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Publications tagged "Human genomics"

Structural variation in human genomics: 6 things to read right now

The significance of structural variation in human genomics is becoming increasingly established in many fields, from cancer to neurology and the mechanisms of rare disease. With research moving at a...

Epigenetics, Cas9-mediated enrichment and novel insights in transcriptome variation: catch up on talks from ASHG 2020

This week we heard from Ariel Gershman, Shruti Iyer and Tuuli Lappalainen on their latest research addressing some of the key challenges in human genomics using nanopore technology. The talks are no...

Blog: cuteSV - a powerful tool to uncover the full spectrum of genomic structural variants

In this blog, Tao Jiang describes his work on the development of the structural variant (SV) caller cuteSV.

Oxford Nanopore Technologies announces new human health and disease study led by the UK National Institute for Health and Care Research (NIHR) BioResource

Oxford Nanopore Technologies, the company delivering a new generation of nanopore-based molecular sensing technology, today announces its participation in a cohort study led by the UK National Insti...

Oxford Nanopore at ASHG 2021: find out how you can use nanopore technology to gain comprehensive, scalable, accurate insights in human genomics

As researchers convene for ASHG online, we’re looking forward to hearing about the very latest in human genomics research using nanopore sequencing over the next few days. We've pulled together some...

Interview: Exploring complex disease in Asian populations with PromethION

with Professor Jianjun Liu of the Genome Institute of Singapore Conducted and written by Jonathan Pugh “long-read sequencing will become the main platform for clinical diagnosis, just because...

From telomere to telomere: the transcriptional and epigenetic state of human repeat elements

Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific genomic innovation and fingerprint individual genomes. Comprehensive analyses of large, composite or arra...

Towards population-scale long-read sequencing

Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the d...

Dysgu: efficient structural variant calling using short or long reads

Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in t...

Jasmine: population-scale structural variant comparison and analysis

The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies...

Cell-free DNA analysis by whole-exome sequencing for hepatocellular carcinoma: a pilot study in Thailand

Liquid biopsy for cell-free DNA (cfDNA) is a non-invasive technique to characterize the genetic profile of a tumor. Despite being a valuable tool, there is no mutational profile of cfDNA from hepato...

Intronic haplotypes in the GBA gene do not predict age at diagnosis of Parkinson's Disease

Background GBA mutations are a common risk factor for Parkinson's disease (PD). A recent study has suggested that GBA haplotypes, identified by intronic variants, can affect age at diagnosis of PD...

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex seg...

Human Chr18 transcriptome dataset combined from the Illumina HiSeq, ONT MinION, and qPCR data

The chromosome-centric dataset was created by applying several technologies of transcriptome profiling. The described dataset is available at NCBI repository (BioProject ID PRJNA635536). The dataset...

Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts

Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excisio...

Whole human genome 5'-mC methylation analysis using long read nanopore sequencing

DNA methylation is a type of epigenetic modification that affects gene expression regulation and is associated with several human diseases. Microarray and short read sequencing technologies are ofte...

The Lithuanian reference genome LT1 - a human de novo genome

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly constructed using 57× of ultra-long nanopore reads and 4...

Interview: The PromethION Experts at VIB

with Mojca Strazisar, Tim De Pooter and Wouter De Coster, members of the VIB Center for Molecular Neurology Conducted and written by Jonathan Pugh “Yields have been exploding in the past few ...

An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics

Background Short tandem repeat (STR) expansion disorders are an important cause of human neurological disease. They have an established role in more than 40 different phenotypes including the myoto...

Interview: Using PromethION for Cancer, Collaborations and more

with Dr Richard Moore, Sequencing Group Leader at the Genome Science Centre, BC Cancer Conducted and written by Jonathan Pugh

Innovations with ultra-long reads

The panel session at London Calling 2021 online saw three leading researchers present their latest work using ultra-long nanopore sequencing reads, obtained using the Ultra-Long DNA Sequencing Kit. ...

Interview: PromethION 24 and human disease research

with Eric Cabannes, Development Laboratory Manager at the Centre National de Recherche en Génomique Humaine (CNRGH) Conducted and written by Jonathan Pugh

The human ribosomal RNA gene is composed of highly homogenized tandem clusters

The structure of the human ribosomal RNA gene clustering region (rDNA) has traditionally been hard to analyze due to its highly repetitive nature. However, the recent development of long-read sequen...

A reference-quality, fully annotated genome from a Puerto Rican individual

Until 2019, the human genome was available in only one fully-annotated version, which was the result of 18 years of continuous improvement and revision. Despite dramatic improvements in sequencing t...

Long-read nanopore sequencing enables accurate confirmation of a recurrent PMS2 insertion–deletion variant located in a region of complex genomic architecture

Targeted next generation sequencing (NGS) is the predominant methodology for the molecular genetic diagnosis of inherited conditions. In many laboratories, NGS-identified variants are routinely vali...

Epigenetic patterns in a complete human genome

The completion of the first telomere-to-telomere human genome, T2T-CHM13, enables exploration of the full epigenome, removing limitations previously imposed by the missing reference sequence. Existi...

Segmental duplications and their variation in a complete human genome

Despite their importance in disease and evolution, highly identical segmental duplications (SDs) have been among the last regions of the human reference genome (GRCh38) to be finished. Based on a co...

The complete sequence of a human genome

In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts a...

Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer

Background Identification of germline variation and somatic mutations is a major issue in human genetics. However, due to the limitations of DNA sequencing technologies and computational algorithms...

Spatially coordinated heterochromatinization of distal short tandem repeats in fragile X syndrome

Short tandem repeat (STR) instability is causally linked to pathologic transcriptional silencing in a subset of repeat expansion disorders. In fragile X syndrome (FXS), instability of a single CGG S...

Heat treatment functionalizes hepatocyte-like cells derived from human embryonic stem cells

Hepatocyte-like cells derived from human pluripotent stem cells (hPSC-HLCs) offer an alternative to primary hepatocytes commonly used for drug screenings and toxicological tests. Although tremendous...

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. Having a high sequencing error of ONT ...

Robust methylation-based classification of brain tumors using nanopore sequencing

DNA methylation-based classification of cancer provides a comprehensive molecular approach to diagnose tumors. In fact, DNA methylation profiling of human brain tumors already profoundly impacts cli...

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. Trinucleotide repeat expansion...

The MinION as a cost-effective technology for diagnostic screening of the SCN1A gene in epilepsy patients

The MinION is a portable DNA sequencer that allows real time sequencing at low capital cost investment. We assessed accuracy and cost-effectivess of the MinION for genetic diagnostic testing of know...

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 cen...

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. For autism spectrum disorders (ASD) cases where pa...

Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks

Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read based phasing. ...

Structural variants in Chinese population and their impact on phenotypes, diseases and population adaptation

A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing (LRS) improves the sensitivity for structural variant (SV) discovery and facilit...

Cas9 targeted enrichment of mobile elements using nanopore sequencing

Mobile element insertions (MEIs) are highly repetitive genomic sequences that contribute to inter- and intra-individual genetic variation and can lead to genetic disorders. Targeted and whole-genome...

Using de novo assembly to identify structural variation of complex immune system gene regions

Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable struct...

Analysis of mitochondrial genome methylation using Nanopore single-molecule sequencing

The level and the biological significance of mitochondrial DNA (mtDNA) methylation in human cells is a controversial topic. Using long-read third-generation sequencing technology, mtDNA methylation ...

Benchmarking challenging small variants with linked and long reads

Genome in a Bottle (GIAB) benchmarks have been widely used to validate clinical sequencing pipelines and develop new variant calling and sequencing methods. Here we use accurate long and linked read...

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 o...

Genetic information insecurity as state of the art

Genetic information is being generated at an increasingly rapid pace, offering advances in science and medicine that are paralleled only by the threats and risk present within the responsible ecosys...

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. Current short-read next-generati...

RNA LEVER mediates long-range regulation of ε-globin by keeping PRC2 in check

Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator required for gene silencing during embryonic development. Previous studies have reported that PRC2 interacts with RNA in a promiscuous...

Engineering radioprotective human cells using the tardigrade damage suppressor protein, DSU

Spaceflight has been documented to produce a number of detrimental effects to physiology and genomic stability, partly a result of Galactic Cosmic Radiation (GCR). In recent years, extensive researc...

The First complete Zoroastrian-Parsi Mitochondria Reference Genome: implications of mitochondrial signatures in an endogamous, non-smoking population

The present-day Zoroastrian-Parsis have roots in ancient pastoralist migrations from circumpolar regions leading to their settlement on the Eurasian Steppes and later, as Indo Iranians in the Fertil...

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-acq...

Higher rates of processed pseudogene acquisition in humans and three great apes revealed by long read assemblies

LINE-1 mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data or human cohorts mostly r...

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 physio...

Large palindromes on the primate X chromosome are preserved by natural selection

Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserve...

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. We developed individual Mitochondrial Genome sequencing (iMiGseq) of full-lengt...

Dynamic Methylome Modification associated with mutational signatures in ageing and etiology of disease

Epigenetic markers and reversible change in the loci of genes regulating critical cell processes, have recently emerged as important biomarkers in the study of disease pathology. The epigenetic chan...

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. Amongst these,...

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 he...

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. H...

VIRUSBreakend: viral integration recognition using single breakends

Integration of viruses into infected host cell DNA can causes DNA damage and can disrupt genes. Recent cost reductions and growth of whole genome sequencing has produced a wealth of data in which vi...

Phospho-RNA sequencing with CircAID-p-seq

Accurate positional information concerning ribosomes and RNA binding proteins with respect to their transcripts is important to understand the global regulatory network underlying protein and RNA fa...

CaBagE: a Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing

A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats. Long-read sequenc...

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex

Alternative splicing is a post-transcriptional regulatory mechanism producing multiple distinct mRNA molecules from a single pre-mRNA. Alternative splicing has a prominent role in the central nervou...

Isoform-level transcriptome Atlas of Macrophage Activation

RNA-seq is routinely used to measure gene expression changes in response to cell perturbation. Genes that are up or down-regulated following perturbation in RNA-seq studies are designated as target ...

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,...

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. Within half a year, since the January 2020 version of NextProt, the numb...

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples

Background High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completenes...

Engineering radioprotective human cells using the tardigrade Damage Suppressor Protein, DSUP

Spaceflight has been documented to produce a number of detrimental effects to physiology and genomic stability, partly a result of Galactic Cosmic Radiation (GCR). In recent years, extensive researc...

precisionFDA Truth Challenge V2:Calling variants from short- and long-reads in difficult-to-map regions

The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20...

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). Methods Embryos with known structural varia...

Control of mitochondrial superoxide production includes programmed mtDNA deletion and restoration

Age-related diseases are intimately linked to mitochondrial impairment. Whether oxidative stress is a major driver of this impairment is still a contentious issue. Here we show that yeast cells ada...

Evaluation of single-molecule sequencing technologies for structural variant detection in two Swedish Human Genomes

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high res...

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. Seco...

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. To investigate the role of SVs in high-altitude adaptation (HAA), we here gene...

Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity after de novo assembly of native full-length hepatitis B virus genomes

Hepatitis B virus (HBV) contains a 3.2 kb DNA genome and causes acute and chronic hepatitis. HBV infection is a global health problem, with 350 million chronically infected people at increased risk ...

Virus-derived variation in diverse human genomes

Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural varian...

Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing

Nanopore sequencing devices read individual RNA strands directly. This facilitates identification of exon linkages and nucleotide modifications; however, using conventional methods the 5' and 3' end...

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. Here, we demonstrate how gene silencing ...

In Vivo Validation of Alternative FDXR Transcripts in Human Blood in Response to Ionizing Radiation

Following cell stress such as ionising radiation (IR) exposure, multiple cellular pathways are activated. We recently demonstrated that ferredoxin reductase (FDXR) has a remarkable IR-induced transc...

A long read mapping method for highly repetitive reference sequences

About 5-10% of the human genome remains inaccessible for functional analysis due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. To enable high-quali...

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, h...

Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants

Background: Despite widespread availability of clinical genetic testing, many individuals with suspected genetic conditions do not have a precise diagnosis. This limits their opportunity to take adv...

Oxford Nanopore announces multiple releases, for high-accuracy, content-rich, high-throughput whole-genome sequencing, and dynamic targeted sequencing

- announced at the 2020 American Society of Human Genetics (ASHG) Meeting. Oxford, UK, 28th October 2020. Oxford Nanopore announces multiple releases that expand and improve its sequencing techno...

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. Next‐Generation...

Benchmarking small variant detection with ONT reveals high performance in challenging regions

Background The development of long read sequencing (LRS) has led to greater access to the human genome. LRS produces long read lengths at the cost of high error rates and has shown to be more useful...

Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using targeted CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

We have developed a generally applicable method based on CRISPR/Cas9-targeted ultra-long read sequencing (CTLR-Seq) to completely and haplotype-specifically resolve, at base-pair resolution, large, ...

Electronic DNA analysis of CSF cell-free tumor DNA to quantify multi-gene molecular response in pediatric high-grade glioma

Purpose Pediatric high-grade glioma (pHGG) diagnosis portends poor prognosis and therapeutic monitoring remains difficult. Tumors release cell-free tumor DNA (cf-tDNA) into cerebrospinal fluid (CSF)...

Single cell transcriptome sequencing on the Nanopore platform with ScNapBar

The current ecosystem of single cell RNA-seq platforms is rapidly expanding, but robust solutions for single cell and single molecule full- length RNA sequencing are virtually absent. A high-through...

Transposable element expression at unique loci in single cells with CELLO-seq

The role of Transposable Elements (TEs) in regulating diverse biological processes, from early development to cancer, is becoming increasing appreciated. However, unlike other biological processes, ...

Assessing the utility of long-read nanopore sequencing for rapid and efficient characterisation of mobile element insertions

Short-read next generation sequencing (NGS) has become the predominant first-line technique used to diagnose patients with rare genetic conditions. Inherent limitations of short-read technology, no...

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 interacti...

Minimal detection and low biological fluctuation of mitochondrial CpG methylation at the single-molecule level

Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is...

Blog: Resolving structural variants causing antithrombin deficiency

In this blog, Alba Sanchis-Juan, Javier Corral, and Belén de la Morena-Barrio describe their research into the genetic basis of thrombophilia, and how nanopore long sequencing reads were needed to r...

The structure, function, and evolution of a complete human chromosome 8

The complete assembly of each human chromosome is essential for understanding human biology and evolution. Using complementary long-read sequencing technologies, we complete the first linear assembl...

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. Here we carried ...

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. Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity h...

Nanopore direct RNA sequencing detects differential expression between human cell populations

Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Therefore, a crucial requirement of RNA sequencing is identifyin...

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). Although thereare many different strategies and approaches, the central premis...

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. We ...

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 nanome...

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 challeng...

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of Transcription Start Sites (TSSs) in several species. Strikingly, ~ ...

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron regulated isoform of Aim2

Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease. We identified a con...

Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing

Purpose Structural variants (SVs) may be an underestimated cause of hereditary cancer syndromes given the current limitations of short-read next-generation sequencing. Here we investigated the util...

Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing

The comprehensive characterization of human leukocyte antigen (HLA) genomic sequences remains a challenging problem. Despite the significant advantages of next-generation sequencing (NGS) in the fie...

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 plasm...

Detection of differential RNA modifications from direct RNA sequencing of human cell lines

Differences in RNA expression can provide insights into the molecular identity of a cell, pathways involved in human diseases, and variation in RNA levels across patients associated with clinical ph...

Long-read human genome sequencing and its applications

Over the past decade, long-read, single-molecule DNA sequencing technologies have emerged as powerful players in genomics. With the ability to generate reads tens to thousands of kilobases in length...

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape o...

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. Here we present the results of our proof of concept Nanop...

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. Current methodologies still face challenges in resolving cis–trans ambiguity ...

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 alongsid...

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 ...

Nanopore sequencing of a forensic STR multiplex reveals loci suitable for single-contributor STR profiling

Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost,...

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. Much of the validation of bioinforma...

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. We implemented who...

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 disor...

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. We develop a universal method (UMIs) to label individual DNA molecules for ...

Amplification-free long read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

A much-debated concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target sites and ...

Location of balanced chromosome-translocation breakpoints by long-read sequencing on the Oxford Nanopore platform

Genomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular...

Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual

Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have re...

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. We perf...

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. Blood-based gene ...

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. We used the MinION platform coupled t...

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 target...

Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information

Background Long DNA reads produced by single-molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short-read DNA fragments. For de novo assembly...

Nanopore sequencing reveals U2AF1 S34F-associated full-length isoforms

U2AF1 S34F is one of the most recurrent splicing factor mutations in lung adenocarcinoma (ADC) and has been shown to cause transcriptome-wide pre-mRNA splicing alterations. While U2AF1 S34F-associat...

Wengan: Efficient and high quality hybrid de novo assembly of human genomes

The continuous improvement of long-read sequencing technologies along with the development of ad-doc algorithms has launched a new de novo assembly era that promises high-quality genomes. However, i...

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...

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

Long-read sequencing (LRS) promises to improve characterization of structural variants (SVs), a major source of genetic diversity. We generated LRS data on 3,622 Icelanders using Oxford Nanopore Tec...

Clinical long-read sequencing of the human mitochondrial genome for mitochondrial disease diagnostics

Purpose Long-read, third generation, sequencing technologies have the potential to improve current state of the art diagnostic strategies. In order to determine if long-read sequencing technologies...

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. However, affordable and fa...

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-ba...

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. Tyrosine kinase inhibitor drugs...

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. The CD1...

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

Higher-order chromatin structure arises from the combinatorial physical interactions of many genomic loci. To investigate this aspect of genome architecture we developed Pore-C, which couples chroma...

A diploid assembly-based benchmark for variants in the Major Histocompatibility Complex

We develop the first human benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle/Personal Genome Project Ashkenazi son (HG002). As a proof-of-principle, we focus on a...

Establishment of an eHAP1 human haploid cell line hybrid reference genome assembled from short and long reads

Background Haploid cell lines are a valuable research tool with broad applicability for genetic assays. As such the fully haploid human cell line, eHAP1, has been used in a wide array of studies. Ho...

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. However, the current state of VXM fails to incorporate donor HLA expression in th...

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 inherite...

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. We develo...

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 mal...

Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study

Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determinin...

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 compa...

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. Fusion gene partner choice and breakpoint-position promiscuity restricts diagno...

Long-read sequencing in deciphering human genetics to a greater depth

Through four decades’ development, DNA sequencing has inched into the era of single-molecule sequencing (SMS), or the third-generation sequencing (TGS), as represented by two distinct technical appr...

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. These include transcripts for Human Leukocyte Antigen (HLA) class I and II receptors which are ...

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 s...

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. GBA mutation carriers have an elevated risk of Parkinson's disease (PD) c...

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 chromo...

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). Targeted RNA next-generation sequencing (NGS) is emerging as a powerful and cli...

Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions

Background Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. Howeve...

Telomere-to-telomere assembly of a complete human X chromosome

After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to...

Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis

Background For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), ...

A multiplex pharmacogenetics assay using the MinION nanopore sequencing device

Aim The MinION nanopore sequencing device opens the opportunity to cost-effective and point-of-care DNA sequencing. We developed a multiplex assay targeting pharmacogenetic variants related to clop...

Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population

Background Next-generation sequencing has allowed for the identification of different genetic variations, which are known to contribute to diseases. Of these, insertions and deletions are the secon...

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly...

Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016

In 2016, a year-long large-scale mumps outbreak occurred in Arkansas among a highly-vaccinated population. A total of 2954 mumps cases were identified during this outbreak. The majority of cases (16...

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 dete...

Resolving MiSeq-generated ambiguities in HLA-DPB1 typing by using the Oxford Nanopore technology

The technical limitations of current next-generation sequencing technologies, combined with an ever-increasing number of human leukocyte antigen (HLA) alleles, forms the basis for the additional amb...

Targeting destabilized DNA G-quadruplexes and aberrant splicing in drug-resistant glioblastoma

Temozolomide (TMZ) is a chemotherapy agent that adds mutagenic adducts to guanine, and is first-line standard of care for the aggressive brain cancer glioblastoma (GBM). Methyl guanine methyl transf...

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-base...

Long read sequencing reveals a novel class of structural aberrations in cancers: identification and characterization of cancerous local amplifications

Here we report identification of a new class of local structural aberrations in lung cancers. The whole-genome sequencing of cell lines using a long read sequencer, PromethION, demonstrated that typ...

Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome

Background Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de no...

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 geno...

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. Preimplantation genetic t...

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. Current methods are limited by the loss of ...

Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability

Long nanopore reads enhance structural variant resolution. Cacace et al. performed whole genome sequencing to investigate an unresolved autosomal dominant dementia family; long reads obtained from P...

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...

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. The wid...

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. Here, we report robust detection of human repeat expansion...

Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions

The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neu...

Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

Background The human genome contains “dark” gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mut...

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore sequencing to evaluate CpG methylation and chromati...

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. The approach is...

Forensic tri-allelic SNP genotyping using nanopore sequencing

The potential and current state-of-the-art of forensic SNP genotyping using nanopore sequencing was investigated with a panel of 16 tri-allelic single nucleotide polymorphisms (SNPs), multiplexing f...

Nanopore native RNA sequencing of a human poly(A) transcriptome

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological...

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...

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. Identification of specific gene fusions can be essential for distinguishing benign f...

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

We sequenced the genome of the Yoruban reference individual NA19240 on the long read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and...

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. Although historically expensive and time consuming, new sequencing te...

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 chro...

Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing

Disease associated chromosomal rearrangements often have break points located within disease causing genes or in their vicinity. The purpose of this study is to characterize a balanced reciprocal tr...

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have thei...

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...

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. Here we show that abnormal ...

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

Background Mutations in GBA cause Gaucher disease when biallelic and are strong risk factors for Parkinson's disease when heterozygous. GBA analysis is complicated by the nearby pseudogene. We aime...

Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing

Background Studies have shown that complex structural variants (cxSVs) contribute to human genomic variation and can cause Mendelian disease. We aimed to identify cxSVs relevant to Mendelian diseas...

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. Pa...

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 id...

Nanopore sequencing and assembly of a human genome with ultra-long reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, re...

"Most complete human genome assembly to date using single tech": Nature Biotech paper from consortium of nine centres use MinION to sequence human genome

Nature Biotechnology has today published a whole human genome assembly using the MinION nanopore DNA sequencer. The consortium of researchers, from nine different institutions, demonstrated the mos...

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 ma...

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. Several studies repor...

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...

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. Here we exploited the long reads of the nan...

Mapping DNA methylation with high-throughput nanopore sequencing

DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer...

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. The MinION has the potential to enable expedited point-o...

The potential impact of nanopore sequencing on human genetics.

Nanopore sequencing has been available to customers for a little over three years. Recently the milestone of sequencing and assembling a human genome on this platform was achieved for the first time...

Linear assembly of a human centromere on the Y chromosome

The human genome reference sequence remains incomplete owing to the challenge of assembling long tracts of near-identical tandem repeats in centromeres. We implemented a nanopore sequencing strategy...

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 assoc...

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-pos...

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 r...

Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing

Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defi...

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-onse...

Rapid re-identification of human samples using portable DNA sequencing

DNA re-identification is used for a broad suite of applications, ranging from cell line authentication to forensics. However, current re-identification schemes suffer from high latency and limited a...

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the ge...

Nanopore sequencing and assembly of a human genome with ultra-long sequence reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, re...

Detecting DNA cytosine methylation using nanopore sequencing

In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanop...

Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

Variations in the genetic code, from single point mutations to large structural or copy number alterations, influence susceptibility, onset, and progression of genetic diseases and tumor transformat...

NA12878 Human Reference on Oxford Nanopore MinION

We have sequenced the CEPH1463 (NA12878/GM12878, Ceph/Utah pedigree) human genome reference standard on the Oxford Nanopore MinION using 1D ligation kits (450 bp/s) using R9.4 chemistry (FLO-MIN106)...

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

Advances in nanopore sequencing technology have enabled investigation of the full catalogue of covalent DNA modifications. We present the first algorithm for the identification of modified nucleotid...

Mapping DNA methylation with high-throughput nanopore sequencing

DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer...

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.. [subscript...

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 seque...

Detecting DNA cytosine methylation using nanopore sequencing

In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanop...