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  1. Article: Single-Molecule Sequencing: Towards Clinical Applications

    Ameur, Adam / Wigard P. Kloosterman / Matthew S. Hestand

    Trends in biotechnology. 2019 Jan., v. 37, no. 1

    2019  

    Abstract: In the past several years, single-molecule sequencing platforms, such as those by Pacific Biosciences and Oxford Nanopore Technologies, have become available to researchers and are currently being tested for clinical applications. They offer ... ...

    Abstract In the past several years, single-molecule sequencing platforms, such as those by Pacific Biosciences and Oxford Nanopore Technologies, have become available to researchers and are currently being tested for clinical applications. They offer exceptionally long reads that permit direct sequencing through regions of the genome inaccessible or difficult to analyze by short-read platforms. This includes disease-causing long repetitive elements, extreme GC content regions, and complex gene loci. Similarly, these platforms enable structural variation characterization at previously unparalleled resolution and direct detection of epigenetic marks in native DNA. Here, we review how these technologies are opening up new clinical avenues that are being applied to pathogenic microorganisms and viruses, constitutional disorders, pharmacogenomics, cancer, and more.
    Keywords DNA ; epigenetics ; genes ; loci ; microorganisms ; nanopores ; neoplasms ; pharmacogenomics ; viruses
    Language English
    Dates of publication 2019-01
    Size p. 72-85.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 47474-5
    ISSN 1879-3096 ; 0167-7799
    ISSN (online) 1879-3096
    ISSN 0167-7799
    DOI 10.1016/j.tibtech.2018.07.013
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: From squiggle to basepair

    Franka J. Rang / Wigard P. Kloosterman / Jeroen de Ridder

    Genome Biology, Vol 19, Iss 1, Pp 1-

    computational approaches for improving nanopore sequencing read accuracy

    2018  Volume 11

    Abstract: Abstract Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a ... ...

    Abstract Abstract Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15%. Here, we review computational approaches determining the nanopore sequencing error rate. Furthermore, we outline strategies for translation of raw sequencing data into base calls for detection of base modifications and for obtaining consensus sequences.
    Keywords Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2018-07-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Author Correction

    Alessio Marcozzi / Myrthe Jager / Martin Elferink / Roy Straver / Joost H. van Ginkel / Boris Peltenburg / Li-Ting Chen / Ivo Renkens / Joyce van Kuik / Chris Terhaard / Remco de Bree / Lot A. Devriese / Stefan M. Willems / Wigard P. Kloosterman / Jeroen de Ridder

    npj Genomic Medicine, Vol 8, Iss 1, Pp 1-

    Accurate detection of circulating tumor DNA using nanopore consensus sequencing

    2023  Volume 1

    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: sv-callers

    Arnold Kuzniar / Jason Maassen / Stefan Verhoeven / Luca Santuari / Carl Shneider / Wigard P. Kloosterman / Jeroen de Ridder

    PeerJ, Vol 8, p e

    a highly portable parallel workflow for structural variant detection in whole-genome sequence data

    2020  Volume 8214

    Abstract: Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still ... ...

    Abstract Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems.
    Keywords Scientific workflow ; Cancer genomics ; Variant calling ; Structural variants ; High-performance computing ; Cloud computing ; Medicine ; R ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Accurate detection of circulating tumor DNA using nanopore consensus sequencing

    Alessio Marcozzi / Myrthe Jager / Martin Elferink / Roy Straver / Joost H. van Ginkel / Boris Peltenburg / Li-Ting Chen / Ivo Renkens / Joyce van Kuik / Chris Terhaard / Remco de Bree / Lot A. Devriese / Stefan M. Willems / Wigard P. Kloosterman / Jeroen de Ridder

    npj Genomic Medicine, Vol 6, Iss 1, Pp 1-

    2021  Volume 11

    Abstract: Abstract 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 ...

    Abstract Abstract 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. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. Here, we describe a new technique, CyclomicsSeq, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule. Consensus calling of the DNA copies increased the base-calling accuracy ~60×, enabling accurate detection of TP53 mutations at frequencies down to 0.02%. We demonstrate that a TP53-specific CyclomicsSeq assay can be successfully used to monitor tumor burden during treatment for head-and-neck cancer patients. CyclomicsSeq can be applied to any genomic locus and offers an accurate diagnostic liquid biopsy approach that can be implemented in clinical workflows.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: A multi-platform reference for somatic structural variation detection

    Jose Espejo Valle-Inclan / Nicolle J.M. Besselink / Ewart de Bruijn / Daniel L. Cameron / Jana Ebler / Joachim Kutzera / Stef van Lieshout / Tobias Marschall / Marcel Nelen / Peter Priestley / Ivo Renkens / Margaretha G.M. Roemer / Markus J. van Roosmalen / Aaron M. Wenger / Bauke Ylstra / Remond J.A. Fijneman / Wigard P. Kloosterman / Edwin Cuppen

    Cell Genomics, Vol 2, Iss 6, Pp 100139- (2022)

    2022  

    Abstract: Summary: Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and ... ...

    Abstract Summary: Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and bioinformatic analysis pipelines. Here, we performed somatic SV analysis of the paired melanoma and normal lymphoblastoid COLO829 cell lines using four different sequencing technologies. Based on the evidence from multiple technologies combined with extensive experimental validation, we compiled a comprehensive set of carefully curated and validated somatic SVs, comprising all SV types. We demonstrate the utility of this resource by determining the SV detection performance as a function of tumor purity and sequence depth, highlighting the importance of assessing these parameters in cancer genomics projects. The truth somatic SV dataset as well as the underlying raw multi-platform sequencing data are freely available and are an important resource for community somatic benchmarking efforts.
    Keywords structural variant ; cancer ; truth set ; benchmarking ; short sequencing read ; long sequencing read ; Genetics ; QH426-470 ; Internal medicine ; RC31-1245
    Subject code 572
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

    Christina Stangl / Sam de Blank / Ivo Renkens / Liset Westera / Tamara Verbeek / Jose Espejo Valle-Inclan / Rocio Chamorro González / Anton G. Henssen / Markus J. van Roosmalen / Ronald W. Stam / Emile E. Voest / Wigard P. Kloosterman / Gijs van Haaften / Glen R. Monroe

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 14

    Abstract: Fusion genes are a hallmarks of cancer, though breakpoint-position promiscuity restricts diagnostic detection. Here, the authors present FUDGE, a CRISPR-Cas9-based enrichment strategy for nanopore sequencing to identify target fusions irrespective of ... ...

    Abstract Fusion genes are a hallmarks of cancer, though breakpoint-position promiscuity restricts diagnostic detection. Here, the authors present FUDGE, a CRISPR-Cas9-based enrichment strategy for nanopore sequencing to identify target fusions irrespective of genomic breakpoint or fusion partner.
    Keywords Science ; Q
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

    Christina Stangl / Sam de Blank / Ivo Renkens / Liset Westera / Tamara Verbeek / Jose Espejo Valle-Inclan / Rocio Chamorro González / Anton G. Henssen / Markus J. van Roosmalen / Ronald W. Stam / Emile E. Voest / Wigard P. Kloosterman / Gijs van Haaften / Glen R. Monroe

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 14

    Abstract: Fusion genes are a hallmarks of cancer, though breakpoint-position promiscuity restricts diagnostic detection. Here, the authors present FUDGE, a CRISPR-Cas9-based enrichment strategy for nanopore sequencing to identify target fusions irrespective of ... ...

    Abstract Fusion genes are a hallmarks of cancer, though breakpoint-position promiscuity restricts diagnostic detection. Here, the authors present FUDGE, a CRISPR-Cas9-based enrichment strategy for nanopore sequencing to identify target fusions irrespective of genomic breakpoint or fusion partner.
    Keywords Science ; Q
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: The presence of extra chromosomes leads to genomic instability

    Verena Passerini / Efrat Ozeri-Galai / Mirjam S. de Pagter / Neysan Donnelly / Sarah Schmalbrock / Wigard P. Kloosterman / Batsheva Kerem / Zuzana Storchová

    Nature Communications, Vol 7, Iss 1, Pp 1-

    2016  Volume 12

    Abstract: One of the hallmarks of cancer cells is aneuploidy, however the molecular effects are poorly understood. Here the authors show that trisomic and tetrasomic cells display increased genomic instability and reduced levels of the helicase MCM2-7. ...

    Abstract One of the hallmarks of cancer cells is aneuploidy, however the molecular effects are poorly understood. Here the authors show that trisomic and tetrasomic cells display increased genomic instability and reduced levels of the helicase MCM2-7.
    Keywords Science ; Q
    Language English
    Publishing date 2016-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

    Jose Espejo Valle-Inclan / Christina Stangl / Anouk C. de Jong / Lisanne F. van Dessel / Markus J. van Roosmalen / Jean C. A. Helmijr / Ivo Renkens / Roel Janssen / Sam de Blank / Chris J. de Witte / John W. M. Martens / Maurice P. H. M. Jansen / Martijn P. Lolkema / Wigard P. Kloosterman

    Genome Medicine, Vol 13, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: Abstract Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. ...

    Abstract Abstract Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of high-grade ovarian and prostate cancer patients and validated on average ten somatic SVs per patient with breakpoint-spanning PCR mini-amplicons. These SVs could be quantified in ctDNA samples of patients with metastatic prostate cancer using a digital PCR assay. The results suggest that SV dynamics correlate with and may improve existing treatment-response biomarkers such as PSA. https://github.com/UMCUGenetics/SHARC .
    Keywords Genomics ; Liquid biopsies ; Nanopore ; Cancer ; Structural variation ; Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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