gene dpcr/ngs editing 4bio · description: this course gives an introduction to next generation...

www.global-engage .com#4BIO

2 7 - 2 8 N o v e m b e r 2 0 1 8ROTTERDAM, THE NETHERLANDS

4BIO SUMMIT: EUROPEqPCR

dPCR/NGSGene

EditingMicrofluidics

WARM WELCOME

4BIO SUMMIT: EUROPE 2018

Global Engage is pleased to announce the 4Bio Summit: Europe, which will feature the most cutting-edge research and technological developments in the fields of qPCR/dPCR, NGS, microfluidics and gene editing. Scientific advancements, coupled with cost reductions in these four areas of research, have contributed to improved diagnosis, monitoring and treatment of disease.

6th qPCR & Digital PCR CongressThese tracks are designed for academic experts working in areas such as molecular biology/diagnostics, liquid biopsies, gene expression, genomics, biomarkers, pathogen detection, and miRNA analysis. The latest developments, opportunities and applications of both dPCR and qPCR will be examined, through case studies across diverse areas such as oncology, infectious diseases, vaccines, clinical applications, microbiology, and other novel applications. Increasing numbers of real-time PCR users are purchasing digital PCR due to the reduction in its cost, absolute quantification, improved sensitivity & precision, and greater robustness. As a result, the qPCR and Digital PCR market is predicted to grow to $4.94 billion by 2021. This conference therefore provides a timely opportunity to learn first-hand about dPCR, whilst also keeping up to date with latest developments and strategies in qPCR.

4th Microfluidics CongressMicrofluidics is a rapidly developing area of research, and scientists are continually discovering the wide range of possibilities the technology can provide. At the intersection of engineering, physics, chemistry, nanotechnology and biotechnology, microfluidics is revolutionizing the way patients are diagnosed, monitored and treated, and is unlocking the potential for reduced reagent consumption and thus, cost. Attracting experts working in all areas of microfluidics, the conference will examine the latest developments in the technologies and techniques being used to progress medical research, as well as well as the challenges being faced and the future of microfluidics. Should you be an expert in developing microfluidics technologies, or a scientist using microfluidics to further medical research, the conference will be an excellent opportunity to learn, share, discuss and engage with the most current microfluidics research and technology.

Gene Editing 1 Day CongressThis Congress will focus on the cutting-edge technologies transforming the field of gene editing today and consider the best strategies for implementing new methods across the field of clinical research, now and for the future. With CRISPR/Cas9 revolutionising the field, this conference will examine how to optimise the delivery of such technology, while also considering how to minimise off-target effects and mutations for the safe and effective delivery of gene editing tools. In addition, our expert panel discussion will explore in-depth the ethical and regulatory challenges in the field of gene editing today, with experts offering their perspectives on current legislation, and how to navigate ethical concerns in light of the growing scope and scale of genome engineering. This conference will therefore provide an opportunity for different disciplines to network and learn from each other, developing the use of gene editing technologies for applications across clinical research as a whole.

• 70+ presentations from academic and industry leaders

• 7+ hours of dedicated networking time

• 10 interactive roundtable discussions

• Extended senior level panel discussions

• A buzzing exhibition hall featuring technology and solution providers in the field

• Poster presentations

EVENT SUMMARY

CONFERENCE SYNOPSIS

• Advancements in qPCR, dPCR and other PCR-based methods

• Comparing methods and systems• Data analysis tools• Challenges of reproducibility/

standardization• Dealing with false positives and other

quality control measures• Assay design, optimization and

validation• Multiplexing• High Resolution Melting analysis

QPCR & DIGITAL PCRSTRATEGY & TECHNOLOGY FOR PCR-BASED METHODS

Applications of PCR-based technologies for:• Absolute quantification• Gene expression analysis• Sequencing sample prep• Clinical test validation• Liquid Biopsies• CTC/ctDNA/cfDNA/mtDNA based

testing• Disease & therapy response monitoring• High-throughput screening• Biomarker discovery• Micro RNA/ncRNA/siRNA applications• Mutation detection• Rare variant detection• Diagnosis and microbiology

CASE STUDIES

Roundtables are informal, small-group interactive discussions on key topics in the field. Discussion leaders will introduce sub-topics/questions for discussion and roundtable attendees are encouraged to participate actively in the session.

1. Liquid Biopsies2. Digital Droplet PCR3. Strategies for Data Analysis4. Standardization, QA & Reproducibility5. Translation of Diagnostic Tech into Clinic

ROUNDTABLE DISCUSSIONS

• Droplet microfluidics• Digital microfluidics• Centrifugal microfluidics• Dielectrophoresis• Paper-based systems• Optofluidics• Inertial microfluidics• Acoustofluidics• Electrokinetics• Gas microflows• Sensing technologies• Modelling and simulation• Microfabrication• 3-D printing of microfluidic devices

MICROFLUIDICSSTRATEGY AND TECHNOLOGY

IN MICROFLUIDICS

• Point-of-care diagnostics and disease monitoring

• Isolation and analysis of CTCs• Single cell analysis• Synthetic biology• Organ-on-a-chip platforms• Lab-on-a-chip• DNA analysis• Biomaterials and tissue engineering• Biomarker analysis• Drug delivery• Cell sorting• High throughput screening

CASE STUDIES AND APPLICATIONS IN MEDICAL RESEARCH

Short presentations from some of the most exciting small and midsize companies in microfluidics

COMPANY SHOWCASE

Roundtables are informal, small-group interactive discussions on key topics in the field. Discussion leaders will introduce sub-topics/questions for discussion and roundtable attendees are encouraged to participate actively in the session.

1. New formats - from paper to 3D printing 2. Droplet microfluidics across the

scales: molecules to cells to organoids3. Organ-on-chip4. Infectious Disease Diagnostics in

Under-Served Communities5. Analyzing Whole Blood Samples in the

Point-of-Care

ROUNDTABLE DISCUSSIONS

In depth analysis of the latest technologies and challenges faced in gene editing, and how to overcome them.• CRISPR/Cas9 • Other technologies

GENE EDITING

GENE EDITING - TECHNOLOGIES

• HDR mediated gene editing• NHEJ mediated gene editing • Base editing • Safe & effective delivery of genome

editing tools– In vivo & ex vivo gene delivery – Viral & Non-Viral Vectors – T-Cell adoptive therapy

GENE EDITING - METHODS & STRATEGIES

• Cancer Immunotherapy• Immunology & Infectious diseases• Neuromuscular disorders • Germline & Somatic Gene Therapy• Antivirals• Antimicrobials

CASE STUDIES

• Navigating Ethical & Regulatory Challenges for the Advancement of Gene Editing

PANEL DISCUSSION

EXPERT SPEAKERS

MIKE MAKRIGIORGOS Professor of Radiation Oncology, Dana Farber Cancer Institute and

Harvard Medical School, USA

STEPHEN BUSTIN Professor of Molecular Medicine,

Anglia Ruskin University, UK

qPCR & DIGITAL PCR

VALERIE TALYCNRS Research Director, Group Leader, Translational Research

and Microfluidics, Paris Descartes University, France

TONY GODFREYAssociate Chair, Surgical

Research; Professor of Surgery, Boston University School of

Medicine, USA

NICOLE PAMMEProfessor in Analytical Chemistry,

University of Hull, UK

CHARLES BAROUD Associate Professor, École

Polytechnique; Research Unit Head, Insitut Pasteur, France

MICROFLUIDICS

NAM TRUNG NGUYENProfessor and Director of Queensland Micro- and

Nanotechnology Centre, Griffith University, Australia

BAS TRIETSCHChief Technology Officer,

Mimetas, The Netherlands


ROBERTO NITSCHAssociate Director, Advanced

Medicines Safety – Drug Safety & Metabolism, AstraZeneca, Sweden

ERIC BENNETTAssociate Professor, University

of Copenhagen, Denmark

GENE EDITING

TIMO FALTUSResearch Fellow, Project

Coordinator of GenomELECTION, Martin Luther University of Halle-

Wittenberg, Germany

SANDRA ACOSTA VERDUGOSenior Postdoctoral Fellow,

Centre for Vascular & Developmental Biology,

Northwestern University, USA

Platinum Sponsors

Gold Sponsors

Other Exhibitors & Sponsors

SPONSORSHIP & EXHIBITION OPPORTUNITIES AVAILABLEFor more details contact Gavin Hambrook or Nick Best at [email protected] or call +44 (0) 1865 849841

EVENT SPONSORS


WORKSHOP PRICES (PER COURSE)

WORKSHOP INFORMATION


Industry - €500Academic - €425

1 course + 4Bio registration - €50 discount2 courses + 4Bio registration - €100 discount

*All workshops include lunch and refreshments

PRE-EVENT WORKSHOP

EXPRESSION BIOMARKERSHow to measure, validate and quality control the workflows in compliance with guidelines

Target audience: Quality managers at medical and diagnostic laboratories, Laboratory personnel at medical and diagnostic laboratories, Pathologists, Biobank personnel, Managers and researchers coordinating or performing

biomarker studies and trial.

Entrance qualifications: Basic molecular biology or similar

Description: During 2015 The International Organization for Standardization (ISO) released Specifications and the European Committee for standardization (CEN) Technical Specifications about the pre-examination process for DNA,

RNA and proteins from several sample types including fresh frozen tissue, formalin fixed tissue, blood and serum/plasma. The specifications are based on results from the FP7-funded project SPIDIA. TATAA Biocenter was partner of SPIDIA and

contributed to the drafting of the new guidelines. These are of great value for reliable and robust sample handling and preparation in a standardized way to ensure measured data are of high quality and comparable across laboratories. The

new guidelines are particularly relevant for accredited laboratories, and also for research and discovery based work, were procedures needs to be standardized and data compared. This course presents the new Specifications and brings them

into context for smooth implementation in your laboratory procedures.

The course contains:• Background about standardization and the pre-analytical process.

• Introduction to the new ISO Specifications and CEN Technical Specifications.• What to consider about the workflow of sampling, storage, transportation and extraction of nucleic acids and proteins.• What to consider about the workflow of sampling, storage, transportation and extraction of nucleic acids and proteins.

• General information and considerations of RNA, DNA and protein extraction.• How to do quality assessment of RNA, DNA and proteins.

Monday 26th November 201810:00-18:00

Course run by TATAA Biocenter

Early registration is recommended www.global-engage.com/event/workshop-tataa-biocenter

MIKAEL KUBISTAProfessor, Czech Academy of Sciences; Chairman

of the Board, and Founder, TATAA Biocenter, Sweden

HOSTED BY

WORKSHOP INFORMATION


WORKSHOP PRICES (PER COURSE)

Industry - €500Academic - €425

1 course + 4Bio registration - €50 discount2 courses + 4Bio registration - €100 discount

*All workshops include lunch and refreshments

POST-EVENT WORKSHOP

NGS LIBRARY CONSTRUCTION AND QUALITY CONTROLFinding the right approach, kit and provider in the jungle

Description: This course gives an introduction to Next Generation Sequencing (NGS) and its many applications. The course will focus on considerations for the NGS experiment design, the different sequencing platforms,

quality control of samples, library preparation techniques, and quantification of libraries for sequencing.

Introduction to NGS:• The history of DNA sequencing

• What are the advantages with NGS? Disadvantages?• What is coverage, index, multiplexing, depth etc…

Applications:• DNA – Whole Genome Sequencing (WGS), targeted resequencing etc.

• RNASeq – Expression analysis, Splice variants detection etc.• Metagenomic sequencing

• Epigenetic sequencing• miRNA

Sample preparation and quality control:• Which starting material can be used for NGS?

• Which quality controls are included in the experimental workflow?• How to choose the right library prep protocol.

Instrumentation:• Which platforms are available?

• How do they work?• How to choose the right library prep protocol.

Thursday 29th November 201808:30-16:30

Course run by TATAA Biocenter

Early registration is recommended www.global-engage.com/event/workshop-tataa-biocenter-2

FILIP STERNTATAA Biocenter

HOSTED BY

CONFIRMED SPEAKERS


JAN RUIJTER (Chair)Principal Investigator (retired), Academic Medical Center, Amsterdam, The Netherlands

STEPHEN BUSTINProfessor of Molecular Medicine, Anglia Ruskin University, UK

HENDRIK EMONSHead of ‘Food and Feed Compliance’ Unit, European Commission’s Joint Research Centre, Health, Consumers & Reference Materials Directorate, Belgium

SENIOR REPRESENTATIVEStilla Technologies

MIKAEL KUBISTAProfessor, Czech Academy of Sciences; Chairman of the Board, and Founder, TATAA Biocenter, Sweden

PER GULDBERGProfessor, Group Leader, Cancer Genetics Lab, Danish Cancer Society, Denmark

NAOMI PARKSenior Staff Scientist, Wellcome Trust Sanger Institute, UK

JULIETTE NECTOUXMolecular Geneticist, Cochin Hospital, Paris, France

SENIOR REPRESENTATIVEIntegrated DNA Technologies

THOMAS EDWARDSPost-doctoral Research Associate, Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, UK

KELLY KAIHARAGlobal Market Development Manager, Bio-Rad Digital Biology Group

LISE LOTTE HANSENAssociate Professor, Department of Biomedicine, Aarhus University, Denmark

MAURICE VAN DEN HOFFAssociate Professor, Department Medical Biology, Amsterdam Universitair

Medische Centra, Location AMC, Amsterdam, The Netherlands

STÉPHANE BRETAGNEProfessor of Medicine, Paris Diderot University; Chair of Parasitology and Mycology,

Saint Louis University Hospital; Deputy Director, French National Reference Centre for Invasive Mycoses and Antifungals, Institut Pasteur, Paris, France

SERGE SHERRERSr. Application Scientist, Nanostring

PETAR PODLESNIYScientific Researcher, CiberNed, IIBB, Barcelona, Spain

VALÉRIE TALYCNRS Research Director, Group Leader, Translational Research and Microfluidics, Paris Descartes University, France

ALEXANDRA BOGOŽALEC KOŠIRResearch Assistant, National Institute of Biology, Department of Biotechnology and Systems Biology, Slovenia

MIKE MAKRIGIORGOSProfessor of Radiation Oncology, Dana Farber Cancer Institute and Harvard Medical School, USA

AMANDA NAAUMVisiting Research Fellow, Queen’s University Belfast, UK; Senior Research Scientist, TRU-ID Ltd., Canada

JÖRG TOSTDirector of the Laboratory for Epigenetics and Environment, National Center for Research in Human Genomics, France

TONY GODFREYAssociate Chair, Surgical Research; Professor of Surgery, Boston University School of Medicine, USA

ULRICH LEHMANNProfessor, Head of the Laboratory of Molecular Diagnostics, Hannover Medical School, Germany

CINDY SMITHSenior Lecturer and Royal Academy of Engineering Senior Research Fellow, Infrastructure and Environment, School of Engineering, University of Glasgow, UK

FLORENT MOULIEREAssistant Professor, Liquid Biopsy Centre/Pathology, University of Cambridge/Amsterdam UMC, UK/Netherlands

LAO SAALCEO, SAGA Diagnostics AB, and Head, Translational Oncogenomics Unit, Lund University Cancer Center, Sweden

BERNHARD ZIMMERMANNVP of Research & Development, Molecular Research, Natera, Inc., USA

MARIE FOLLOHead of Lighthouse Core Facility, Center for Translational Cell Research, Dept. of Internal Medicine I, Medical Center, Faculty of Medicine - University of Freiburg, Germany

JARI LOUHELAINENAssociate Professor of Biochemistry, University of Helsinki, Finland

RUUD JANSENMedical Molecular Biologist, Regional Laboratory for Public Health Kennemerland, The Netherlands

NICOLAS YEUNGScientist, DuPont Nutrition & Health, Finland

KEVIN P NICHOLSGroup Manager, BacteriaDx, Intellectual Ventures Laboratory, USA

FRANÇOIS-XAVIER SICOTSenior Product Manager, Takara Bio Europe

ERNST BÖHMHead of QC, Biomay AG, Austria

qPCR & DIGITAL PCR

CONFIRMED SPEAKERS

NAM-TRUNG NGUYENProfessor and Director of Queensland Micro- and Nanotechnology Centre, Griffith University, Australia

THOMAS FRANKEProfessor in Biomedical Engineering, University of Glasgow, UK

LINAS MAZUTISProfessor, Institute of Biotechnology, Vilnius University, Lithuania

ELISA HEMMIGPostdoctoral Researcher, IBM Zurich Research Laboratory, Switzerland

JONATHAN COOPERProfessor, Wolfson Chair of Bioengineering, University of Glasgow, UK

MINA HOORFARProfessor and Director of the School of Engineering, University of British Columbia, Canada

MARTYN BOUTELLEProfessor of Biomedical Sensors Engineering, Imperial College London, UK

TUOMAS KNOWLESProfessor of Biophysics & Biophysical Chemistry, University of Cambridge, UK

CHARLES BAROUDAssociate Professor, École Polytechnique; Research Unit Head, Insitut Pasteur, France

NICOLE PAMMEProfessor in Analytical Chemistry, University of Hull, UK

JEROEN LAMMERTYNProfessor, Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, Belgium

SÉVERINE LE GACAssociate Professor, Applied Microfluidics for BioEngineering Research, University of Twente, The Netherlands

JAAP DEN TOONDERProfessor, Chair of the Microsystems Group, Eindhoven University of Technology, The Netherlands

KARINA WEBERGroup Leader, Leibniz Institute of Photonic Technology, Germany

SAMI ELLOUZEGroup Leader, Microfluidics Assay Development & Screening Platform, HiFiBiO Therapeutics, France

MARIAN REHAKDirector of R&D, Sphere Fluidics, UK

MAXIME DROBOTHead of Products, Elveflow

JAN MADSENProfessor, Deputy Director at DTU Compute, Section Head, Department of Applied Mathematics and Computer Science, Technical University of Denmark

DANIEL LEVNERChief Technology Officer, Emulate, Inc., USA

BAS TRIETSCHChief Technology Officer, Mimetas, The Netherlands

VINCENT LINDERFounder and President, CDP BioMedical Consulting, Portugal

MARCO SERRAPost-doc, Institut Curie, France


MICROFLUIDICS

qPCR & DIGITAL PCR

STEFAN RÖDIGERGroup Leader, Institute of Biotechnology, Brandenburg University of Technology Cottbus – Senftenberg, Germany

BAS BRINKHOFPostdoc, Engineering Science, University of Oxford, UK

KRISTI KRUUSMAAHead of Research, Universal DX Diagnostics, Spain

CONFIRMED SPEAKERS GENE EDITING

ERIC BENNETTAssociate Professor, University of Copenhagen, Denmark

ROBERTO NITSCHAssociate Director, Advanced Medicines Safety – Drug Safety & Metabolism, AstraZeneca, Sweden

ANDREW WOODWellcome Trust Sir Henry Dale Fellow at the MRC Human Genetics Unit, University of Edinburgh, UK

SANDRA ACOSTA VERDUGOSenior Postdoctoral Fellow, Centre for Vascular & Developmental Biology, Northwestern University, USA

ALASDAIR RUSSELLHead, Pre-Clinical Editing, Cancer Research UK Cambridge Institute, University of Cambridge, United Kingdom

GUILLERMO MONTOYAAssociate Professor, Novo Nordisk Foundation Centre for Protein Research, Denmark

BASIL HUBBARDAssociate Professor & Canada Research Chair, University of Alberta, Canada

TIMO FALTUSResearch Fellow, Project Coordinator of GenomELECTION, Martin Luther University of Halle-Wittenberg, Germany

BERT SMEETSProfessor in Clinical Genomics, Maastricht University, The Netherlands

BEN HOUGHTONResearch Associate, UCL (University College of London), United Kingdom

JOHN PARRINGTONAssociate Professor, University of Oxford, United Kingdom

DYLAN PHILLIPSLecturer in Genetics, IBERS, University of Aberystwyth, United Kingdom

POSTER PRESENTATIONS

MAKING A POSTER PRESENTATION

Poster presentation sessions will take place in breaks and alongside the other breakout sessions of the conference. Your presentation will be displayed in a dedicated area, with the other accepted posters from industry and academic presenters. We also issue a poster eBook to all attendees with your full abstract in and can share your poster as a PDF after the meeting if you desire (optional). Whether looking for funding, employment opportunities, or simply wanting to share your work with a like-minded and focused group, these are an excellent way to join the heart of this congress.

In order to present a poster at the congress you need to be registered as a delegate. Please note that there is limited space available and poster space is assigned on a first come first served basis (subject to checks and successful registration). We charge an admin fee of €100 to industry delegates to present, that goes towards the shared cost of providing the poster presentation area and display boards, guides etc. This fee is waived for those representing academic institutions and not for profit organisations.

CONGRESS SCHEDULE DAY 1 TUESDAY 27TH NOVEMBER 2018

08:00-08:50

Global Engage Welcome Address and Morning Chair’s Opening Remarks: Jan Ruijter, Principal Investigator (retired), Academic Medical Center, Amsterdam, The Netherlands


Registration & Refreshments

09:00-09:40

QPCR & DIGITAL PCR METHODS FLOW CONTROL & DROPLETS IN MICROFLUIDICS

09:00-09:40

KEYNOTE ADDRESS:STEPHEN BUSTINProfessor of Molecular Medicine, Anglia Ruskin University, UKThings you may not know about the PCRAnyone using the polymerase chain (PCR)

reaction in 2018 employs enzymes, buffers and instruments that are a vast improvement on what they would have used thirty years ago. But do our assay designs and methods really reflect these advances or do we need to revise some of our practices? I shall demonstrate the need to modify some assay design parameters, encourage the implementation of effortless revisions to PCR protocols and reveal surprising conclusions about PCR reagents. The aim, as ever, is to update the reliability and appropriateness of the PCR, which continues to be a core molecular technique.

KEYNOTE ADDRESS:NAM-TRUNG NGUYENProfessor and Director of Queensland Micro- and Nanotechnology Centre, Griffith University, AustraliaLiquid marble based digital microfluidics: fundamental physics and applications

Liquid marbles (LMs) are droplets with volume of typically microliters coated with hydrophobic powder. The versatility, ease of use and low cost make LMs an attractive platform for digital microfluidics. The talk will report our recent discoveries in the physics of liquid marbles (LMs) that allow them to serve as miniature labs. First, a novel LM manipulation technique using dielectrophoresis (DEP) will be reported. Using this manipulation technique, the coalescence of two LMs was demonstrated via vertical collision. Next, the robustness of LMs was investigated in terms of evaporation and structural deformation. We demonstrated that a LM cluster can survive thermal cycling conditions up to 95°C in a humidity controlled environment. The robustness of a LM in terms of elasticity was also investigated. Experimental results were compared with simulation based on coarse grained molecular dynamics. The above proof-of-concept data show that liquid marbles are suitable for applications such as large-scale three-dimensional cell culture and high-throughput digital PCR.

09:40-10:15

09:40-10:15

HENDRIK EMONSHead of ‘Food and Feed Compliance’ Unit, European Commission’s Joint Research Centre, Health, Consumers & Reference Materials Directorate, BelgiumDigital PCR for nucleic acid quantification

The quantification of nucleic acids or their fragments has been advanced significantly in recent years by the development of several so-called digital PCR (dPCR) techniques. An overview on the current achievable analytical performance characteristics of dPCR methods will be presented in combination with points for attention and limitations of corresponding analytical procedures. Moreover, recommendations for dPCR method validations will be

THOMAS FRANKEProfessor in Biomedical Engineering, University of Glasgow, UKTopic: Droplets - using traps for immobilization and incubation

08:50-09:00

Global Engage Welcome Address and Morning Chair’s Opening Remarks:

08:50-09:00

Global Engage Welcome Address and Morning Chair’s Opening Remarks:

08:50-09:0009:00-09:40

GENE EDITING

09:40-10:15

KEYNOTE ADDRESS:ERIC BENNETTAssociate Professor, University of Copenhagen, DenmarkCellular indel outcomes and dynamics induced by different CRISPR/Cas9 delivery formats

• Methodologies for absolute identification of cellular CRISPR/Cas9 induced indel events

• Plasmid-, piggyback-, lenti- and RNP –CRISPR/Cas9 delivery • Indel formation dynamics and profiles induced by various

CRISPR/Cas9 delivery methods Accurate and sensitive detection of indels induced by precise gene targeting in cells requires detection methodologies that are accurate, precise and sensitive. The indel detection by amplicon analysis method (IDAA) possess the necessary detection specificity and sensitivity down to single base indel discrimination differences in cells, that however comes at a fraction of the cost and speed of sequencing based indel detection methodologies based on next generation sequencing. Thus, IDAA is ideally suited for CRISPR/Cas9 based cell line engineering, gRNA validation and in vitro and ex vivo indel profiling and quantification. The presentation will present features of CRISPR/Cas9 induced indel dynamics and profiles and translational aspects of the IDAA methodology in ex vivo gene targeting regimes.

ANDREW WOODWellcome Trust Sir Henry Dale Fellow at the MRC Human Genetics Unit, University of Edinburgh, UK How chromatin modifications influence CRISPR mutagenesis at on- and off-target sites

• We present a new experimental system to study how CRISPR-Cas9 and other genome editing tools are affected by different chromatin states in primary cells.

• We find that transcriptionally repressed chromatin significantly impedes CRISPR-Cas9 mutagenesis when Cas9 exposure is brief or expression is low, but the effect is negligible upon prolonged or high-level Cas9 exposure. Neither the size of



11:55-12:20

MIKAEL KUBISTAProfessor, Czech Academy of Sciences; Chairman of the Board, and Founder, TATAA Biocenter, SwedenTwo-tailed PCR for Precision Diagnostics

We present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on novel chemistry called Two-tailed PCR. Two-tailed PCR takes advantage of target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of 7 logs and a sensitivity sufficient to detect less than ten target miRNA molecules. The reverse transcription step can be multiplexed and it allows for rapid testing with a total analysis time of less than 2.5 hours.

11:55-12:20

LINAS MAZUTISProfessor, Institute of Biotechnology, Vilnius University, LithuaniaDroplet microfluidics technology for single-cell biology research

Recent developments in single-cell functional assays and single-cell sequencing have opened new possibilities to many branches of biological sciences. Droplet microfluidics technology plays a key role in this progress; it provides ultra-high-throughput capabilities, reduced reagent cost and improved reaction sensitivity. In this talk I will present a few recent droplet-microfluidics developments of our group for single-cell biology research. I will finish my talk by showing how these tools enabled us to build a high-dimensional, single-cell transcriptional atlas of human breast tumors comprising over 47.000 individual immune cells. We find that the increased heterogeneity of intratumoral cells of both lymphoid and myeloid cell lineages occupy markedly expanded contiguous phenotypic space in comparison to normal breast tissue.

09:40-10:15

09:40-10:15

outlined. Application examples will be discussed from the areas of quantifying nucleic acids for clinical diagnostics and for monitoring genetically modified food or feed as well as for establishing reliable calibration systems for GMO analysis. Continued

09:40-10:15

10:15-10:45

SOLUTION PROVIDER PRESENTATION:SENIOR REPRESENTATIVEStilla TechnologiesTitle TBC

10:15-10:45

For sponsorship opportunities contact Gavin Hambrook / Nick Best: [email protected] /

+44 (0) 1865 849841

SOLUTION PROVIDER PRESENTATION

10:15-10:45

Morning Refreshments / Even Numbered Poster Presentations / One-to-One Meetings10:45-11:5511:55-12:20

ROBERTO NITSCHAssociate Director, Advanced Medicines Safety – Drug Safety & Metabolism, AstraZeneca, SwedenCRISPR at the crosstalk between efficacy and safety: in vitro, in vivo, in clinics

CRISPR represents the major innovation in the field of genome manipulation. Its simplistic mechanism and flexible, multi-component modularity (enzyme + gRNA) make it one of the most useful tools in molecular biology. However, the simplicity of editing genomes with CRISPR engaged the scientific community to think about its application to the clinic without a thorough consideration of any potential intrinsic harmful effects. The major drawback of CRISPR is currently represented by its Off-Target activity, which can cause unwanted disruption of gene functions and more broadly, genomic instability. In fact, highly frequent double-strand breaks generated on the Off-Targets loci could trigger On- to Off-Target chromosomal translocations, which result detrimental to the fitness of the targeted cell. In order to move CRISPR closer to the clinics, we need to improve both efficacy and safety and broaden the spectrum of applications to more target organs in vivo and ex vivo.

KEVIN P NICHOLSGroup Manager, BacteriaDx, Intellectual Ventures Laboratory, USADigital Assays: There’s Plenty of Room in the Middle

In digital assays, targets are partitioned into separate compartments, which are processed to give ON/OFF signals (usually with amplification) depending on whether the compartments have target entities. Digital assays have been developed to detect various target types, including nucleic acids, proteins, and cells. Typically, these assays are considered to require monodisperse droplets to enable accurate counting. In this talk, we describe a simple statistical correction that enables highly polydisperse mixtures of droplet sizes to be utilized with nearly equivalent accuracy as monodisperse emulsions. We expect this will enable a wide variety of new types of digital assay instruments with reduced cost or increased capabilities.

11:55-12:20

Indels nor the ratio of mutations arising from NHEJ or HDR is affected by chromatin modifications in these assays

• Nucleotide mismatches between the sgRNA and target site disproportionately affect mutagenesis in transcriptionally repressed chromatin, which has major implications for the prediction and avoidance of off-target mutagenesis.

SOLUTION PROVIDER PRESENTATION:SENIOR REPRESENTATIVEIntegrated DNA Technologies



12:20-12:45

NAOMI PARKSenior Staff Scientist, Wellcome Trust Sanger Institute, UKStreamlining the genotyping service at the Sanger

Institute using Multiplex PCR and NGS• Small scale genotyping at Sanger has been

carried out for over a decade using platforms which require bespoke equipment, taking a large amount of laboratory space

• Genotyping at Sanger is largely used for “finger printing” prior to whole genome sequencing and for tracking malaria parasite diversity

• We developed an alternative bespoke high-throughput amplicon sequencing pipeline requiring no up-front sample quantification or normalisation

• Up to 1536 samples may be pooled on a single lane of Miseq sequencing

• The pipeline is LIMS tracked and post sequencing genotype calling is fully automated

NICOLAS YEUNGScientist, DuPont Nutrition & Health, FinlandThe application of Droplet Digital PCR for probiotic consumption monitoring during a human clinical trial

The gold standard for monitoring the consumption of probiotic strains during a clinical trial has been real time quantitative PCR (qPCR). With the advent of droplet digital PCR (ddPCR) and the benefits of higher sensitivity, intrinsic quantification and decreased effect of PCR inhibitors, it has become an increasingly powerful tool in the field of strain-specific bacterial detection and enumeration.

12:20-12:45

12:20-12:45

KARINA WEBERGroup Leader, Leibniz Institute of Photonic Technology, GermanyMolecular and spectroscopic droplet-

based platforms in bioanalyticsWithin this contribution we will introduce our droplet-based platform for life science application. In doing so, the droplets serve as a reaction chamber and it is achieved that small sample volumes are analyzed in a high throughput. Two of our applications will be described in more detail, firstly for DNA amplification towards digital PCR. With the help of intercalating dyes, the successful duplication can be indicated by means of fluorescence-based detection and thus the presence of the corresponding pathogen. Furthermore, the droplets serve as a detection chamber for metabolites and bacteria based on surface-enhanced Raman spectroscopy (SERS). For this purpose, metallic nanoparticles are mixed with the substances of interest and the molecular-specific Raman modes are enhanced by several orders of magnitude.

12:20-12:45

ALASDAIR RUSSELLHead, Pre-Clinical Editing, Cancer Research UK Cambridge Institute, University of Cambridge, United Kingdom

Allele-specific correction of a putative pathogenic mutation in a primary immunodeficiency patient’s cellsOver 6000 monogenic human diseases are potentially amenable to curative CRISPR medicine. Here we develop, and successfully apply, an allele-specific targeting approach to selectively correct a pathogenic heterozygous SNV in cells from a patient with Primary Immunodeficiency disease. In partnership with the 100K Genomes Project, whole genome sequencing of peripheral blood identified a putative pathogenic mutation in the IFR8 gene within a family diagnosed with primary immunodeficiency. Importantly, mutations in IRF8 have been implicated in selective depletion of dendritic cells in patients, leading to immunodeficiency. Dermal fibroblasts were isolated from an affected patient, expanded in vitro, and reprogrammed into a pluripotent state (iPSCs). These cells were then subjected to CRISPR/Cas9 editing. Exploiting the proximity of the patient’s pathogenic mutation to guide seed sequence, we prototyped various approaches to target only the diseased allele, leaving the wild-type allele untouched. We demonstrate that by combining the enhanced specificity Cas9 variant, eSpCas9, with chemically synthesised sgRNAs with altered CRISPR target sequences, we were able to preferentially target the mutant allele in vitro. Using this approach in iPSCs allowed the generation of two independent corrected iPSC clones, each with no detectable off-target events. We have thus demonstrated 'proof of concept' of selective targeting of diseased alleles in patient-derived cells.



GUILLERMO MONTOYAAssociate Professor, Novo Nordisk Foundation Centre for Protein Research, DenmarkStructural Biology of

Genome Editing: How RNA-guided endonucleases cut specific regions of the Genome• Cpf1 is a class 2 type V CRISPR-Cas single

RNA-guided endonuclease that has been harnessed for genome editing based on its ability to generate specific dsDNA breaks. I will in my seminar address the molecular mechanism that control the specificity and cleavage mechanisms of Cpf1.

• We have determined the crystal structure of Francisella novicida Cpf1(FnCpf1) in complex with the triple strand R-loop formed after target DNA cleavage. The structure reveals a unique machinery for target DNA unwinding

Lunch13:15-14:15

14:15-14:40

LISE LOTTE HANSENAssociate Professor, Department of Biomedicine, Aarhus University, DenmarkMethylation-Sensitive High-Resolution Melting

(MS-HRM) for sensitive DNA methylation assessment• MS-HRM is a method for locus specific

assessment of DNA methylation.• The unique primer design we use for MS-

HRM, ensures a high sensitivity that can be adjusted to meet the dynamic range required for the specific experiment.

• The performance of MS-HRM under challenging conditions will be discussed. Examples of using highly degraded or limited amount of template DNA will be presented.

• Further, the performance of MS-HRM with regard to assessment of methylation of imprinted and heterogeneously methylated

METHOD DEVELOPMENT

STÉPHANE BRETAGNEProfessor of Medicine, Paris Diderot University; Chair of Parasitology and Mycology, Saint Louis University

Hospital; Deputy Director, French National Reference Centre for Invasive Mycoses and Antifungals, Institut Pasteur, Paris, FranceChallenges in establishing a PCR assay for the diagnosis of invasive aspergillosisInvasive aspergillosis (IA) is the leading cause of invasive fungal diseases in patients with haematological conditions. Because of the high mortality rate, a lot of PCR assays have been developped to anticipate the diagnosis based on mycology and antigen detection. For physiopathological reasons, the amount of circulating DNA is very low, and there is an urgent need for basic studies to elucidate the origin and kinetics of Aspergillus DNA in blood. This low amount exacerbates all the pitfalls

14:15-14:40

PCR & MICROBIOLOGY

14:15-14:40

MICROFLUIDICS-BASED DIAGNOSTICS & BIOSENSING

14:15-14:40

GENE EDITING

JAN MADSENProfessor, Deputy Director at DTU Compute, Section Head, Department of Applied Mathematics and Computer Science, Technical University of Denmark

A Programmable General-Purpose Lab-on-ChipA key turning point for the evolution of modern computers was the introduction of the general-purpose computer architecture which allowed the computer to be programmed after hardware fabrication. This allowed hardware to be designed bottom-up, providing a hardware independent programming interface which could then be compiled from a high-level programming language, effectively separating the design of hardware (processor) and software (application). Today, microfluidic Lab-on-Chip are still mainly developed as hardcoded applications using

12:45-13:15

SOLUTION PROVIDER PRESENTATION:FRANÇOIS-XAVIER SICOTSenior Product Manager, Takara Bio Europe

Flexible, high-throughput qPCR for gene expression and genotyping analysisSmartChip™ Real-Time PCR System enables high-throughput real-time PCR for gene expression or single nucleotide polymorphism (SNP) genotyping analysis. Learn about the features of the system and hear about some of the exciting research that has been enabled by the SmartChip system, including studies on antibiotic

10:15-10:45

For sponsorship opportunities contact Gavin Hambrook / Nick Best:

[email protected] / +44 (0) 1865 849841


12:45-13:15

12:45-13:15

SOLUTION PROVIDER PRESENTATION:MAXIME DROBOTHead of Products, Elveflow

BERT SMEETSProfessor in Clinical Genomics, Maastricht University, The NetherlandsTowards autologous muscle stem cell therapy for genetic muscular disorders

• Use of autologous muscle stem cells for systemic treatment of myopathy

• Treatment of patients with mitochondrial DNA mutation without correction of the genetic defect

• Correction of the genetic defect in patients with nuclear genetic neuromuscular disease

Track Chair: Ernst Böhm, Head of QC, Biomay AG, Austria Track Chair:

Track Chair: Vincent Linder, Founder and President, CDP BioMedical Consulting, Portugal

Track Chair:



15:05-15:30

JARI LOUHELAINENAssociate Professor of Biochemistry, University of Helsinki, FinlandEvaluation of PCR/qPCR inhibitors, with effect of

various polymerases and extraction methods: not all approaches are created equalFor successful PCR and qPCR analysis the

15:05-15:30

RUUD JANSENMedical Molecular Biologist, Regional Laboratory for Public Health Kennemerland, The Netherlands

MYcrobiota analysis in routine diagnosticsThe field of microbiota studies has come of age and is now ready to enter the

15:05-15:30

MINA HOORFARProfessor and Director of the School of Engineering, University of British Columbia, CanadaAdvanced Biomedical and

Environmental Diagnostics through Microfluidic Olfaction TechnologyGas chromatography-mass spectrometry are

15:05-15:30

BASIL HUBBARDAssociate Professor & Canada Research Chair, University of Alberta, CanadaImproving the specificity of CRISPR/Cas9 using

chemically-modified guide RNAs• Off-target DNA binding and cleavage is a

major concern when using the CRISPR/Cas9 system

• We will discuss our recent finding that incorporation of bridged nucleic acids (BNAs) into crRNAs dramatically improves Cas9 endonuclease specificity

• In addition, we will present on-going work examining the effect of BNAs and other chemical modifications on the DNA-binding specificity of Cas9

14:40-15:05

MAURICE VAN DEN HOFFAssociate Professor, Department Medical Biology, Amsterdam Universitair Medische Centra, Location

AMC, Amsterdam, The NetherlandsIntegration of DNA melting curve analysis in qPCR data analysisQuantitive PCR (qPCR) reactions often amplify off-target products in addition to the correct product thus biasing the qualitative and quantitative outcome. To correct these measurement results, we developed a program to analyze melting curve data to identify melting peaks belonging to the correct product or artefacts. The program and the correction method were tested and validated with more than 100 different validated qPCR assays in different biological tissues and model experiments. The identification of the presence of the correct product will improve the sensitivity of Sybr Green I-based assays, avoiding erroneous diagnosis. The correction of the observed target quantities in the presence of artefact amplification results in more efficient and more reliable quantitative analysis of qPCR experiments.

14:40-15:05

THOMAS EDWARDSPost-doctoral Research Associate, Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, UK

Strategies for highly multiplexed qPCR based diagnostics for anti-microbial resistance• AMR is a high priority area for diagnostic

development, and high-plexy tests are desirable due to complex resistance mechanisms

• I will present, gram negative bacterial speciation panels and diagnostic evaluation data for ESBLs, AmpCs and Carbapenemases

• Evaluation data on 7 year longitudinal study at the Royal University Hospital Liverpool, UK

14:40-15:05

14:40-15:05

ELISA HEMMIGPostdoctoral Researcher, IBM Zurich Research Laboratory, SwitzerlandNew microfluidic modules for miniaturized

immunoassays using electrowetting and capillary self-assemblyPoint-of-care diagnostics are critical for identifying diseases near patients, quickly, and in many settings and scenarios. One of our contribution to the field of microfluidics is the development of capillary-driven microfluidic chips for highly miniaturized immunoassays. In this talk, I will briefly introduce the fundamentals of capillary flow and describe some of the main microfluidic functional elements required for implementing immunoassays. I will show how stop-and-go control of liquid flow is achieved in microfluidic chips using electrowetting and also present a novel approach for integrating receptors inside closed microfluidic devices using capillary self-assembly of functionalized microbeads. Altogether, capillary-driven elements allow for the manipulation of samples and reagents with unprecedented precision and control, paving the way for the next generation of point-of-care diagnostic devices.

BEN HOUGHTONResearch Associate, UCL (University College of London), United KingdomPresentation on Genome Editing case study

14:15-14:40

of the PCR, hence the difficulties in obtaining assays with the same limit of detection, making comparison between the published results difficult. For respiratory specimens, the results seem encouraging but the issue of DNA extraction and quantification of the results are not solved. Once a technical consensus is achieved, it remains to show whether the integration of qPCR in the diagnostic strategy of IA can improve the prognosis.

14:15-14:40

14:15-14:40

14:15-14:40

loci, will be discussed.• A MS-HRM LINE1 assay will be presented,

which allows for quantitative assessment of global DNA methylation changes.

passive operations, even though microfluidic technologies have the potential to scale. We argue that such scaling will require active components and the ability to abstract basic operations to a level similar to that of classical computation and presents a digital microfluidic-based general-purpose Lab-on-Chip that can be programmed after fabrication.

to form a crRNA-DNA hybrid and a displaced DNA strand inside FnCpf1.

• Our study reveals a singular working model of RNA-guided DNA cleavage by Cpf1, providing new avenues for redesign of Cpf1 and development of new genome editing tools.



15:30-16:00

SOLUTION PROVIDER PRESENTATION:SERGE SHERRERSr. Application Scientist, NanostringHigh plex gene expression faster than qPCR & simpler than NGS - case studyGene expression is an essential molecular biology technique for most researchers. There are some intrinsic technical challenges in current gene

expression solutions like qPCR and RNASeq, like uncertain reproducibility, long workflow and limited multiplexing capabilities. The session will explain how to avoid the current challenges and present results produced with the Nanostring gene expression solution in cancer and other applications. Learn about NanoString’s enzyme-free, multi-analyte quantification platform and hybridization chemistry that is 100% digital. The technology can accelerate your research beyond RT-PCR and RNAseq and can be used for analyzing mRNA, miRNA, CNV, Fusions, SNV, and protein. 15:30-16:00

15:30-16:00

15:05-15:30

quality and amount of the target template is crucial. If starting material is either degraded, damaged or the reaction is inhibited, the results can be misleading, dubious and outright negative. Typically, template DNA-related problems are encountered when “non-standard” samples are being analysed, i.e. samples recovered from crime scenes, archaeological digs, or recovered from aged cadavers. Prediction of appearance (DNA phenotyping) of unknown missing persons and offenders is especially crucial in forensic cases which have no other evidence available. We have examined the effect of various known and candidate inhibitors, as well as methods to successfully amplify regions of interest from compromised samples. These variables include inhibitors (components of clay, common household chemicals), selected polymerases and storage methods.

15:05-15:30

diagnostic field for the benefit of patient care. Microbiota diagnostics gives insight in the presence of all live, dead and fastidious bacteria in clinical samples in contrast to specific PCR or culture. Here we report on the evaluation of an ‘end-to-end’ microbiota profiling platform (MYcrobiota), which combines micelle 16S rRNA PCR/NGS with an easy-to-use bioinformatics pipeline. As an example, we studied 23 culture negative synovial fluid samples from suspected sceptic arthritis and demonstrated the presence of bacterial DNA in seven samples. These samples contained fastidious anaerobic species that were left uncultured. This study demonstrates the benefits of MYcrobiota for diagnosing sceptic arthritis and its potential on improving patient care.

15:05-15:30

considered as “gold standards” for detection of volatile organic compounds (VOCs). However, they are bulky, expensive, and require highly skilled personnel. An alternative technique is electronic-noses (e-noses) that with a sensor array and pattern recognition methods mimic the mammalian olfactory system. However, the drift and need for recalibration of the sensor array limit the broad use of e-noses. We present a practical solution involving a single sensor for which the drift compensation and recalibration is much simpler than e-noses. In essence, the single metal oxide semiconductor sensor embedded into a microchannel provides a unique “smell print” due to diffusion and adsorption phenomena. The effect of ambient along with different applications of the proposed microfluidic-based artificial olfaction system will be presented.

15:05-15:30

Continued

SANDRA ACOSTA VERDUGOSenior Postdoctoral Fellow, Centre for Vascular & Developmental Biology, Northwestern University, USA

2-HHR: an efficient method for bi-allelic homologous recombination in mouse embryonic stem cellsTargeted genome editing in mouse embryonic stem cells (ESCs) is a powerful resource to functionally characterize genes and regulatory elements. The use of the CRISPR/Cas9 genome editing approach has remarkably improved the time and efficiency of targeted recombination. However, the efficiency of this protocol is still far from ideal when aiming for bi-allelic homologous recombination, requiring at least two independent targeting recombination events. Here we describe an improved protocol that uses two gRNAs flanking the selected targeted region, leading to highly efficient homologous recombination in mouse ESCs. The bi-allelic recombination targeting efficiency is over 90% when using two gRNAs together with the inhibition of non-homologous end-joint repair. Moreover, this technique is compatible with the generation of knocked-in mice and the use of ESC-derived differentiation protocols, therefore facilitating and accelerating the gene targeting in mice and ESCs.

VINCENT LINDERFounder and President, CDP BioMedical Consulting, PortugalCommercialization of Microfluidic Devices for

Point-of-Care ApplicationsThis presentation will focus on the commercialization challenges specific to microfluidic devices for Point-of-Care (PoC) applications. At an early stage of development, strategies can focus on de-risking analytical and clinical performances and may overlook other critical aspects of the design. For a successful commercialization effort, it is essential to implement at the onset of the program a comprehensive vision encompassing the patient presenting in a PoC setting, the PoC user and all the steps needed to obtain an actionable test result. This presentation will focus on selected commercialization challenges and discuss directions/solutions to overcome them.



16:50-17:15

ALEXANDRA BOGOŽALEC KOŠIRResearch Assistant, National Institute of Biology, Department of Biotechnology and Systems Biology, Slovenia

Optimization of GMO quantification – from qPCR to multiplex dPCRGenetically modified organisms (GMOs) have been present on the world market for more than 20 years. In this time many countries, including the European Union, implemented a labelling system for products containing GMOs based on a certain threshold. Today, real-time quantitative PCR (qPCR) is the standard approach for GMO quantification. However, with the rise of complexity of products containing GMOs and the rise of abundancy of GMOs in general, a new approach is needed. To overcome these issues we have:• Used 3 platforms, BioRad - QX100/200,

Fluidigm – Biomark, Stilla – Naica• Transferred simplex qPCR methods to

simplex and duplex dPCR assays for quantification of GMOs in complex samples exhibiting high inhibition

• Designed and evaluate multiplex assays for more time- and cost-effective quantification.

16:50-17:15

PETAR PODLESNIYScientific Researcher, CiberNed, IIBB, Barcelona, SpainSelfie-dPCR: Absolute measurement of gene expression and replication

• Limitations of reference gene based normalization in qPCR and dPCR

• Concept of Selfie-dPCR • Specificity, accuracy and precision of the

approach• Applications for absolute quantification of

gene expression of single/multiple/variable copy genes expression between tissues, transgene models and species

• Study of the DNA replication using Selfie-dPCR

• Design strategies and technical notes • Possibilities which Selfie-dPCR opens for

reproducible and comparable nucleic acids quantification

16:50-17:15

MARTYN BOUTELLEProfessor of Biomedical Sensors Engineering, Imperial College London, UKPortable microfluidic devices for continuous human tissue monitoring

16:50-17:15

TIMO FALTUSResearch Fellow, Project Coordinator of GenomELECTION, Martin Luther University of Halle-Wittenberg, Germany

The Legal and Medico-Ethical Framework of Basic Research Using Genome Editing and of the Translation of Genome Editing Therapies• Getting aware of the different legal framework

of basic research and application-oriented research in genome editing research.

• Avoiding legal pitfalls in translating genome editing based therapy approaches from bench to bedside.

• Where, when, and how to go for legal and scientific advice for a successful translation.

17:15-18:05

ROUNDTABLE DISCUSSIONS:Table 1: Liquid biopsiesMIKAEL KUBISTAProfessor, Czech Academy of Sciences; Chairman of the Board, and Founder, TATAA Biocenter, Sweden

• Goals and objectives (personalized medicine, theranostics, monitoring, primary diagnostics)

• Challenges (actionability, one tube, sensitivity, specificity)

• Quality control (reliability)• Standardization & guidelines (reproducibility)

Table 2: Droplet-based digital PCRVALÉRIE TALYCNRS Research Director, Group Leader, Translational

17:15-17:40

CINDY SMITHSenior Lecturer and Royal Academy of Engineering Senior Research Fellow, Infrastructure and Environment, School of

Engineering, University of Glasgow, UKEvaluating the impact of RNA integrity and reverse transcription strategy on quantification and diversity of bacterial transcripts from environmental samplesQuantification of gene transcripts from environmental samples is a powerful approach to unravel the functioning of microbial communities. It can, however, be adversely affected by the quality and integrity of the RNA used. We evaluated the impact of RNA integrity on transcript quantification via RT-Q-PCR and bacterial community composition via Illumina MiSeq of 16S

17:15-17:40

JEROEN LAMMERTYNProfessor, Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, Belgium

Self-powered and easy-to-integrate heating system for on-chip temperature dependent bioassays in low resource settingsHere, we present a tuneable electric-free system enabling localized on-chip heating for point-of-care (POC) applications in low-resource settings (LRS). As heat source, the exothermic reaction of nucleating supercooled sodium acetate trihydrate (SAT) was exploited. A finite element method was applied to model heat transfer through the chip. To initiate the nucleation reaction an innovative finger-press activation mechanism was developed. This system was

PANEL DISCUSSION:Navigating Ethical & Regulatory Challenges for the Advancement of Gene Editing• Existing legal frameworks for gene editing

applications• Ethical concerns in light of the growing

scope and scale of genome engineering• Regulatory advice from leading experts for

the progress of safe scientific researchTIMO FALTUSResearch Fellow, Project Coordinator of GenomELECTION, Martin Luther University of Halle-Wittenberg, GermanyJOHN PARRINGTONAssociate Professor, University of Oxford, United Kingdom

17:15-18:05

Afternoon Refreshments / Odd Numbered Poster Presentations / One-to-One Meetings16:00-16:50



17:15-18:15

Research and Microfluidics, Paris Descartes University, France• Available platforms• Setting up of assays• Samples preparations • Comparison qPCR/dPCR and dPCR/NGS• Implementation of mutations based assays

or methylations based assay, also integrity based assays

Table 3: Gene expression analysis in the digital(PCR) era.PETAR PODLESNIYScientific Researcher, CiberNed, IIBB, Barcelona, Spain

This round table will be focused on the unprecedented possibilities which the digital PCR technologies are opening in the field of gene expression analysis.•Detecting of fine events of physiologically relevant gene regulation.•Comparison the expression levels between cell types, tissues and model organisms.•General technical considerations.•The emerging possibility to construct a “digital image” of the nucleic acids composition of a living cell by employing digital PCR.

Table 4: Strategies for data analysisSTEFAN RÖDIGERGroup Leader, Institute of Biotechnology, Brandenberg

University of Technology Cottbus – Senftenberg, GermanyReproducibility is a central element of science. Results that have already been obtained must be replicable by using the same and new samples or data. In recent years, there has been growing evidence that science is confronted with a crisis of reproducibility. Researchers indicated that about 2/3 of the results were not reproducible in certain areas of research. These results are dramatic and require efforts to counteract non-reproducibility. In the discussion round, central questions and data analysis strategies will be defined and options for action derived.• Are we facing a reproducibility crisis that

effects diagnostics and healthcare or is it

17:15-17:40

rRNA and two mRNA gene targets (amoA and glnA) in sequentially degraded RNA extracted from coastal sediments. Subsequently, we evaluated the impact of the reverses transcriptase strategy (enzyme choice and priming) on quantification and amplicon sequencing of transcripts from complex sediment mixed microbial communities. Here the choice of RT enzyme and priming strategy resulted in significant difference in quantification and community composition from the exact same sample. Based on results, we set forth recommendations for transcript quantification from environmental samples and propose a new RNA integrity index to assess the quality of extracted RNA.

17:15-17:40

integrated within our SIMPLE technology1,2, with the aim to create a standalone generic system supporting isothermal nucleic acid amplification tests (NAATs), immunoassays or other temperature-dependent bioassays.

17:15-18:05

17:40-18:05

AMANDA NAAUMVisiting Research Fellow, Queen’s University Belfast, UK; Senior Research Scientist, TRU-ID Ltd., CanadaSeafood Identification in

the Field: Portable Real-Time PCR for Fish and Shrimp SpeciesSeafood fraud, particularly the substitution of one species for another, continues to be a global issue. Differentiation of species via DNA-based methods can help identify and combat this problem, but accessibility to testing, and incorporation into the supply chain remain problematic. Real-time PCR is a rapid and effective method for performing screening for target species. Using portable equipment and specially designed sample preparation protocols, reliable field testing can be done to screen for seafood mislabelling using real-time PCR. This presentation details case studies in fish and shrimp species identification using the two3 device from Biomeme paired with easy-to-use kits that require no specialized lab equipment for sample preparation. The procedures allow anyone with minimal training to carry out species identification. This simple, portable approach allows DNA testing using real-time PCR to be more fully integrated into the food supply chain, helping to better identify and combat food fraud.

17:40-18:15

CLOSING KEYNOTE ADDRESS: JONATHAN COOPERProfessor, Wolfson Chair of Bioengineering, University of Glasgow, UK

Origami Paper Folding for Low Cost DNA Diagnostics in Rural Communities Rapid, low-cost, species-specific information based upon DNA testing is becoming key to informing the treatment of patients with infectious disease. Populations in remote, under-served communities would benefit from this information, if available, enabling the correct treatment of infections. For example, such highly sensitive assays will become increasingly important in global efforts for disease elimination where the diagnosis of asymptomatic patients is important for the identification of disease reservoirs. However, healthcare workers face practical and logistical issues in the implementation of such tests, which often involve complex instrumentation and centralized laboratories. We have now demonstrated a multiplexed paper-based microfluidic technology that combines origami paper folding for sample-processing with lateral-flow detection and a simple visualisation system. The studies were performed in village schools in Eastern Uganda with individual diagnoses being completed in <1hr.

DYLAN PHILLIPSLecturer in Genetics, IBERS, University of Aberystwyth, United Kingdom



Chair's Closing Remarks / End of Day 118:15

Networking Drinks Reception18:15-19:15

17:15-18:15

merely an academic concern?• How can open source software help to

improve strategies for data analysis?• Is the flood of publications, or the publication

process, symptom or cause of non-reproducibility?

• How can we detect non-reproducible results even at early stages of research?

• Could machine learning (artificial intelligence) help us to counteract non-reproducibility?

17:15-18:05

17:40-18:05

Continued

17:40-18:15

Continued Continued

CONGRESS SCHEDULE DAY 2 WEDNESDAY 28TH NOVEMBER 2018

08:20-09:00

Track Chair: Bas Brinkhof, Postdoc, Engineering Science, University of Oxford, UK

Refreshments

LIQUID BIOPSIES & CTDNA ANALYSIS ORGAN-ON-A-CHIP

Track Chair: Mina Hoorfar, Professor and Director of the School of Engineering, University of British Columbia, Canada

09:00-09:35

KEYNOTE ADDRESS:MIKE MAKRIGIORGOSProfessor of Radiation Oncology, Dana Farber Cancer Institute and Harvard Medical School, USANovel digital PCR and mutation enrichment technologies for the analysis of clinically

relevant DNA alterations in liquid biopsiesWith the increasing interest in treatment assessment using liquid biopsy and circulating DNA, sensitive and multiplexed detection of tumor-derived alterations in blood are desirable. We provide novel forms of digital PCR, as well as mutation enrichment-based real time PCR methods that (a) enable several orders of magnitude improvement of detecting mutations or microsatellite instability than currently possible; (b) are highly multiplex-able; (c) reduce cost of analysis. Application in circulating DNA from clinical cancer samples will be presented.

09:00-09:35

KEYNOTE ADDRESS:DANIEL LEVNERChief Technology Officer, Emulate, Inc., USAOrgans-on-Chips: A Platform for Drug Development and Disease ModelingOrgan-Chips - such as the Lung-, Liver-, Brain-

and Intestine-Chips - are micro-engineered systems that display physiological functions consistent with human in vivo. Each Organ-Chip contains fluidic channels lined by living human cells that are cultured under continuous flow and mechanical forces. Organ-Chips recreate key aspects of the in vivo cellular microenvironment, leading to recapitulation of human biology well beyond the capabilities of conventional in vitro models. Accordingly, Organ-Chips enable the study of normal physiology, pathophysiology, and mechanisms of action or toxicity in an organ-specific context. In this presentation, we will highlight studies from collaborative efforts across our Human Emulation System with various academic and industry partners to demonstrate the utility of the system as a more predictive human-relevant platform for efficacy, safety and mechanistic studies.

09:35-10:00

CHARLES BAROUDAssociate Professor, École Polytechnique; Research Unit Head, Insitut Pasteur, FranceSpheroid culture and screening in an integrated microfluidic deviceIn this presentation I will present our platform

for the culture and screening of 3D cell spheroids. The platform provides access to single-cell measurements on more than 100,000 cells, in situ within more than 10,000 spheroids. I will also show how to build complex tissues, screen small molecules, or study host-pathogen or immuno-therapy interactions.

09:35-10:00

JÖRG TOSTDirector of the Laboratory for Epigenetics and Environment, National Center for Research in Human Genomics (CNRGH), CEA- Institute for Biology Francois Jacob, FranceIdentification of rare mutations and DNA

methylation patterns in cell-free DNA using multiplexed Enhanced-ice-COLD-PCRCirculating cell-free DNA (ccfDNA) has great potential for non-invasive diagnostics and monitoring of treatment response. We have developed Enhanced-ice-COLD-PCR for mutation detection and identification, which allows the enrichment of mutations permitting the sensitive detection and multiplexed sequence identification of mutations within three hours. This assay permits the reliable detection of down to 0.1 % mutated sequences in a wild-type background while maintaining quantitative accuracy as compared with dPCR. We have recently extended the applications to the analysis of methylated molecules in primary tumors and ccfDNA. Enhanced-ice-COLD-PCR has been applied to different collections of cancer samples including repeated plasma samples from patients undergoing mutation-specific treatments and enables detection of mutations in samples, which appear wild-type using standard detection technologies.

10:00-10:30

SOLUTION PROVIDER PRESENTATION:KELLY KAIHARAGlobal Market Development Manager, Bio-Rad Digital Biology Group7 Years in: Bio-Rad and the next steps for Droplet Digital PCR

10:00-10:30

For sponsorship opportunities contact Gavin Hambrook / Nick Best:

[email protected] / +44 (0) 1865 849841


Morning Refreshments / Poster Presentations / One-to-One Meetings10:30-11:50


11:50-12:05

TONY GODFREYAssociate Chair, Surgical Research; Professor of Surgery, Boston University School of Medicine, USAOptimization of barcoded NGS library construction and application to liquid biopsy for cancer monitoring

SiMSenSeq is a barcoded NGS library construction approach that facilitates detection of rare variant alleles at frequencies <0.1%. SiMSen-Seq is perfectly suited for applications that require multiplexing beyond the capability of digital PCR but do not require large genome coverage provided by other ultra-sensitive NGS approaches. For example, the flexible multiplexing

11:50-12:05

SÉVERINE LE GACAssociate Professor, Applied Microfluidics for BioEngineering Research, University of Twente, The NetherlandsTumor-on-a-chip model to study nanomedicine penetration

Nanomedicines hold great promises as imaging and therapeutic agents. However, their penetration in stroma-rich tumor is challenging, which limits their applicability. To evaluate the penetration and efficiency of nanomedicines, dedicated in vitro models are required that recapitulate essential features of the tumor microenvironment. Here, we report a tumor-on-a-chip platform, which consists of a 3D


ROUNDTABLE DISCUSSIONS:Table 1: New formats - from paper to 3D printingNICOLE PAMMEProfessor in Analytical Chemistry, University of Hull, UK■ What are the opportunities and challenges with

new formats such as paper or fibre based microfluidic devices or 3D printed chip devices?• What implications does this have for the manufacture and

use of the '2-dimensional' polymer and glass devices the microfluidics community has mainly worked with so far?

Table 2: Droplet microfluidics across the scales: molecules to cells to organoidsCHARLES BAROUDAssociate Professor, École Polytechnique; Research Unit Head, Insitut Pasteur, France

• Droplets have proven to be exquisite for detecting molecules (DNA, proteins, ...) at high throughput. What is the future of this research now that standards have emerged?

• Manipulating cells has proved to be more challenging. Are there questions for which droplets are uniquely well adapted?

• How can we go beyond single-cell studies to look at complex 3D structures?

Table 3: Organ-on-a-chipDANIEL LEVNERChief Technology Officer, Emulate, Inc., USA

Table 4: Infectious Disease Diagnostics in Under-Served CommunitiesJON COOPERProfessor, Wolfson Chair of Bioengineering, University of Glasgow, UK

• What are the drivers for new diagnostic tests in under-served communities?

• How do the criteria for diagnostics differ in the developed world from those needed in rural communities?

• How do devices differ when used for individual screening against population screening?

Table 5: Analyzing Whole Blood Samples in the Point-of-CareVINCENT LINDERFounder and President, CDP BioMedical Consulting, Portugal

Many assays measure analytes present in plasma/serum, and in centralized laboratory settings blood cell separation is routinely performed before assaying the samples. In Point-of-Care (PoC) settings, blood cell separation is, however, often not available. When developing a PoC device:

12:20-12:45

FLORENT MOULIEREAssistant Professor, Liquid Biopsy Centre/Pathology, University of Cambridge/Amsterdam UMC, UK/NetherlandsBoosting non-invasive cancer genomics with fragment size analysis of plasma cell-free DNA

The sensitivity for detecting the presence of genomic changes in circulating tumour DNA (ctDNA) is limited by its low concentration in plasma. Here I will present new approaches tailoring sequencing to the biological properties of ctDNA for improving the detection of rare mutant molecules. In particular, we studied the feasibility for enrichment of ctDNA by physical and in-silico size selection in plasma samples collected from multiple cancer types. Size selection of short DNA fragments enriches for ctDNA, unlocking untargeted genome-wide sequencing for liquid biopsy.

ULRICH LEHMANNProfessor, Head of the Laboratory of Molecular Diagnostics, Hannover Medical School, GermanyIntroducing liquid biopsy into routine diagnostics in molecular pathology – challenges and perspectives• FDA approval of the first liquid biopsy test in

the middle of 2016 (for EGFR T790M).• A range of methods for analysis of free circulating DNA in

blood samples has be evaluated.• Many methodological questions have been addressed and

solved since then.• My talk focusses on key pre-analytical, logistic and analytical

challenges and problems still to be solved.• The list of possible and already realized applications is steadily

growing and will be critically discussed.

12:05-12:20

12:20-13:10


11:50-12:05

afforded by SiMSen-Seq can be leveraged to generate patient-specific mutation detection panels to monitor treatment response and recurrence in cell-free plasma DNA from cancer patients or to detect clinically actionable evolution of tumors during targeted therapy. This talk will discuss recent applications and reproducibility of SiMSen-Seq, the effect of polymerase fidelity on error correction in barcoded NGS and will introduce a new protocol for single-tube SiMSen-Seq.

11:50-12:05

tumor spheroid, prepared from a co-culture of breast tumor cells and fibroblasts, trapped in a microfluidic chamber.

Lunch13:10-14:10

12:45-13:10

KRISTI KRUUSMAAHead of Research, Universal DX Diagnostics, SpainMSRE-qPCR for multiplexed analysis of DNA methylation can be accurately used for detection and validation of colorectal cancer-specific biomarkers in liquid biopsy samples

12:05-12:20

MARCO SERRAPost-doc, Institut Curie, FranceMagnetic solid supports handling in droplet microfluidics: application to DNA clean-up and size selection for NGS libraries preparation



14:35-15:00

BERNHARD ZIMMERMANNVP of Research & Development, Molecular Research, Natera, Inc., USAMonitoring circulatory tumor DNA (ctDNA) with patient specific multiplex PCR assaysSignatera™ RUO is the first individualized

pan-cancer circulating tumor DNA platform showing promising results in research studies for monitoring treatment response, detecting minimal residual disease and predicting disease recurrence. I will present analytical validation of the test down to 0.01% VAF (tumor fraction) and data from clinical studies in lung cancer, bladder cancer and colorectal cancer, where ctDNA is detected in plasma of patients up to one year ahead of clinical detection of relapse, with 100% specificity, and demonstrably higher sensitivity than ddPCR.

14:10-14:35

LAO SAALCEO, SAGA Diagnostics AB, and Head, Translational Oncogenomics Unit, Lund University Cancer Center, SwedenApplications of ultrasensitive circulating tumor DNA measurements to 0.001% VAF in cancer liquid biopsies using SAGAsafe (IBSAFE) digital chemistry

• Increasingly, rare sequence variants are important to identify and quantify in research and healthcare, and in particular within cancer research and oncology such as in circulating tumor DNA (ctDNA)

• In sequence variant quantification, polymerase errors inevitably introduce false-positive signals in qPCR, dPCR, and NGS workflows which hinders performance and negatively impacts their lower limits of detection (LoD)

• SAGAsafe (IBSAFE) is an improved dPCR-compatible method for highly sensitive and specific detection of SNVs that is ultrasensitive to a lower LoD of 0.001% variant allele frequency (VAF)

• Example applications of IBSAFE/SAGAsafe in non-small cell lung cancer, breast cancer, melanoma, and acute myeloid leukemia will be presented

LIQUID BIOPSIES, CTDNA ANALYSIS & DDPCR ORGAN-ON-A-CHIP

14:10-14:35

JAAP DEN TOONDERProfessor, Chair of the Microsystems Group, Eindhoven University of Technology, The NetherlandsCancer on a Chip: a microfluidic platform to study cancer cell invasion

Microfluidics technology offers the possibility to create devices in which chemical, mechanical, and physical conditions can be precisely controlled. This makes it possible to realize well-defined micro-environments to realize advanced multi-cellular culture systems to investigate tissue and organ function, and to recreate aspects of diseases to understand processes and mechanisms in disease progression. In this talk, I will present our microfluidic platforms and show how we use these to understand disease progression. In particular, I will focus on our “cancer-on-chip” devices, which we have applied to study the influence of the structure of the extra-cellular matrix on the invasive behavior of a number of breast cancer cell types with known different metastatic behavior.

TUOMAS KNOWLESProfessor of Biophysics & Biophysical Chemistry, University of Cambridge, UKTopic: Microfluidics for protein biophysics

14:35-15:00

15:00-15:25

MARIE FOLLOHead of Lighthouse Core Facility, Center for Translational Cell Research, Dept. of Internal Medicine I, Medical Center, Faculty of Medicine - University of Freiburg, GermanyDevelopment of ddPCR assays for the

detection of KRAS and NRAS mutations in circulating tumor DNA in patients with pancreatic cancerThe detection of circulating tumor DNA (ctDNA) from patients with solid tumors shows great promise in the areas of diagnosis and treatment monitoring. The sensitivity of droplet digital PCR (ddPCR) makes it a powerful tool for the detection of low-abundance mutations in patient plasma. We have focused on the development of assays for the detection of typical activating mutations found within the KRAS and NRAS oncogenes in patients with pancreatic cancer through the use of a Bio-Rad QX100 ddPCR system, as well as on the development of duplexed and multiplexed screening assays for these mutations.

15:00-15:50

COMPANY SHOWCASE:3x 15 minute presentations

BAS TRIETSCHMimetasChief Technology Officer, Mimetas, The Netherlands

SAMI ELLOUZEInDrop functional assay applied for antibody drug discoveryGroup Leader, Microfluidics Assay Development & Screening Platform, HiFiBiO Therapeutics, France

• Hifibio introduction• Hifibio platform• Screening technology• InDrop functional assay• Monitoring of multiple pathway at single cell level• Functional antibody drug discovery

MARIAN REHAKDirector of R&D, Sphere Fluidics, UKCyto-Mine® - An integrated microfluidic platform for a high-throughput single cell analysisA number of different techniques are currently

used in the biopharmaceutical discovery and development workflows. These include single cell assessment, identification, imaging and dispensing into individual wells of microtitre plates (MTPs). Traditionally, different instruments would be required for each technique; which is costly, time-consuming and requires extensive lab space that increases the risk of sample contamination. Picodroplet technology allow for

15:25-15:50

PER GULDBERGProfessor, Group Leader, Cancer Genetics Lab, Danish Cancer Society, DenmarkUrine as a liquid biopsy for highly sensitive detection of bladder cancerIt has been known for decades that bladder

tumors shed cells into the urine. However, to convert such “proof of concept” into a clinical useful test for bladder cancer can be complicated. This paper discusses various factors that can affect the sensitivity of urine-based tests, including 1) diagnostic coverage of DNA biomarkers, 2) cancer-to-normal cell ratio, 3) detection of rare molecules using ddPCR, and 4) the stochastic



15:50-16:15

JULIETTE NECTOUXMolecular Geneticist, Cochin Hospital, Paris, FranceNon-invasive prenatal diagnosis of monogenic disorders using droplet digital PCRThe deployment of ddPCR for cell-free DNA

analysis has opened the way for noninvasive prenatal testing (NIPT) of monogenic disorders. However, to date, it is proposed only in rare cases for exclusion of paternal/sporadic mutations, the study of the maternally-inherited mutations remaining complex because of the predominance of maternal DNA background. In this context, ddPCR represents an appropriate tool for the analysis of the fetal genotype. Since 2013, >200 samples have been collected from families at risk of transmitting monogenic disorder. Two types of applications have been developed:• Qualitative detection of sequences absent from the maternal

genome, which allows proposing NIPT in clinical practice for sporadic mutations involved in achondroplasia, but also for paternal mutations involved in neurofibromatosis type 1 and cystic fibrosis.

• Quantitative detection of sequences identical to the maternal genome, taking into account the mode of transmission, the nature of the mutation and the fetal fraction.

15:50-16:15

Conference Close16:15

15:00-15:50

sophisticated, fast and sensitive manipulation of cells at the single cell level. Cyto-Mine® technology is the first integrated device to automatically perform allowing for automated cell assessment, hit identification and sorting, and a hit dispening in a single compact system. This high-throughput instrument uses picodroplet technology and microfluidics to process around up to 40 million heterogeneous mammalian cells in 4-6 hours.

15:25-15:50

nature of tumor-cell shedding. Addressing all of these factors have led to the development of a urine-based test for bladder cancer, which has a very high sensitivity and therefore may replace the current golden standard, cystoscopy.

NICOLE PAMMEProfessor in Analytical Chemistry, University of Hull, UKTitle TBC

VENUE INFORMATION

Postillion Convention Centre WTC RotterdamParkeergarage Beurs-WTC,Rodezand 19,3011 AM Rotterdamwww.postillionhotels.com/en-gb/conferenties-events/rotterdam-convention-centre

In the vibrant heart of the Rotterdam metropolis: you cannot get more central than this. Wherever you are in the world, a World Trade Center is a special place. It is an (inter)national corporate community, in a unique building that meets the highest standards. From high-spec office space to high-tech meeting rooms, shops, restaurants and a wide range of additional services.• A non-stop high-speed train runs between Rotterdam and Schiphol

(Amsterdam airport) every 20 minutes. The journey time is 20 minutes. Cost €22 Euros

• Located in the city centre (surrounded by shops, architecture, museums, restaurants and the Port of Rotterdam)

• Walking distance from the international train station• Rotterdam – The Hague airport with flights to at least 30

international destinations is a short taxi ride• A large number of parking facilities can be found in the area• A wide variety of hotels are within walking distance. (Details will be• sent to you in your welcome letter when you register)


gene dpcr/ngs editing 4bio · description: this course gives an introduction to next generation...

Documents