Genomic diagnostics beyond the sequence

Deliverables

Expanded database of plasmids from clinical isolates

Expanded database of unsequenced plasmids. An expanded database with >100 previously non-sequenced plasmids from clinical isolates, each plasmid with its clinical phenotype.

Fully sequenced and validated database of bacterial DNA

Fully validated database of sequenced bacterial DNA. A database of sequenced bacterial DNA, both chromosomal and plasmids, that has been validated with experiments on >20 of the plasmids and >20 of the bacterial strains in the database.

Dissemination plan

Toolbox for identification of bacteria and plasmids

Comprehensive toolbox for identification of bacteria and plasmids. Fully working and validated software as well as experimental protocols adapted to clinical situations for identification of barcode patterns along DNA for both bacterial identification and characterization of antibiotic resistance

Project logo, leaflets, presentation & website
International conference

Publications

Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays

Author(s): Tslil Gabrieli, Hila Sharim, Gil Nifker, Jonathan Jeffet, Tamar Shahal, Rani Arielly, Michal Levi-Sakin, Lily Hoch, Nissim Arbib, Yael Michaeli, Yuval Ebenstein
Published in: ACS Nano, 2018, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.8b03023

A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA

Author(s): Jochem Deen, Su Wang, Sven Van Snick, Volker Leen, Kris Janssen, Johan Hofkens, Robert K Neely
Published in: Nucleic Acids Research, Issue 46/11, 2018, Page(s) e64-e64, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky184

Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers

Author(s): Noa Gilat, Tzlil Tabachnik, Amit Shwartz, Tamar Shahal, Dmitry Torchinsky, Yael Michaeli, Gil Nifker, Shahar Zirkin, Yuval Ebenstein
Published in: Clinical Epigenetics, Issue 9/1, 2017, ISSN 1868-7075
Publisher: Springer Verlag
DOI: 10.1186/s13148-017-0368-9

Sensing Native Protein Solution Structures Using a Solid-state Nanopore: Unraveling the States of VEGF

Author(s): Nitinun Varongchayakul, Diana Huttner, Mark W. Grinstaff, Amit Meller
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-19332-y

Optical DNA mapping in nanofluidic devices: principles and applications

Author(s): Vilhelm Müller, Fredrik Westerlund
Published in: Lab on a Chip, Issue 17/4, 2017, Page(s) 579-590, ISSN 1473-0197
Publisher: Royal Society of Chemistry
DOI: 10.1039/c6lc01439a

Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach

Author(s): 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
Published in: PLOS ONE, Issue 13/3, 2018, Page(s) e0193900, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0193900

Open channel deterministic lateral displacement for particle and cell sorting

Author(s): Trung S. H. Tran, Bao D. Ho, Jason P. Beech, Jonas O. Tegenfeldt
Published in: Lab Chip, Issue 17/21, 2017, Page(s) 3592-3600, ISSN 1473-0197
Publisher: Royal Society of Chemistry
DOI: 10.1039/C7LC00707H

Broad spectrum detection of DNA damage by Repair Assisted Damage Detection (RADD)

Author(s): Nathaniel W. Holton, Yuval Ebenstein, Natalie R. Gassman
Published in: DNA Repair, Issue 66-67, 2018, Page(s) 42-49, ISSN 1568-7864
Publisher: Elsevier BV
DOI: 10.1016/j.dnarep.2018.04.007

Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools

Author(s): Karolin Frykholm, Lena K. Nyberg, Fredrik Westerlund
Published in: Integrative Biology, Issue 9/8, 2017, Page(s) 650-661, ISSN 1757-9694
Publisher: Royal Society of Chemistry
DOI: 10.1039/c7ib00085e

Real-time visualization and sub-diffraction limit localization of nanometer-scale pore formation by dielectric breakdown

Author(s): Adam Zrehen, Tal Gilboa, Amit Meller
Published in: Nanoscale, Issue 9/42, 2017, Page(s) 16437-16445, ISSN 2040-3364
Publisher: Royal Society of Chemistry
DOI: 10.1039/c7nr02629c

Chapter Fourteen - Single-Molecule Characterization of DNA–Protein Interactions Using Nanopore Biosensors

Author(s): A.H. Squires, T. Gilboa, C. Torfstein, N. Varongchayakul, A. Meller
Published in: Methods in Enzymology, 2017, Page(s) 353-385, ISSN 0076-6879
Publisher: Academic Press
DOI: 10.1016/bs.mie.2016.08.010

Methyltransferase-directed covalent coupling of fluorophores to DNA

Author(s): Milena Helmer Lauer, Charlotte Vranken, Jochem Deen, Wout Frederickx, Willem Vanderlinden, Nathaniel Wand, Volker Leen, Marcelo H. Gehlen, Johan Hofkens, Robert K. Neely
Published in: Chemical Science, Issue 8/5, 2017, Page(s) 3804-3811, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/C6SC04229E

Irys Extract

Author(s): Rani Arielly, Yuval Ebenstein
Published in: Bioinformatics, Issue 34/1, 2017, Page(s) 134-136, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btx437

Noise reduction in single time frame optical DNA maps

Author(s): Paola C. Torche, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
Published in: PLOS ONE, Issue 12/6, 2017, Page(s) e0179041, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0179041

Methyltransferase-Directed Labeling of Biomolecules and its Applications

Author(s): Jochem Deen, Charlotte Vranken, Volker Leen, Robert K. Neely, Kris P. F. Janssen, Johan Hofkens
Published in: Angewandte Chemie International Edition, Issue 56/19, 2017, Page(s) 5182-5200, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201608625

Separation of pathogenic bacteria by chain length

Author(s): Jason P. Beech, Bao Dang Ho, Geneviève Garriss, Vitor Oliveira, Birgitta Henriques-Normark, Jonas O. Tegenfeldt
Published in: Analytica Chimica Acta, Issue 1000, 2018, Page(s) 223-231, ISSN 0003-2670
Publisher: Elsevier BV
DOI: 10.1016/j.aca.2017.11.050

Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores

Author(s): Tal Gilboa, Chen Torfstein, Matyas Juhasz, Assaf Grunwald, Yuval Ebenstein, Elmar Weinhold, Amit Meller
Published in: ACS Nano, Issue 10/9, 2016, Page(s) 8861-8870, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.6b04748

Super-Resolution Genome Mapping in Silicon Nanochannels

Author(s): 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
Published in: ACS Nano, Issue 10/11, 2016, Page(s) 9823-9830, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.6b05398

Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

Author(s): 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
Published in: Scientific Reports, Issue 6, 2016, Page(s) 30410, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep30410

Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping

Author(s): Vilhelm Müller, Nahid Karami, Lena K. Nyberg, Christoffer Pichler, Paola C. Torche Pedreschi, Saair Quaderi, Joachim Fritzsche, Tobias Ambjörnsson, Christina Åhrén, Fredrik Westerlund
Published in: ACS Infectious Diseases, Issue 2/5, 2016, Page(s) 322-328, ISSN 2373-8227
Publisher: ACS Publications
DOI: 10.1021/acsinfecdis.6b00017

Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping

Author(s): Vilhelm Müller, Fredrika Rajer, Karolin Frykholm, Lena K. Nyberg, Saair Quaderi, Joachim Fritzsche, Erik Kristiansson, Tobias Ambjörnsson, Linus Sandegren, Fredrik Westerlund
Published in: Scientific Reports, Issue 6, 2016, Page(s) 37938, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep37938

Light-Enhancing Plasmonic-Nanopore Biosensor for Superior Single-Molecule Detection

Author(s): Ossama N. Assad, Tal Gilboa, Joshua Spitzberg, Matyas Juhasz, Elmar Weinhold, Amit Meller
Published in: Advanced Materials, 2016, Page(s) 1605442, ISSN 0935-9648
Publisher: United Nations Industrial Developement Organization
DOI: 10.1002/adma.201605442

Single-molecule protein sensing in a nanopore: a tutorial

Author(s): Nitinun Varongchayakul, Jiaxi Song, Amit Meller, Mark W. Grinstaff
Published in: Chemical Society Reviews, Issue 47/23, 2018, Page(s) 8512-8524, ISSN 0306-0012
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8cs00106e

Analytical epigenetics: single-molecule optical detection of DNA and histone modifications

Author(s): Christian Heck, Yael Michaeli, Ilko Bald, Yuval Ebenstein
Published in: Current Opinion in Biotechnology, Issue 55, 2019, Page(s) 151-158, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2018.09.006

Hypersensitive quantification of global 5-hydroxymethylcytosine by chemoenzymatic tagging

Author(s): Tamar Shahal, Omri Koren, Gabi Shefer, Naftali Stern, Yuval Ebenstein
Published in: Analytica Chimica Acta, Issue 1038, 2018, Page(s) 87-96, ISSN 0003-2670
Publisher: Elsevier BV
DOI: 10.1016/j.aca.2018.08.035

Microfluidic DNA combing for parallel single-molecule analysis

Author(s): Shuyi Wu, Jonathan Jeffet, Assaf Grunwald, Hila Sharim, Noa Gilat, Dmitry Torchinsky, Quanshui Zheng, Shahar Zirkin, Luping Xu, Yuval Ebenstein
Published in: Nanotechnology, Issue 30/4, 2019, Page(s) 045101, ISSN 0957-4484
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-6528/aaeddc

Optically-Monitored Nanopore Fabrication Using a Focused Laser Beam

Author(s): Tal Gilboa, Adam Zrehen, Arik Girsault, Amit Meller
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-28136-z

DNA barcodes for rapid, whole genome, single-molecule analyses

Author(s): Nathaniel O Wand, Darren A Smith, Andrew A Wilkinson, Ashleigh E Rushton, Stephen J W Busby, Iain B Styles, Robert K Neely
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz212

Enzyme-free optical DNA mapping of the human genome using competitive binding

Author(s): Vilhelm Müller, Albertas Dvirnas, John Andersson, Vandana Singh, Sriram KK, Pegah Johansson, Yuval Ebenstein, Tobias Ambjörnsson, Fredrik Westerlund
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz489

Long-read single-molecule maps of the functional methylome

Author(s): 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
Published in: Genome Research, Issue 29/4, 2019, Page(s) 646-656, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.240739.118

Intellectual Property Rights

METHODS OF DETECTING 5-HYDROXYMETHYLCYTOSINE AND DIAGNOSING OF CANCER

Application/Publication number: WO 2017081689
Date: 2017-05-18