BeyondSeq
Genomic diagnostics beyond the sequence
Total Cost €
0EC-Contrib. €
0Partnership
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Project "BeyondSeq" data sheet
The following table provides information about the project.
| Coordinator |
TEL AVIV UNIVERSITY
Organization address contact info |
| 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.
| # | ||||
|---|---|---|---|---|
| 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
| 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 |
|---|---|---|---|
| 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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