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Publications tagged "Cancer research"

Structural variation & cancer: top 7 things to read right now

Somatic mutations are the driving force behind cancer development, and structural variations (SVs) are more and more being recognised as an important class of these mutations. The detection of SVs i...

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...

Mayo Clinic and Oxford Nanopore announce collaboration to advance precision medicine for cancer and genetic disorders

Joint development collaboration to bring leading-edge nanopore sequencing into clinical laboratories at Mayo Clinic to increase understanding and improve treatment of cancer and genetic disorders

American Association of Cancer Research: Oxford Nanopore showcases breakthrough technology to generate most comprehensive insights into cancer genomes

Meet our team of nanopore experts in booth #801 and mark your calendars for our industry spotlight workshop on Tuesday, 18th April at 12:30PM (EST). The genetic underpinnings of cancer are diverse...

Oxford Nanopore and 4bases announce collaboration to combine nanopore sequencing devices and 4bases kits to support rapid, high-accuracy analyses in human and cancer genetics

Oxford Nanopore’s devices with 4bases kits will enable decentralised, flexible scalability with a significant decrease in turnaround time for clinical researchers in Italy and Switzerland, with a fi...

Oxford Nanopore Technologies and Cyclomics begin developer testing on non-invasive method for accurate and fast detection of molecules associated with cancer

Research collaboration has resulted in new ‘liquid biopsy’ research workflow using nanopore sequencing to detect molecules that are associated with cancer, circulating in blood

Interview: Rapid leukemia classification using nanopore sequencing

Mélanie Sagniez is a PhD student in Bioinformatics at CHU Sainte-Justine Research Center & Department of Biochemistry and Molecular Medicine, Université de Montréal in Canada, where she focuss...

Interview: Optimisation and validation of a nanopore-based sequencing method for potential molecular testing of CNS tumours

Mashiat Mimosa is a research-based MSc. student at University of Toronto’s Department of Laboratory Medicine and Pathobiology where her work focusses on cancer research, neuro-oncology, and genomi...

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...

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

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...

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...

Personalized genome assembly for accurate cancer somatic mutation discovery using cancer-normal paired reference samples

The use of personalized genome assembly as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but never been systematically investigated. Here we addr...

Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. There are different mutational mechanisms causing s...

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...

Oncogenic fusion protein anchors to histone acetyltransferase complex to the coding region of active genes

A chromosomal translocation found in cannibalistic acute myeloid leukemia (AML) leads to an in-frame fusion of the transcription elongation repressor ZMYND11 to MBTD1, a subunit of the NuA4/TIP60 hi...

Epstein-Barr virus long non-coding RNA RPMS1 full-length spliceome in transformed epithelial tissue

Epstein-Barr virus is associated with two types of epithelial neoplasms, nasopharyngeal carcinoma and gastric adenocarcinoma. The viral long non-coding RNA RPMS1 is the most abundantly expressed pol...

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 ori...

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. Diverse molecular approaches are currently used for the mol...

Highly accurate barcode and UMI error correction using dual nucleotide dimer blocks allows direct single-cell nanopore transcriptome sequencing

Droplet-based single-cell sequencing techniques have provided unprecedented insight into cellular heterogeneities within tissues. However, these approaches only allow for the measurement of the dist...

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. However, littl...

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...

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. Here, we optimized an in vivo genetic screening strategy for evaluating dependencies in acute myeloid leuk...

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

DNA replication timing and three-dimensional (3D) genome organisation occur across large domains associated with distinct epigenome patterns to functionally compartmentalise genome regulation. Howev...

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,...

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 in...

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 ...

Two new papers further demonstrate the role adaptive sampling could play in understanding genetic disease

Two new papers published in Nature Biotech today, from teams at the University of Nottingham and Johns Hopkins University, demonstrate the use of real-time nanopore sequencing and adaptive sampling ...

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...

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 ...

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)...

Blog: Copy number variation analysis from plasma: is it feasible using nanopore sequencing?

In this blog, Filippo Martignano shares his research into copy number variation (CNV) analysis in cancer, from cell-free DNA samples, using shallow whole-genome sequencing.

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. Contiguous and compl...

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...

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 ...

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 ...

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...

Precise characterization of somatic structural variations and mobile element insertions from paired long-read sequencing data with nanomonsv

We introduce our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. Using paired lo...

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...

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...

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. Here, we used a long-read nanopore-based sequen...

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...

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...

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...

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...

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. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirab...

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 canc...

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...

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...

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...

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...

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...

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...

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...

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 ...

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...

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as ant...

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-length isoform changes may better elucidate the functional consequences of these mutations. We report nanopor...

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...

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. Third-generation sequencing platforms such as si...

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...

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. I...

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...

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...

Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events

Background Laboratory assays evaluating the effect of DNA sequence variants on BRCA1 mRNA splicing may contribute to classification by providing molecular evidence. However, our knowledge of normal...

Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer

Here, we employed cDNA amplicon sequencing using a long-read portable sequencer, MinION, to characterize various types of mutations in cancer-related genes, namely, EGFR, KRAS, NRAS and NF1. For hom...

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...

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...

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...

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). A broad spectrum of molecular techniques has been employ...

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. Not only do the reads (or paired-...

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. This leads to partial recove...