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BeyondSeq

Genomic diagnostics beyond the sequence

Total Cost €

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EC-Contrib. €

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Partnership

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 BeyondSeq project word cloud

Explore the words cloud of the BeyondSeq project. It provides you a very rough idea of what is the project "BeyondSeq" about.

hematological    reagents    genetic    cultures    reads    lung    amounts    mapping    resistance    ngs    atrophy    single    bridge    diagnostics    screens    lesions    epigenetic    bias    assays    resolving    profiling    amplification    commercialization    ready    medically    colorectal    hardware    proof    prototype    sequencing    variations    diagnosis    prone    malignancies    biopsy    samples    markers    chromosome    individual    layout    suffer    resolution    antibiotic    technologies    preventing    diagnostic    imposed    domains    optical    validation    stage    point    generation    barcoding    ultimately    rare    micro    spinal    platforms    tools    inhomogeneous    unamplified    cytogenetic    genomic    automated    software    aberrations    gap    erasure    throughput    analyzing    contrast    correlating    molecules    limitations    prevent    dna    infections    pcr    extraction    preparation    base    damage    toolbox    prognosis    tumor    data    circulating    quantification    readout    mutations    cancer    muscular    provides    bacterial    native    types   

Project "BeyondSeq" data sheet

The following table provides information about the project.

Coordinator
TEL AVIV UNIVERSITY 

Organization address
address: RAMAT AVIV
city: TEL AVIV
postcode: 69978
website: http://www.tau.ac.il/

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Israel [IL]
 Project website http://www.beyondseq.eu
 Total cost 6˙034˙026 €
 EC max contribution 6˙034˙026 € (100%)
 Programme 1. H2020-EU.3.1.3. (Treating and managing disease)
 Code Call H2020-PHC-2014-two-stage
 Funding Scheme RIA
 Starting year 2015
 Duration (year-month-day) from 2015-05-01   to  2019-04-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    TEL AVIV UNIVERSITY IL (TEL AVIV) coordinator 1˙147˙250.00
2    TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY IL (HAIFA) participant 844˙475.00
3    CHALMERS TEKNISKA HOEGSKOLA AB SE (GOETEBORG) participant 840˙361.00
4    LUNDS UNIVERSITET SE (LUND) participant 799˙863.00
5    KATHOLIEKE UNIVERSITEIT LEUVEN BE (LEUVEN) participant 778˙312.00
6    THE UNIVERSITY OF BIRMINGHAM UK (BIRMINGHAM) participant 703˙578.00
7    GENOMIC VISION SA FR (BAGNEUX) participant 674˙497.00
8    IMPASARA LIMITED UK (LONDON) participant 245˙687.00

Map

 Project objective

Cytogenetic diagnostic approaches provide information on the single-chromosome level but suffer from low resolution and throughput. In contrast, next generation sequencing (NGS) based diagnostics provides single base resolution and high throughput but suffer from short reads that prevent analysis of large genomic aberrations as well as being prone to PCR-amplification bias and erasure of epigenetic information. This proposal aims to bridge the gap between these domains by analyzing long individual DNA molecules without PCR-amplification via utilization of emerging optical DNA mapping technologies. We specifically address three types of challenges to current genomic based diagnostics: 1. Loss of relevant information such as DNA damage lesions, rare mutations or epigenetic markers following PCR amplification. 2. Limitations in resolving long-range variations in genomic layout and correlating them with single point mutations, preventing large scale screens. 3. Limitations imposed by the sample such as low sample amounts (micro biopsy, circulating tumor DNA) or inhomogeneous/highly variable samples (bacterial cultures). We will develop a robust toolbox for integrated genetic and epigenetic profiling of single DNA molecules that will include automated sample preparation of native unamplified DNA as well as the hardware and software platforms and analysis tools for readout, extraction and quantification of medically relevant genomic information. This technology will be used to develop a set of specific, proof of principle diagnostic assays based on optical barcoding of individual DNA molecules. These assays will address: -Bacterial infections and antibiotic resistance -Diagnosis/prognosis tools for hematological malignancies -Spinal Muscular Atrophy -Early diagnosis of colorectal and lung cancer. Ultimately our project will provide reagents, prototype DNA barcoding devices and data analysis software ready for large scale validation and early stage commercialization.

 Deliverables

List of deliverables.
Expanded database of plasmids from clinical isolates Documents, reports 2020-02-06 14:55:08
Toolbox for identification of bacteria and plasmids Demonstrators, pilots, prototypes 2020-02-06 14:55:08
International conference Other 2020-02-06 14:55:08
Dissemination plan Documents, reports 2020-02-06 14:55:06
Project logo, leaflets, presentation & website Other 2020-02-06 14:55:06
Fully sequenced and validated database of bacterial DNA Documents, reports 2020-02-06 14:55:06

Take a look to the deliverables list in detail:  detailed list of BeyondSeq deliverables.

 Publications

year authors and title journal last update
List of publications.
2019 Vilhelm Müller, Albertas Dvirnas, John Andersson, Vandana Singh, Sriram KK, Pegah Johansson, Yuval Ebenstein, Tobias Ambjörnsson, Fredrik Westerlund
Enzyme-free optical DNA mapping of the human genome using competitive binding
published pages: , ISSN: 0305-1048, DOI: 10.1093/nar/gkz489
Nucleic Acids Research 2020-02-06
2019 Hila Sharim, Assaf Grunwald, Tslil Gabrieli, Yael Michaeli, Sapir Margalit, Dmitry Torchinsky, Rani Arielly, Gil Nifker, Matyas Juhasz, Felix Gularek, Miguel Almalvez, Brandon Dufault, Sreetama Sen Chandra, Alexander Liu, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Kathryn R. Wagner, Jonathan Pevsner, Jeff Reifenberger, Ernest T. Lam, Alex R. Hastie, Han Cao, Hayk Barseghyan, Elmar Weinhold, Y
Long-read single-molecule maps of the functional methylome
published pages: 646-656, ISSN: 1088-9051, DOI: 10.1101/gr.240739.118
Genome Research 29/4 2020-02-06
2018 Nathaniel W. Holton, Yuval Ebenstein, Natalie R. Gassman
Broad spectrum detection of DNA damage by Repair Assisted Damage Detection (RADD)
published pages: 42-49, ISSN: 1568-7864, DOI: 10.1016/j.dnarep.2018.04.007
DNA Repair 66-67 2020-02-06
2018 Jochem Deen, Su Wang, Sven Van Snick, Volker Leen, Kris Janssen, Johan Hofkens, Robert K Neely
A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA
published pages: e64-e64, ISSN: 0305-1048, DOI: 10.1093/nar/gky184
Nucleic Acids Research 46/11 2020-02-06
2017 Adam Zrehen, Tal Gilboa, Amit Meller
Real-time visualization and sub-diffraction limit localization of nanometer-scale pore formation by dielectric breakdown
published pages: 16437-16445, ISSN: 2040-3364, DOI: 10.1039/c7nr02629c
Nanoscale 9/42 2020-02-06
2018 Jason P. Beech, Bao Dang Ho, Geneviève Garriss, Vitor Oliveira, Birgitta Henriques-Normark, Jonas O. Tegenfeldt
Separation of pathogenic bacteria by chain length
published pages: 223-231, ISSN: 0003-2670, DOI: 10.1016/j.aca.2017.11.050
Analytica Chimica Acta 1000 2020-02-06
2017 Rani Arielly, Yuval Ebenstein
Irys Extract
published pages: 134-136, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btx437
Bioinformatics 34/1 2020-02-06
2017 A.H. Squires, T. Gilboa, C. Torfstein, N. Varongchayakul, A. Meller
Chapter Fourteen - Single-Molecule Characterization of DNA–Protein Interactions Using Nanopore Biosensors
published pages: 353-385, ISSN: 0076-6879, DOI: 10.1016/bs.mie.2016.08.010
Methods in Enzymology 2020-02-06
2018 Albertas Dvirnas, Christoffer Pichler, Callum L. Stewart, Saair Quaderi, Lena K. Nyberg, Vilhelm Müller, Santosh Kumar Bikkarolla, Erik Kristiansson, Linus Sandegren, Fredrik Westerlund, Tobias Ambjörnsson
Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach
published pages: e0193900, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0193900
PLOS ONE 13/3 2020-02-06
2017 Milena Helmer Lauer, Charlotte Vranken, Jochem Deen, Wout Frederickx, Willem Vanderlinden, Nathaniel Wand, Volker Leen, Marcelo H. Gehlen, Johan Hofkens, Robert K. Neely
Methyltransferase-directed covalent coupling of fluorophores to DNA
published pages: 3804-3811, ISSN: 2041-6520, DOI: 10.1039/C6SC04229E
Chemical Science 8/5 2020-02-06
2017 Noa Gilat, Tzlil Tabachnik, Amit Shwartz, Tamar Shahal, Dmitry Torchinsky, Yael Michaeli, Gil Nifker, Shahar Zirkin, Yuval Ebenstein
Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers
published pages: , ISSN: 1868-7075, DOI: 10.1186/s13148-017-0368-9
Clinical Epigenetics 9/1 2020-02-06
2018 Nitinun Varongchayakul, Diana Huttner, Mark W. Grinstaff, Amit Meller
Sensing Native Protein Solution Structures Using a Solid-state Nanopore: Unraveling the States of VEGF
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-19332-y
Scientific Reports 8/1 2020-02-06
2017 Trung S. H. Tran, Bao D. Ho, Jason P. Beech, Jonas O. Tegenfeldt
Open channel deterministic lateral displacement for particle and cell sorting
published pages: 3592-3600, ISSN: 1473-0197, DOI: 10.1039/C7LC00707H
Lab Chip 17/21 2020-02-06
2017 Jochem Deen, Charlotte Vranken, Volker Leen, Robert K. Neely, Kris P. F. Janssen, Johan Hofkens
Methyltransferase-Directed Labeling of Biomolecules and its Applications
published pages: 5182-5200, ISSN: 1433-7851, DOI: 10.1002/anie.201608625
Angewandte Chemie International Edition 56/19 2020-02-06
2018 Tslil Gabrieli, Hila Sharim, Gil Nifker, Jonathan Jeffet, Tamar Shahal, Rani Arielly, Michal Levi-Sakin, Lily Hoch, Nissim Arbib, Yael Michaeli, Yuval Ebenstein
Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays
published pages: , ISSN: 1936-0851, DOI: 10.1021/acsnano.8b03023
ACS Nano 2020-02-06
2017 Vilhelm Müller, Fredrik Westerlund
Optical DNA mapping in nanofluidic devices: principles and applications
published pages: 579-590, ISSN: 1473-0197, DOI: 10.1039/c6lc01439a
Lab on a Chip 17/4 2020-02-06
2017 Karolin Frykholm, Lena K. Nyberg, Fredrik Westerlund
Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools
published pages: 650-661, ISSN: 1757-9694, DOI: 10.1039/c7ib00085e
Integrative Biology 9/8 2020-02-06
2019 Nathaniel O Wand, Darren A Smith, Andrew A Wilkinson, Ashleigh E Rushton, Stephen J W Busby, Iain B Styles, Robert K Neely
DNA barcodes for rapid, whole genome, single-molecule analyses
published pages: , ISSN: 0305-1048, DOI: 10.1093/nar/gkz212
Nucleic Acids Research 2020-02-06
2019 Shuyi Wu, Jonathan Jeffet, Assaf Grunwald, Hila Sharim, Noa Gilat, Dmitry Torchinsky, Quanshui Zheng, Shahar Zirkin, Luping Xu, Yuval Ebenstein
Microfluidic DNA combing for parallel single-molecule analysis
published pages: 45101, ISSN: 0957-4484, DOI: 10.1088/1361-6528/aaeddc
Nanotechnology 30/4 2020-02-06
2018 Tamar Shahal, Omri Koren, Gabi Shefer, Naftali Stern, Yuval Ebenstein
Hypersensitive quantification of global 5-hydroxymethylcytosine by chemoenzymatic tagging
published pages: 87-96, ISSN: 0003-2670, DOI: 10.1016/j.aca.2018.08.035
Analytica Chimica Acta 1038 2020-02-06
2019 Christian Heck, Yael Michaeli, Ilko Bald, Yuval Ebenstein
Analytical epigenetics: single-molecule optical detection of DNA and histone modifications
published pages: 151-158, ISSN: 0958-1669, DOI: 10.1016/j.copbio.2018.09.006
Current Opinion in Biotechnology 55 2020-02-06
2018 Tal Gilboa, Adam Zrehen, Arik Girsault, Amit Meller
Optically-Monitored Nanopore Fabrication Using a Focused Laser Beam
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-28136-z
Scientific Reports 8/1 2020-02-06
2016 Jonathan Jeffet, Asaf Kobo, Tianxiang Su, Assaf Grunwald, Ori Green, Adam N. Nilsson, Eli Eisenberg, Tobias Ambjörnsson, Fredrik Westerlund, Elmar Weinhold, Doron Shabat, Prashant K. Purohit, Yuval Ebenstein
Super-Resolution Genome Mapping in Silicon Nanochannels
published pages: 9823-9830, ISSN: 1936-0851, DOI: 10.1021/acsnano.6b05398
ACS Nano 10/11 2020-02-06
2016 Lena K. Nyberg, Saair Quaderi, Gustav Emilsson, Nahid Karami, Erik Lagerstedt, Vilhelm Müller, Charleston Noble, Susanna Hammarberg, Adam N. Nilsson, Fei Sjöberg, Joachim Fritzsche, Erik Kristiansson, Linus Sandegren, Tobias Ambjörnsson, Fredrik Westerlund
Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
published pages: 30410, ISSN: 2045-2322, DOI: 10.1038/srep30410
Scientific Reports 6 2020-02-06
2016 Ossama N. Assad, Tal Gilboa, Joshua Spitzberg, Matyas Juhasz, Elmar Weinhold, Amit Meller
Light-Enhancing Plasmonic-Nanopore Biosensor for Superior Single-Molecule Detection
published pages: 1605442, ISSN: 0935-9648, DOI: 10.1002/adma.201605442
Advanced Materials 2020-02-06
2016 Vilhelm Müller, Fredrika Rajer, Karolin Frykholm, Lena K. Nyberg, Saair Quaderi, Joachim Fritzsche, Erik Kristiansson, Tobias Ambjörnsson, Linus Sandegren, Fredrik Westerlund
Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping
published pages: 37938, ISSN: 2045-2322, DOI: 10.1038/srep37938
Scientific Reports 6 2020-02-06
2016 Vilhelm Müller, Nahid Karami, Lena K. Nyberg, Christoffer Pichler, Paola C. Torche Pedreschi, Saair Quaderi, Joachim Fritzsche, Tobias Ambjörnsson, Christina Åhrén, Fredrik Westerlund
Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping
published pages: 322-328, ISSN: 2373-8227, DOI: 10.1021/acsinfecdis.6b00017
ACS Infectious Diseases 2/5 2020-02-06
2016 Tal Gilboa, Chen Torfstein, Matyas Juhasz, Assaf Grunwald, Yuval Ebenstein, Elmar Weinhold, Amit Meller
Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores
published pages: 8861-8870, ISSN: 1936-0851, DOI: 10.1021/acsnano.6b04748
ACS Nano 10/9 2020-02-06

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