensing in a cystic fibrosis isolate of Pseudomonas aeruginosa

The opportunistic pathogen Pseudomonas aeruginosa is a leading cause of airway infection in cystic fibrosis (CF) patients. P.

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Rapid and cost-efficient Enterovirus genotyping from clinical samples using Flongle Flow Cells

Enteroviruses affect millions of people worldwide and are of significant clinical importance. The standard method for enterovirus identification and genotyping still relies on Sanger sequencing of short diagnostic amplicons.

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Nanopore sequencing of the glucocerebrosidase (GBA) gene in a New Zealand Parkinsons disease cohort

Mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder.

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The diagnostic chronic lymphocytic leukaemia genome by nanopore sequencing

Chronic lymphocytic leukaemia (CLL) is characterised by considerable clinical and biological heterogeneity, with specific recurrent genomic alterations, including TP53 mutations, deletions of chromosome 17p, and IgHV mutational status, impacting on response to chemo-immunotherapy and tar

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Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing

Detection of chromosomal translocation is a key component in diagnosis and management of acute myeloid leukemia (AML).

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Cas9-based enrichment and single-molecule sequencing for precise characterization of genomic duplications

The widespread use of genome-wide diagnostic screening methods has greatly increased the frequency with which incidental (but possibly pathogenic) copy number changes affecting single genes are detected. These findings require validation to allow appropriate clinical management.

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Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential.

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Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy.

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MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing

Recent evidence suggests a role for the gut microbiome in the development and progression of colorectal cancer. In this study we compare MinION sequencing with meta-transcriptomics and amplicon-based sequencing for microbiome analysis of colorectal tumour tissue samples.

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Severe haemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing

Background
No F8 genetic abnormality is detected in about 2% of severe haemophilia A patients using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal.

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Distinguishing between carrier and noncarrier embryos with the use of long-read sequencing in preimplantation genetic testing for reciprocal translocations

Balanced reciprocal translocation carriers are usually phenotypically normal but are at an increased risk of infertility, recurrent miscarriage or having affected children.

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Targeted nanopore sequencing with Cas9-guided adapter ligation

Despite recent improvements in sequencing methods, there remains a need for assays that provide high sequencing depth and comprehensive variant detection.

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Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications

CYP2D6 is one of the most important and widely studied genes in pharmacogenetics but it is highly polymorphic, can be affected by different forms of structural variation, and has a nearby pseudogene with highly similar sequence; therefore, its accurate genotyping and structural r

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Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease

Neuronal intranuclear inclusion disease (NIID) is a progressive neurodegenerative disease that is characterized by eosinophilic hyaline intranuclear inclusions in neuronal and somatic cells.

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Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads

Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide.

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Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

Enterococcus faecium is a gut commensal of many mammals but is also recognized as a major nosocomial human pathogen, as it is listed on the WHO global priority list of multi-drug resistant organisms.

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MinION Nanopore Sequencing of Multiple Displacement Amplified Mycobacteria DNA Direct from Sputum

Sequencing of pathogen DNA directly from clinical samples offers the possibilities of rapid diagnosis, faster antimicrobial resistance prediction and enhanced outbreak investigation.

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ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin

Objectives
This study compares the genome of an ST131 CMY-2-producing Escherichia coli isolate from a Danish patient with other ST131 CMY-2-producing E. coli isolates of both human and animal origin.

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Lytic Transcriptome Dataset of Varicella Zoster Virus Generated by Long-Read Sequencing

Varicella zoster virus (VZV) belongs to the Alphaherpesvirinae subfamily of the Herpesviridae family. The presented data report is aimed toward providing a new, comprehensive transcript catalog of VZV using a long-read sequencing approach for the first time.

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A comprehensive overview of FCGR3A gene variability by full-length gene sequencing including the identification of V158F polymorphism

The FCGR3A gene encodes for the receptor important for antibody-dependent natural killer cell-mediated cytotoxicity. FCGR3A gene polymorphisms could affect the success of monoclonal antibody therapy.

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A nanopore sequencing–based assay for rapid detection of gene fusions

Structural chromosomal rearrangements leading to gene fusions are strong driver mutations in a variety of tumors.

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Human-Specific Abnormal Alternative Splicing of Wild-Type PKD1 Induces Premature Termination of Polycystin-1

Background The major form of autosomal dominant polycystic kidney disease is caused by heterozygous mutations in PKD1, the gene that encodes polycystin-1 (PC1).

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MinION rapid sequencing: Review of potential applications in neurosurgery

Background: Gene sequencing has played an integral role in the advancement and understanding of disease pathology and treatment.

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Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia

We report a customized gene panel assay based on multiplex long-PCR followed by third generation sequencing on nanopore technology (MinION), designed to analyze five frequently mutated genes in chronic lymphocytic leukemia (CLL): TP53, NOTCH1, BIRC3, SF3B1 and MYD88.

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Rapid confirmation of the Zaire Ebola Virus in the outbreak of the Equateur province in the Democratic Republic of Congo: implications for public health interventions

Ten days after the declaration of the Ebola outbreak in the Equateur Province of the Democratic Republic of Congo, rapid identification of the species Zaire Ebolavirus (EBOV) using partial gene amplification and nanopore sequencing backed up the use of the rVSV-ZEBOV vaccine in the ring vaccinati

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Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

Next generation sequencing (NGS) is challenged by structural and copy number variations larger than the typical read length of several hundred bases.

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Paternally inherited cis-regulatory structural variants are associated with autism

The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD.

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Genomic and epidemiological monitoring of yellow fever virus transmission potential

The yellow fever virus (YFV) epidemic that began in Dec 2016 in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes sp. vectors highlights the urgent need to monitor the risk of re-establishment of domestic YFV transmission in the Americas.

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Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy

Epilepsy is a common neurological disorder, and mutations in genes encoding ion channels or neurotransmitter receptors are frequent causes of monogenic forms of epilepsy.

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Rapid preimplantation genetic screening (PGS) using a handheld, nanopore-based, DNA sequencer

Objective: To determine if a handheld, nanopore-based DNA sequencer can be used for rapid preimplantation genetic screening (PGS).

Design: Retrospective study. Setting: Academic medical center.

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Long-read sequencing reveals the splicing profile of the calcium channel gene CACNA1C in human brain

RNA splicing is a key mechanism linking genetic variation and complex diseases, including schizophrenia. Splicing profiles are particularly diverse in the brain, but it is difficult to accurately identify and quantify full-length isoforms using standard approaches.
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Culture-independent analysis of liver abscess using nanopore sequencing

The identification of microbial species has depended predominantly upon culture-based techniques. However, the difficulty with which types of organisms are cultured implies that the grown species may be overrepresented by both cultivation and plate counts.

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Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

OBJECTIVE: Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak.

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Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris

Background: Candida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak of C.

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Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for personalized monitoring of residual disease in chronic myeloid leukemia patients

For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts.

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Barcoding analysis of HIV drug resistance mutations using Oxford Nanopore MinION (ONT) sequencing

Determination of HIV drug resistance (HIVDR) is becoming an integral baseline HIV evaluation for newly infected subjects, as the level of pre-treatment resistance is increasing worldwide.

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Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

Genetic changes causing brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and is a determinant of neuronal number in the mammalian cortex.

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Mitochondrial heteroplasmy is responsible for Atovaquone drug resistance in Plasmodium falciparum

Malaria is the most significant parasitic disease affecting humans, with 212 million cases and 429,000 deaths in 20151, and resistance to existing drugs endangers the global malaria elimination campaign. Atovaquone (ATO) is a safe and potent antimalarial drug that acts on cytochrome b (cyt.

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Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

Background.

Klebsiella pneumoniae is a leading cause of extended-spectrum beta-lactamase (ESBL) producing hospital-associated infections, for which elderly patients are at increased risk.

Methods.

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Campylobacter fetus meningitis confirmed by a 16S rRNA gene analysis using the MinION nanopore sequencer, South Korea, 2016

C. fetus should be considered a possible cause of bacterial meningitis, especially in immunocompromised patients with accompanying gastrointestinal symptoms. Nanopore sequencing of the 16S rRNA gene allowed the identification of C. fetus at the subspecies level.

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Picky comprehensively detects high-resolution structural variants in nanopore long reads

Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data.

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Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates

Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates.
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First two cases of severe multifocal infections caused by Klebsiella pneumoniae in Switzerland: characterization of an atypical non-K1/K2-serotype strain causing liver abscess and endocarditis

Background

We describe the first two multifocal invasive infections due to Klebsiella pneumoniae recently observed in Switzerland.

Methods

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A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer

Background

A simple and accurate molecular diagnostic method for malaria is urgently needed due to the limitations of conventional microscopic examination.

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Accurate typing of class I human leukocyte antigen by Oxford nanopore sequencing

Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability.

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Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples

The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility.

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Hand-held rapid whole genome nanopore sequencing to predict neisseria gonorrhoeae antibiotic susceptibility: steps towards clinic based tailored antimicrobial therapy

Next generation sequencing can accurately predict antibiotic susceptibility in Neisseria gonorrhoeae (NG) allowing preservation of first-line treatments in the face of widespread antimicrobial resistance (AMR).

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Mutational analysis in BCR-ABL1 positive leukemia by deep sequencing based on nanopore MinION technology

We report a third-generation sequencing assay on nanopore technology (MinION) for detecting BCR-ABL1 KD mutations and compare the results to a Sanger sequencing(SS)-based test in 24 Philadelphia-positive (Ph +) leukemia cases.

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Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy

Subtelomeric macrosatellite repeats are difficult to sequence using conventional sequencing methods owing to the high similarity among repeat units and high GC content. Sequencing these repetitive regions is challenging, even with recent improvements in sequencing technologies.

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Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer’s disease

Premature termination codon (PTC) mutations in the ATP-Binding Cassette, Sub-Family A, Member 7 gene (ABCA7) have recently been identified as intermediate-to-high penetrant risk factor for late-onset Alzheimer’s disease (LOAD).

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Non-invasive diagnosis of cutaneous leishmaniasis by the direct boil loop-mediated isothermal amplification method and MinION™ nanopore sequencing

Cutaneous leishmaniasis (CL) is gaining attention as a public health problem. We present two cases of CL imported from Syria and Venezuela in Japan.

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Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks.

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TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

Background

The assessment of TP53 mutational status is becoming a routine clinical practice for chronic lymphocytic leukemia patients (CLL).

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MinION sequencing of malaria parasites

The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate.

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Nanopore sequencing for metagenomic diagnosis of infectious diseases

Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing is now feasible, but has been limited to date by concerns regarding sensitivity and sample-to-answer turnaround times.

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Sara Goodwin, CSHL: Rapid CNV Characterisation of clinical cancer samples on the Oxford Nanopore MinION

Sara Goodwin of Coldspring Harbour Laboratory talks to the Oxford Nanopore Community at London Calling.

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Clive Brown, CTO of Oxford Nanopore, talks at the London Calling conference

Clive is Chief Technology Officer at Oxford Nanopore. On the Executive team, he is responsible for all of the Company’s product-development activities.

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How MinION is Changing my Research in Infectious Diseases Diagnostics

A presentation to the MinION Community by Dr Justin O’Grady, Lecturer in Medical Microbiology, University of East Anglia.

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Rapid Short-Read Sequencing and Aneuploidy Detection using MinION Nanopore Technology

A presentation to the MinION Community by Dr Zev Williams, Assistant Professor, Department of Obstetrics & Gynecology and Women’s Health, Assistant Professor, Department of Genetics, Albert Einstein College of Medicine.

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Getting the Flu: Exploring Influenza Virus Evolutionary Dynamics by Single Molecule Sequencing

Elodie Ghedin - Professor of Biology and member of the Center for Genomics and Systems Biology, New York University - talks to the MinION community.

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NGS for Public Health Microbiology

Dr Catherine Arnold, Consultant Clinical Scientist in Molecular Microbiology at Public Health England talks to the MinION Community about NGS for Public Health Microbiology.

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De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging.

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Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology

Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software.

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Clonal expansion of Escherichia coli ST38 carrying chromosomally-integrated OXA-48 carbapenemase gene

Many isolates of Escherichia coli carrying blaOXA-48 referred to Public Health England’s national reference laboratory during 2014 and 2015 shared similar pulsed-field gel electrophoresis (PFGE) profiles, despite coming from patients in multiple hospitals and regions.

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Nanopore sequencing detects structural variants in cancer

Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300bp) of 2nd generation sequencing.

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Rapid short-read sequencing and aneuploidy detection using MinION nanopore technology

MinION™ is a memory stick-sized, nanopore-based sequencer primarily designed for single-molecule sequencing of long DNA fragments (>6 kb).

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Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions.

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Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain

Pandoraea species, in particular Pandoraea apista, are opportunistic, multidrug-resistant pathogens in persons with cystic fibrosis (CF).

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Noninvasive Prenatal Testing by Nanopore Sequencing of Maternal Plasma DNA: Feasibility Assessment

Noninvasive prenatal testing (NIPT) by maternal plasma DNA sequencing is now clinically available for screening fetal chromosomal aneuploidies; these tests have close to 99% sensitivity..

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MinION nanopore sequencing of an influenza genome

Influenza epidemics and pandemics have significant impacts on economies, morbidity and mortality worldwide. The ability to rapidly, and accurately, sequence influenza viruses is instrumental in the prevention and mitigation of influenza.

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An epidemiological river metagenome based on MinION

River waters worldwide are impacted by disease-causing agents including bacteria, protists, flatworms, viruses, and harmful algae that derive from domestic sewage and farm runoff, and/or are emergent due to nutrient pollution and climate change.

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Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital.

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Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information.

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Mitochondrial Genome Acquisition Restores Respiratory Function and Tumorigenic Potential of Cancer Cells Without Mitochondrial DNA

We report that tumor cells without mitochondrial DNA (mtDNA) show delayed tumor growth, and that tumor formation is associated with acquisition of mtDNA from host cells.

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