11-12 July 2016, Philadelphia, USA

www.globalengage.co.uk/digital-and-qpcr.html

2nd qPCR and Digital PCR Congress: USA DEVELOPMENTS & POTENTIAL OF qPCR & dPCR AS A TOOL FOR PROGRESSING MOLECULAR BIOLOGY RESEARCH Global Engage is pleased to announce the 2nd year of the American leg of our successful qPCR & Digital PCR series, which will be co-located with our Microfluidics Congress on 11-12 July 2016 in Philadelphia. Bringing together over 150 industry and academic experts working in areas such as molecular biology/diagnostics, gene expression, genomics, biomarkers, pathogen detection, GMO, mRNA, NGS, bioinformatics and data management, the congress will examine the latest developments, opportunities and applications of both dPCR and qPCR through case studies across diverse areas such as oncology, infectious diseases, vaccines, prenatal diagnostics, clinical applications, microbiology, food microbiology, environmental testing and other novel applications. With increasing numbers of real-time PCR users purchasing digital PCR due to the reduction in its cost, absolute quantification, improved sensitivity, precision and greater robustness; and with the gene amplification market predicted to grow to $2.2 billion by 2017, this conference provides a timely opportunity to learn first-hand about dPCR whilst also keeping up to date with latest developments and strategies in qPCR. The conference will provide an interactive networking forum to both further develop and answer your queries through a vibrant exhibition room full of technology providers showcasing their technologies and other solutions, poster presentation sessions, expert led case study presentations and interactive Q&A panel discussions from a 50-strong speaker faculty examining topics on five separate tracks covering Confirmed Speakers Include:

Nick Papadopoulos Professor and Director of Translational Genetics, Johns Hopkins University

Joel Tellinghuisen Emeritus Professor of Chemistry, Vanderbilt University

G. Mike Makrigiorgos Professor of Radiation Oncology, Dana Farber Cancer Institute and Harvard Medical School

Conference Synopsis Day 1 – Stream One Digital PCR: Applications & Possibilities

Introduction, benefits, future development of dPCR

Comparing dPCR to qPCR

Converting to dPCR and choosing your system

Validation of dPCR

Complimenting digital PCR with other technologies including NGS

Multiplexing in digital PCR

Detection of patient-specific mutations

Applications for precision medicine Day 1 – Stream Two

A) qPCR: Strategies & Developments

Developments in qPCR methods

MIQE guidelines & standardisation

qPCR/RT-PCR assay design, optimisation & validation

Sample preparation & quality control methods

Detection, quantification and sequencing of RNA

Automation of qPCR methods

Bioinformatics and data analysis

Multiplexing

Parallel sequencing

B) Food Case Studies

qPCR in food research

Detection and identification of food pathogens

GMO quantification in food

Day 2 – Stream One Healthcare Case Studies

Clinical/Diagnostic applications

Oncology (rare variant detection, monitoring therapy response, early relapse detection.)

Neurological disorders

Prenatal diagnostics

Infectious diseases

Biomarker discovery

Micro RNA/ncRNA/siRNA applications

Gene expression and synthesis

Single cell analysis

Liquid Biopsies Day 2 – Stream Two Plant and Water Case Studies

Environmental Sampling

Water contamination analysis with dPCR and qPCR

qPCR in plant research

Detection and identification of plant pathogens/bacteria

Gene expression analysis

Confirmed Speakers:

Fred Kramer Professor of Microbiology, Biochemistry and Molecular Genetics, Public Health Research Institute, Rutgers University Patricia Silveyra Assistant Professor, Pennsylvania State University Derek Ostertag Head of R&D Diagnostics, Tocagen Shu Chen Research Scientist and Manager, Agriculture and Food Laboratory, University of Guelph Valerie Taly Group Leader, University of Paris Descartes Hendrik Viljoen Professor and Chair of Chemical and Bimolecular Engineering, University of Nebraska-Lincoln Bob Dorazio Research Statistician, US Geological Survey Greg McCollum Research Plant Physiologist, US Department of Agriculture Katia Sol-Church Director Nemours Biomolecular Core Lab Alfred I. duPont Hospital for Children Rémi Dangla CEO and Co-Founder, Stilla Technologies

Wayne Barnes Associate Professor, Washington University Medical School, St Louis Joel Tellinghuisen Emeritus Professor of Chemistry, Vanderbilt University

Rachel Noble Professor and Director of Institute for the Environment, University of North Carolina Institute of Marine Sciences Jerald Radich Director the Molecular Oncology Lab and Member of Clinical Research Division, Fred Hutchinson Cancer Center Mojca Milavec Senior Research Specialised Associate National Institute of Biology, Slovenia

John Griffith Principal Scientist & Coordinator of Molecular Technology, Southern California Coastal Water Research Project

Sandra Koseoglu Associate Principal Scientist, Pharmacology and Cellular Pharmacology, Merck Research Laboratories Tigst Demeke Program Manager of Grain Biotechnology Research, Canadian Grain Commission Tiong Gim Aw Assistant Professor, School of Public Health and Tropical Medicine, Tulane University Erica Romsos, Forensic Scientist, Biomolecular Measurements Division, Applied Genetics, National Institute of Standards and Technology

Nick Papadopoulos Professor and Director of Translational Genetics, Johns Hopkins University Ronald Rabin Chief, Laboratory of Immunobiochemistry, US Food and Drug Administration Piotr Garstecki Associate Professor, Institute of Physical Chemistry, Polish Academy of Sciences G. Mike Makrigiorgos Professor of Radiation Oncology, Dana Farber Cancer Institute and Harvard Medical School Musaddeq Hussain Principal Scientist, Merck Laboratories Guillaume Pavlovic Head of Genetic Engineering and Model Validation Department, Mouse Clinical Institute, France

Anne Eischeid Research Scientist, US Food and Drug Administration, Center of Food Safety and Applied Nutrition Rachel Tam Senior Scientific Researcher, Genentech Jean Beagle Ristaino William Neal Reynolds Distinguished Professor, North Carolina State University John Thomas Bradshaw Senior Development Scientist, Artel

2nd qPCR & Digital PCR Congress: USA – 11-12 July 2016, Philadelphia, USA

Confirmed Speakers Continued:

Stream Chair: Sony Agrawal Senior Scientist, Merck Laboratories Sarmitha Sathiamoorthy Scientist, Sanofi Pasteur, Canada Sabine Hellwig R&D Scientist, ARUP Laboratories Bahram Arezi R&D Operating Manager, Diagnostics & Genomics Group, Agilent Technologies Inc

Chetan Bettegowda Assistant Professor of Neurosurgery and Oncology, Johns Hopkins University Marie Bugarel Research Assistant Professor, Texas Tech University

Sanjiv Shah Microbiologist, US Environmental Protection Agency Johnson Ng CEO, JN Medsys

Konrad Faulstich Director of Business Development, BioNTech Jie Wang Researcher, Martin Chilvers’ Lab, Department of Plant, Soil and Microbial Sciences, Michigan State University Maria Mayda Senior Scientist, ATCC Cody Youngbull Research Professor, Arizona State University

The 2nd qPCR and Digital PCR Congress USA is co-located with: The Microfluidics Congress USA

http://www.globalengage.co.uk/microfluidics-usa.html

Venue

Hilton Philadelphia City Avenue 4200 CITY AVENUE, PHILADELPHIA, PENNSYLVANIA, 19131, USA

A discounted group rate is available to all attendees. Details of how to book are available on registration. Space is limited and accommodation is available on a first come basis.

For more information please contact Steve Hambrook, Conference Director, Global Engage Ltd.

steve@globalengage.co.uk +44 (0) 1865 849841

2nd qPCR & Digital PCR Congress: USA – 11-12 July 2016, Philadelphia, USA

2nd qPCR and Digital PCR Congress USA - Sponsors 2016

Gold Sponsors

Supporting Sponsors

2nd qPCR and Digital PCR Congress USA – 11-12 July 2016, Philadelphia, USA

For more information please contact Steve Hambrook, Conference Director, Global Engage Ltd.

steve@globalengage.co.uk +44 (0) 1865 849841

08.00-08.50 Registration & Coffee – Renaissance & Grand Salon

08.50-09.00 Garden Ballroom Global Engage Welcome Address Stream Chair’s Opening Remarks: Ronald Rabin – Chief of Immunobiochemistry, US Food and Drug Administration

09.00-09.35 Keynote Address Detection of Rare Mutations in Biological Fluids: Challenges and Opportunities

Somatic mutations are cancer specific biomarkers that reveal the presence of cancer when present in cell free DNA or DNA derived from biological fluids.

The number of circulating tumor DNA molecules with somatic mutations is very small compared to that of DNA molecules with wild type sequence making their detection challenging.

Accurate detection of rare mutations in biological fluids provides the opportunity to develop non-invasive tests for the clinical management of cancer patients.

Confirmed: Nickolas Papadopoulos, Professor of Oncology and Director of Translational Genetics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University

09.35-10.05 Keynote Address Types I and II Interferons at the Respiratory Epithelial Barrier

Analysis of interferon stimulated genes that function as transcription factors reveals non-redundant functions for interferon-beta and interferon-lambda1

Combinatorial effects of interferon-beta and interferon-lambda1 can be modeled with a cuboid equation

Small can be beautiful too: targeted qRT-PCR can be revealing at a fraction of the cost of transcriptome analysis

Confirmed: Ronald Rabin, Chief, Laboratory of Immunobiochemistry, US Food and Drug Administration

10.05-10.35 Solution Provider Presentation Introducing the Naica™ System for Crystal Digital™ PCR Stilla Technologies unveils its unique technology for high precision genetic analysis: Crystal Digital PCR. Taking advantage of cutting-edge microfluidic innovations, this technology relies on a single consumable to perform on-chip PCR in monolayer droplet arrays. A key feature of Crystal Digital PCR is the combination of powerful image analysis and intuitive visual inspection of droplet crystals to characterize and count partitions, which offers an unmatched confidence in digital PCR results. The Naica system leverages the key assets of Crystal Digital PCR in a compact, fast and easy-to-use solution, uniquely equipped with a 3-color multiplexing capacity.

Confirmed: Rémi Dangla – CEO of Stilla Technologies

10.35-11.45 Morning Refreshments – Renaissance & Grand Salon Poster Presentation Sessions and One-to-One Partnering Meetings

Stream 1 – Digital PCR: Possibilities & Opportunities Garden Ballroom

Stream Chair: Ronald Rabin – Chief of Immunobiochemistry, US Food and Drug Administration

Stream 2 – qPCR: Strategies & Developments Salon Venezia

Stream Chair: Sony Agrawal – Senior Scientist, Merck Laboratories

11.45-12.10 Color-Coded Molecular Beacons for Multiplex Digital PCR Assays Every droplet of a digital PCR assay can contain as many as 35 different highly specific molecular beacon probes that are each tagged with a different combination of three out of seven available fluorescent colors. All of the molecular beacons remain dark except for those whose probe sequence is exactly complementary to a target sequence within the amplicons that are generated in a droplet. Because each droplet is a screening assay, as many as 35 rare mutations (for example, mutations relevant to cancer diagnosis, prognosis, and treatment that may be present in a “liquid biopsy") can be simultaneously and accurately quantitated with an instrument that can distinguish the fluorescent colors that are present.

Confirmed: Fred Kramer, Professor of Microbiology, Biochemistry and Molecular Genetics, Public Health Research Institute, Rutgers University

Developing Automated Absolute qPCR Capabilities to Evaluate Antiviral Potencies

Absolute qPCR of viral and host DNA copy numbers enables accurate monitoring of antiviral effects of test samples.

Development of a robust assay requires an evaluation of biological parameters, PCR efficiencies, and assay metrics.

Automation enables higher throughput while minimizing variability. Special consideration needs to be taken when employing automation to ensure that assay metrics are not affected as throughput is scaled.

Confirmed: Sandra Koseoglu, Associate Principal Scientist, Pharmacology, Cellular Pharmacology, Merck Research Laboratories

Agenda: Day One – Monday 11th July 2016

For more information please contact Steve Hambrook, Conference Director, Global Engage Ltd.

steve@globalengage.co.uk +44 (0) 1865 849841

12.10-12.35 Evaluation of Digital PCR as a Primary Method for Measurement for Production of a Reference Material

Use of digital PCR to assign values for a NIST Standard Reference Material

Importance of evaluation various assays and platforms

Assessment of bias and assigning uncertainty when assigning values

Confirmed: Erica Romsos, Forensic Scientist, Biomolecular Measurements Division, Applied Genetics, National Institute of Standards and Technology, USA

Design of a qPCR Assay to Confirm a Positive Adventitious Agent Signal by HTS in a Biological Product

Detection of Adventitious Agents in Vaccines and Biological Products

Use of Next-Generation Sequencing in adventitious agent testing to address gaps in current testing package

Follow-up of positive Next-Generation Sequencing signals using qPCR assays

Confirmed: Sarmitha Sathiamoorthy, Scientist, Sanofi Pasteur, Canada

12.35-13.00 Digital PCR for Biological and Synthetic Standards Biological and synthetic nucleic acid standards are a particular form of standardized nucleic acids that can be used for multiple applications such as controls, checking the metrological traceability of DNA/RNA products, validating analytical measurement methods, and for calibration of instruments. Given the intended use of these nucleic acids, a precise, reliable and reproducible quantification process is vital to define them as standards. This presentation will discuss the benefits and challenges of digital PCR and how this technology has been used at ATCC for absolute quantification of Nucleic acid-based products.

Confirmed: Maria Mayda, Senior Scientist, ATCC

Better qPCR through Statistics

Scale-independent markers for the quantification cycle Cq, like the second-derivative maximum or relative threshold, perform better than the absolute threshold.

For small copy number N0, the dispersion of Cq in replicate experiments is dominated by Poisson statistics , making it possible to estimate N0 directly from the Cq variance; the method is useful for N0 in the range 10-200, with relative precision (2/n)1/2 (20% for 50 replicates).

Relative expression is commonly estimated using the Cq method, or the Cq,adj method, where in the latter, there is allowance for variability in the amplification efficiency AE; for the

often-use “standard curve” design, nonlinear least squares can be used to estimate Cq,adj and its uncertainty, with automatic inclusion of uncertainty in the AEs.

Confirmed: Joel Tellinghuisen, Emeritus Professor, Vanderbilt University, USA

13.00-13.30 Solution Provider Presentation Accuracy Matters When Transferring a Quantitative, Bench-top Assay to Automation: Understanding Method Transfer Pitfalls

Assays are usually performed on the benchtop using handheld pipettes before they are transferred to an automated liquid handling platform

The manual assay should be directly compared to the automated assay for consistencies in pipetting performance.

Undetected differences in accuracy will impact the integrity of the assay as the automation process continues.

Confirmed: John Thomas Bradshaw, Senior Development Scientist, Artel

13.30-14.25 Lunch and One-to-One Partnering Meetings – Renaissance & Grand Salon

Stream Chair: Rémi Dangla – CEO, Stilla Technologies Stream Chair: Sony Agrawal – Senior Scientist, Merck Laboratories

14.25-14.50 Detection Limits of Digital PCR Assays and their Influence in Presence-Absence Surveys of Environmental DNA The digital PCR (dPCR) assay can potentially be used to estimate low concentrations of nucleic acids with greater accuracy and precision than other assays. This potential is particularly important in the quantification of environmental DNA (eDNA), which is often used to identify the presence of an animal species not easily detected by traditional survey methods. In this application it is essential to establish an unambiguous reference point (or detection limit) for the presence of eDNA. We developed a statistical model for estimating dPCR-based limits of detection from serial dilution experiments with known standards. We illustrated the benefits of this approach by analyzing samples of grass carp eDNA collected in ponds known to contain different numbers of grass carp.

Confirmed: Robert Dorazio, Research Statistician, US Geological Survey

Opportunities for Expedited Isothermal PCR

Review of the Recombinase Polymerase Amplification (RPA) process and identification of the rate limiting steps. Experiments are shown in which DNA amplification occurs under conditions of rotational turbulent flow. A mathematical model is used to demonstrate how to use RPA for qPCR applications.

Two utilities of expedited RPA are discussed: the use of super paramagnetic nanoparticles (SPMNPs) to retrieve target DNA from the lysate onto the mechanical stirrer and the collection of cells by SPMNPs from a clinical sample for analysis by RPA.

New opportunities for expedited RPA. Some applications in agriculture and medicine will be discussed as well as the development of a system for unmanned aerial vehicle applications.

Confirmed: Hendrik Viljoen, Professor and Chair of Chemical and Biomolecular Engineering, University of Nebraska, USA

Day One continued – Monday 11th July 2016

For more information please contact Steve Hambrook, Conference Director, Global Engage Ltd.

steve@globalengage.co.uk +44 (0) 1865 849841

14.50-15.15 Digital PCR Assays for the Use in Point-of-Care Systems and on Standard Real-Time Devices

Digital PCR assays introduced absolute quantitation yet, in the classic format they require massively large number of partitions of the sample.

Here we describe two innovative approaches that maximize the information gain from each partition and reduce the required number of compartments by orders of magnitude.

An explicit algorithm for designing multi-volume/dilution assays allows to independently tailor the precision and dynamic range to the particular application.

We also describe the first synergistic digital-analogue assay, that can be run on standard Real-Time PCR devices, with multiple tests fitted on a single well-plate, combining absolute quantitation with high precision and dynamic range.

Both methods are described in terms of ready-to-use explicit design and analysis formulas and open up new grounds for the use of digital assaying technologies.

Confirmed: Piotr Garstecki, Professor, Group Leader, Institute of Physical Chemistry, Polish Academy of Sciences, Poland

Identification of miRNA Biomarkers for Pediatric Lung Disease using PCR Profiling

Using miRNAs as biomarkers and diagnostic tools for human lung diseases: selecting the best sample source.

Bronchopulmonary dysplasia and Pulmonary Hypertension in the preterm infant, using miRNA profiling to identify patients and risk and therapeutic targets.

Common technical challenges when profiling by PCR, strategies for data analysis and interpretation.

Confirmed: Patricia Silveyra, PhD Assistant Professor, Department of Pediatrics, The Pennsylvania State University College of Medicine, USA

15.15-15.45 Solution Provider Presentation Serial Monitoring of ctDNA by Picoliter Digital PCR Liquid biopsy diagnostic assays are increasingly recognized as valuable additions to clinical oncology practice. Detecting point mutations and other somatic alterations in plasma circulating tumor DNA (ctDNA) in an often overwhelming background of healthy cell-free DNA requires highly sensitive analysis methods. Using picoliter droplet digital PCR (dPCR) we are able to detect ctDNA to a sensitivity of 2 copies per milliliter plasma. In ongoing studies we use dPCR detection of somatic point mutations, such as EGFR T790M and BRAF V600E, to serially monitor cancer patient samples.

Confirmed: Sabine Hellwig, R&D Scientist, ARUP Laboratories

15.45-16.35 Afternoon Refreshments – Renaissance & Grand Salon Poster Presentation Sessions and One-to-One Partnering Meetings

Stream 1 – Digital PCR: Possibilities & Opportunities Garden Ballroom

Stream 2 – Food Case Studies Salon Venezia

16.35-17.00 Ultra-sensitive Mutational Analysis in Cell-free DNA by Digital PCR Cell-free DNA in plasma offers a non-invasive approach to monitor tumour molecular profiling in real-time, detection of emerging genomic alterations associated with drug resistance, clarifying cancer prognosis and diagnosis of cancer progression. We developed an ultra-sensitive ddPCR approach to detect actionable mutations in cfDNA. We will show the validation of this ddPCR platform using commercially available DNA controls, FFPE tissues and cfDNA matched samples and compared this approach to other orthogonal technologies, including qPCR and NGS and achieved 100% concordance across these platforms. DdPCR can detect mutations down to 0.03% allele frequency with 100% sensitivity and specificity. DdPCR platform enables the development of a non-invasive method to overcome existing challenges to provide molecular understanding of patient’s tumour evolution and aid in the development of personalized cancer therapies.

Confirmed: Rachel Tam, Senior Scientist, Genentech

A Single-Codon Gain-of-Function Mutation that Converts Taq DNA Polymerase to be able to Catalyze RT-PCR, LAMP, and RT-LAMP, and be Resistant to Chocolate, Black Pepper and Blood We report a single amino acid change to Taq DNA polymerase that confers a multiplicity of new or increased powers. The single-mutant Taq enzyme can now catalyse RT-PCR (albeit only 200 or so bases), LAMP and RT-LAMP, and inhibitors found in blood and food are now so insignificant that DNA and RNA purification can be reduced or even dispensed with in many diagnostic, safety and forensic assays that amplify RNA or DNA sequences. It was results from non-negative negative controls that led to the discovery of the LAMP ability of the full-length Taq mutant (vs. the N-terminal deletion Klentaq1) and also the RT activity (the no-RT control). The mutated amino acid is not near DNA or the active site in the crystal structures.

Confirmed: Wayne Barnes, Associate Professor, Department of Biochemistry and Molecular Biophysics, Washington University Medical School in St Louis, USA

Day One continued – Monday 11th July 2016

For more information please contact Steve Hambrook, Conference Director, Global Engage Ltd.

steve@globalengage.co.uk +44 (0) 1865 849841

17.00-17.25 Innovative Methods in Quantitating Host Residual DNA in Biologic Drugs

Host residual DNA as impurity in a biologic drug is currently quantified by DNA extraction followed by qPCR

We have developed methods for direct qPCR without DNA extraction from mAb drugs

We have applied direct methods in digital PCR based residual DNA quantification

Confirmed: Musaddeq Hussain, Principal Scientist, Merck Laboratories

Molecular Determination of the most prevalent Salmonella Serotypes

Development of 41 real-time molecular biomarkers targeting serotype-specific clustered regularly interspaced short palindromic repeat (CRISPR) spacers for the 30 most prevalent Salmonella serotypes, including Agona, Senftenberg, Dublin, SaintPaul, Anatum, Derby, Braenderup, Newport, Bovismorbificans, Montevideo, Heidelberg, Napoli, Enteritidis, Gallinarum, Tennessee, Schwarzengrund, Infantis, Virchow, Hadar, ParatyphiA, ParatyphiB, ParatyphiC, Choleraesuis, Hessarek, Weltevreden, Brandenburg, Panama, Kottbus, Typhimurium, and variants.

Validation of the markers using an high-throughput real-time PCR platform and in silico investigation

Utilization of this assay as a first screening step to identify the most frequently encountered serotypes, to facilitate and fasten the process of serotype determination, which can be particularly important in the case of outbreak investigation.

Confirmed: Marie Bugarel, Research Assistant Professor, Texas Tech University

17.25-17.50 Exploring the Potential of dPCR for the Development of Reference Measurement Procedure

Comparison of one qPCR and two dPCR platforms for quantification of CMV

Quantification of CMV by dPCR (without extraction)

Inter-laboratory comparison of methods for quantification of CMV (4 laboratories, 3 dPCR platforms)

Confirmed: Mojca Milavec, Senior Research Specialised Associate, Department of Biotechnology and Systems Biology, National Institute of Biology, Slovenia

Quantitative Real-time PCR for Detection of Food Allergens QPCR is a highly sensitive and specific detection method for allergenic foods. This talk will focus on development of qPCR methods for detection of crustacean shellfish. For this work, group-specific assays were developed for shrimp, crab, and lobster using mitochondrial 12S and 16S gene sequences. The method was evaluated for detection of crustaceans at concentrations from 0.1 to 105 ppm (mg/kg) in a variety of food matrices and processing conditions, including foods with inherently low DNA content, acidic pH, and foods treated with high temperature and pressure. With the exception of combined conditions of high temperature, high pressure, and acidic pH, the assays were linear over 6-8 orders of magnitude, with high reaction efficiencies and detection limits of approximately 0.1 to 1 ppm.

Confirmed: Anne Eischeid, Research Scientist, US Food and Drug Administration, Center for Food Safety and Applied Nutrition

17.50-18.15 Applications of Droplet DigitalTM PCR in Food and Feed Testing: Challenges and Solutions

Droplet Digital PCR (ddPCR) methods will be presented for quantification of meat species (bovine, porcine, chicken and turkey) and GMO in food and feed samples.

Challenges and solutions encountered in the method validation process will be discussed, especially those relating to sample matrices, reference materials, DNA QC and controls.

Examples of method evaluation over time and “real-world” application of the methods for testing food and feed samples will be presented.

Confirmed: Shu Chen, Research Scientist, Manager, Agriculture and Food Laboratory, University of Guelph, Canada

18.15 Chair’s Closing Remarks and End of Day 1

18.15-19.15 Networking Drinks Reception – Renaissance & Grand Salon

Day One continued – Monday 11th July 2016

For more information please contact Steve Hambrook, Conference Director, Global Engage Ltd.

steve@globalengage.co.uk +44 (0) 1865 849841

08.00-08.35 Registration, One-to-One Networking Meetings, & Coffee – Renaissance & Grand Salon

08.35-08.40 Versailles Room Global Engage Welcome Address Stream Chair’s Opening Remarks: Tania Konry, Assistant Professor, Department of Pharmaceutical Sciences, Northeastern University, USA

08.40-09.15 Keynote Address Extraction and Detection of Sparse Pathogens from Biological Fluids at the Microfluidics Scale The molecular diagnosis of blood infections is challenging because pathogens exist in the bloodstream in very low concentrations. Consequently, such sparse target populations typically require DNA extraction and purification from large volume biofluids. This work utilizes the advances in microfluidic technologies to demonstrate initially whether pathogens are present. If so, then a second phase of DNA extraction and identification of the specific pathogens present is performed. Magnetic bead assays and current-wire manipulation enable the initial sensing step. Immiscible phase filtration (IPF) for nucleic acid purification and electrowetting-on dielectric (EWD) droplet actuation are combined on a hybrid microfluidic device that translates from large volume sample-to-small-volume analysis. After IPF reduces the sample volume from a milliliter-sized lysate to a microliter-sized eluent, EWD can be used to automatically prepare the PCR mixture. The extent of purification obtained per IPF wash, and hence the number of washes needed for uninhibited qPCR, are determined via on-chip UV absorbance. The performance of on-chip qPCR, particularly the copy number to threshold cycle correlation, is characterized. Lastly, the above developments accumulate to an experiment that includes the following on-chip steps: DNA purification by IPF, PCR mixture preparation via EWD, and target quantification using qPCR - thereby demonstrating the core procedures in the proposed approach.

Confirmed: Richard Fair, Lord-Chandran Professor of Engineering, Department of Electrical and Computer Engineering, Duke University, USA

Stream 1 – Healthcare Case Studies Garden Ballroom

Stream Chair: Johnson Ng – CEO, JN Medsys

Stream 2 – Plant and Water Case Studies Salon Venezia

Stream Chair: Sanjiv Shah – Microbiologist, US Environmental Protection Agency

09.20-09.50 Keynote Address Novel Methods for Enrichment of Mutations and Differentially Methylated Sequences from Tumor and Liquid Biopsy DNA Circulating DNA is poised to become a widely used tool for repeated assessment of cancer mutation and methylation status during the course of therapy. Removing the high excess wild type DNA fraction from circulating DNA allows enrichment of variant DNA and boosts the potential of all endpoint detection technologies, including sequencing. We present Nuclease-assisted Mutation Enrichment, NaME, a simple and powerful approach to remove wild type DNA from large gene pools simultaneously, in order to focus sequencing on clinically relevant DNA alterations. This single-step approach retains current sample preparation protocols almost unchanged and combines seamlessly with downstream technologies such as HRM, COLD-PCR, ddPCR and next generation sequencing. Application in clinical samples and liquid biopsies will be presented.

Confirmed: Mike Makrigiorgos, Professor of Radiation Oncology, Dana Farber Cancer Institute and Harvard Medical School, USA

Late Blight: A Re-emerging Plant Disease that Threatens Global Food Security

Plant pathogens cause losses estimated to be as high as $30 billion per year and the risk of spread of pathogens globally with trade requires continued monitoring and improved diagnostic capabilities.

Late blight caused by Phytophthora infestans causes a devastating disease of potato and tomato and was responsible for the Irish potato famine.

Her work on the population genetics of historical epidemics of the pathogen and the population structure of present day late blight outbreaks will be discussed as well as the pioneering research techniques on 150-year-old historic herbarium specimens.

Confirmed: Jean Beagle Ristaino, William Neal Reynolds Distinguished Professor, North Carolina State University

9.50-10.20 Solution Provider Presentation Accurate quantification and qualification of FFPE samples by qPCR increases success rate of NGS library prep and sequencing FFPE tissue archiving is the most widely used method for clinical sample preservation, and provides a valuable source of diverse genetic information for cancer biomarker discovery. DNA recovered from FFPE tissues exhibits varying degrees of fragmentation, cross-linking, deamination, depurination and other lesions due to formalin fixation, paraffinization, and storage conditions; and as a result, NGS library preparation is often challenging. To increase success with FFPE-derived DNA, we developed a qPCR-based method to determine quantity of amplifiable DNA and extent of degradation. As we will show, qPCR integrity scores are highly correlated with pre-capture PCR yield and sequencing metrics, and can be used as a guide to determine appropriate sequencing depth for optimal coverage

Confirmed: Bahram Arezi, R&D Operating Manager, Diagnostics & Genomics Group, Agilent Technologies Inc

10.20-11.25 Morning Refreshments – Renaissance & Grand Salon Poster Presentation Sessions and One-to-One Partnering Meetings

11.25-11.55 Solution Provider Presentation Tube-strip digital PCR for sensitive and high-throughput quantification of cell-free DNA in liquid biopsy Digital PCR is one of the fastest growing technologies for genetic analyses. Sample partitioning, where a PCR sample is divided into a large number of partitions such that each contains only 0 or 1 target DNA copy, is an important step in digital PCR. However sample partitioning is technically complex to achieve. Here, we introduce tube-strip digital PCR on the Clarity system. Sample partitioning requires just 1 min and is performed on a high-density chip within a conventional PCR tube-strip. Workflow is fast and easy, with the flexibility to perform up to 96 reactions per run. We show how the Clarity digital PCR system is an attractive platform for performing for sensitive and high-throughput quantification of cell-free DNA in liquid biopsy.

Confirmed: Johnson Ng, CEO, JN Medsys

Day Two – Tuesday 12th July 2016

11.55-12.20 Tumor Derived Cell Free DNA as a Diagnostic Tool for Human Malignancies Human malignancies shed molecules of cell free DNA into the bloodstream and adjacent bio-fluids. These molecules of cell free tumor DNA can be distinguished from the background normal DNA by the presence of somatic mutations. Using sensitive digital approaches, we are now able to detect and track tumor DNA levels over time. Such an approach can theoretically be applied for applications related to screening, disease monitoring and treatment response.

Confirmed: Chetan Bettegowda, Assistant Professor of Neurosurgery, Johns Hopkins University, USA

qPCR in Plant Pathology to address Etiology, Epidemiology and Disease Risk Assessment

Strategies utilized for plant pathogen diagnostic assay development – loci of choice, target region copy number variations, and assay validation

Detection and quantification of pathogens from plant and soil samples

Case studies: Fusarium and Phytophthora assay development and application

Confirmed: Jie Wang, Researcher, Martin Chilvers’ Lab, Department of Plant, Soil and Microbial Sciences, Michigan State University

12.20-12.45 Aneuploidy Screening of Embryonic Stem Cell Clones by Metaphase Karyotyping and Droplet Digital Polymerase Chain Reaction The successful germ line transmission of a mutated allele in embryonic stem (ES) cells depends on karyotypic integrity. Classical methods for the identification of aneuploidy involve cytological analyses that both are time consuming and require rare expertise to identify mouse chromosome. We validated a PCR based method as an alternative to classical karyotype analysis that enables laboratories that are non-specialist or work with large numbers of clones to precisely assess ES cells for the most common aneuploidy found in ES cells prior to microinjection to maintain high level of germ line transmission potential. This method can be applied to any other cell line (iPS, human cells …) to evaluate the karyotypic integrity.

Confirmed: Guillaume Pavlovic, Head of Genetic Engineering and Model Validation Department, Mouse Clinical Institute, France

Digital PCR Detection of Candidatus Liberibacter Species in Citrus and Asian Citrus Psyllids

Worldwide citrus production is being devastated by Huanglongbing (HLB), a disease associated with Candidatus Liberibacter sp. (CLas) a bacterial pathogen, vectored by insects known as citrus psyllids (ACP). Confirmation of CLas infection has important regulatory consequences and is an essential component of HLB management.

Currently, CLas infection can only be confirmed via PCR technology, and quantitative real time PCR is the USDA APHIS approved protocol for survey. Suspect samples must be confirmed by conventional PCR. Digital PCR may provide a more sensitive assay for confirmation of infection.

We have compared detection of CLas via digital PCR with quantitative real time PCR and conventional PCR. Our results indicate digital PCR may serve as alternative to conventional PCR for confirmation of CLas infection.

Confirmed: Greg McCollum, Research Plant Physiologist, USDA Agricultural Research Service

12.45-13.10 Digital PCR: A Tool for Clinical Investigations of Pediatric-onset Genetic Disorders

Establishments of new digital PCR services for bench to bedside translational research, a core lab perspective

Copy number variation in Spinal Muscular Atrophy, dPCR as a tool for genotype/phenotype correlation

Complex genomic rearrangements at the PLP1 locus, dPCR as a deliverable for breakpoint studies

Confirmed: Katia Sol-Church, Director Nemours Biomolecular Core Lab Alfred I. duPont Hospital for Children

Effects of DNA-related Factors on Droplet Digital PCR for Absolute Quantification of Genetically Engineered Traits

Low levels of genetically engineered traits were analyzed with RainDance droplet dPCR system

The effects of source of DNA and treatment of DNA on droplet dPCR results were investigated

Absolute quantification of GE traits in non-target DNA was investigated using droplet dPCR

Confirmed: Tigst Demeke, Research Scientist. Canadian Grain Commission, Grain Research Laboratory

13.10-14.10 Lunch – Renaissance & Grand Salon

Stream Chair: Valerie Taly - Group Leader, University of Paris Descartes

Stream Chair: Sanjiv Shah – Microbiologist, US Environmental Protection Agency

14.10-14.35 MammaTyper – Making Breast Cancer Stratification Reproducible Breast cancer has been recognized as multiple diseases, each subtype requiring a different therapy. Correct determination of the subtype of breast cancer is therefore crucial to therapeutic choice and patient’s prognosis on survival. MammaTyper, a CE/IVD marked test, combines proven medical principles with state-of-the art RT-qPCR measurement technology to conclude the subtype of breast cancer. The test determines the gene expression level of markers, which are recommended by guidelines and provides results with highest precision and reproducibility. Analytical and clinical validation data are provided and precision as well as clinical utility in adjuvant and neo-adjuvant setting is discussed. A CE/IVD certified optimized and simplified process for sample preparation from FFPE tissue material is also revealed

Confirmed: Konrad Faulstich, Director of Business Development and Project Management, BioNTech

Using Quantitative PCR and Digital PCR for Fecal Pollution Source Tracking in Environmental Waters The detection of the origin of fecal pollution in complex watersheds is beginning to take a prominent place in hazard identification and risk management policies. Microbial source tracking (MST) is a field that has developed molecular methods to differentiate various sources of fecal contamination from humans and animals. Most of the MST methods utilize genetic markers, which are host-specific, or library independent, and rely mainly on quantitative PCR without cultivation of the microorganisms. This presentation will focus on the use of qPCR- and digital PCR-based MST for determining the sources of fecal pollution in watersheds in Michigan.

Confirmed: Tiong Gim Aw, Assistant Professor, School of Public Health and Tropical Medicine, Tulane University

Day Two continued – Tuesday 12th July 2016

For more information please contact Steve Hambrook, Conference Director, Global Engage Ltd.

steve@globalengage.co.uk +44 (0) 1865 849841

14.35-15.00 The use of Digital Detection in Leukemia Digital detection allows for the detection of rare transcripts or leukemia cells, which is important in the quantification of residual disease, as well as understanding clonal selection and expansion. This talk we describe the various ways digital analysis can be used in the research and management of leukemia patients, especially in the context of discontinuation strategies in chronic myeloid leukemia.

Confirmed: Jerald Radich, Director the Molecular Oncology Lab and Member of Clinical Research Division, Fred Hutchinson Cancer Center, Professor of Medicine, University of Washington School of Medicine, USA

Development of Flow Through Automated Digital PCR Instrument for Environmental Water Monitoring Environmental water quality is typically monitored using growth-based methods that take 18 - 72 hours to result. However, water contamination events are ephemeral and have often dispersed before health officials can act to issue warnings against water contact and protect the public from exposure to potential pathogens. qPCR methods to measure microbial targets are faster, but still require water samples to be returned to the laboratory for testing. Here we describe development of a field-portable ddPCR instrument. This technology has the potential to revolutionize how environmental water monitoring is conducted by allowing technicians to analyze samples in near real time and to follow microbial contamination back to its source.

Confirmed: John Griffith, Principal Scientist and Coordinator of Molecular Technology, Southern California Coastal Water Research Project, USA

15.00-15.25 Droplet Digital PCR, Liquid Biopsies and Patient Follow-up Droplet digital PCR allows for analysis of specific genetic markers with high sensitivity and precision Analysis of liquid biopsies by digital PCR is a highly pertinent tool for patient follow up and treatment management Illustrative examples will be presented both for different markers and different cancer types.

Confirmed: Valerie Taly, Group Leader, University of Paris Descartes, France

Quantifying Pathogenic Viruses and Bacteria using Digital Droplet PCR in Complex Water Samples Digital droplet PCR (ddPCR)-based quantification of viral and bacterial pathogens in complex water and shellfish samples has the power to revolutionize monitoring and surveillance. For example, in recreational waters, quantification of norovirus and adenovirus at detection limits relevant to swimmers and surfers was previously not possible. However, with the advent of improved capture and detection techniques detection limits relevant to human health are attainable. We have analyzed a range of complex water and shellfish samples for specific viral and bacterial pathogens and will illustrate the possibilities for improved future water quality management using ddPCR, including hazard identification, QMRA, and improved notification. The importance of attention to detail for sample processing, quantification of standards, and assessments of recovery and inhibition will be featured.

Confirmed: Rachel Noble, Professor and Director of the Institute for the Environment, University of North Carolina Institute for Marine Sciences, USA

15.25-15.55 Afternoon Refreshments – Renaissance & Grand Salon Poster Presentation Sessions

15.55-16.20 Biomarker Identification and Viral Tracking of Cancer-Selective Immunotherapy Drug Product in Recurrent High Grade Glioma Clinical Trials Toca 511 (vocimagene amiretrorepvec) is an investigational retroviral replicating vector that encodes the transgene cytosine deaminase. Toca 511 can be delivered by multiple routes and selectively infects and spreads in tumor cells. Subsequent oral administration of investigational 5-fluorocytosine (Toca FC) results in formation of the antineoplastic drug 5-fluorouracil within infected tumors. Thus, clinically, treatment with Toca 511 and extended-release 5-FC (Toca FC) is designed to selectively destroy tumor cells within the body, while leaving healthy cells unharmed. This presentation will focus on the viral drug monitoring program and biomarker identification program using real time and digital PCR assays to support current phase I and II clinical trials.

Confirmed: Derek Ostertag, Head of R&D Diagnostics, Tocagen Inc

Enteric Virus Monitoring Under U.S. EPA’s Unregulated Contaminant Monitoring Rule Between 2013 and 2015, the U.S. EPA conducted enteric virus monitoring of 800 undisinfected ground water wells in the U.S. under the third round of Unregulated Contaminant Monitoring Rule. The monitoring targeted enteroviruses and noroviruses, which were listed on U.S.EPA’s Candidate Contaminant List 3. qPCR along with cell culture was used for enterovirus detection while only qPCR was used for norovirus detection. Although qPCR did not determine viability of the viruses, it was used as tool to determine ground water vulnerability. The presentation will discuss the methods and process used for the implementation of this study and the monitoring results.

Confirmed: Sanjiv Shah, Microbiologist, National Homeland Security Research Center, US Environmental Protection Agency

16.20-16.45 An Autonomous, Miniaturized Digital Droplet PCR Instrument for Field Deployable DNA Quantification

Digital Droplet PCR Instrument Developed for Long-Range Autonomous Underwater Vehicle

Fully integrated sample preparation, droplet generation, thermocycling and detection in a single miniaturized field-deployed package

Improves the rate, sensitivity, and dynamic range at which environmental samples may be continuously sampled and analyzed in situ.

Confirmed: Cody Youngbull, Professor, Arizona State University

16.45 Chair’s Closing Remarks and Conference Close

Day Two continued – Tuesday 12th July 2016

Workshop Organiser

2 Day Course: MIQE – How to get Good Quality Control in qPCR

Are you working with qPCR? Do you have control of the quality in all the steps of the analysis

procedure? This course will go deep into the MIQE guidelines, describe the important steps in

RNA and DNA analysis with qPCR and how you should work to fulfil the guidelines. To

follow the guidelines will give you a better control of the quality of your results. The course

is theoretical with a few practical computer-based exercises. The course content includes:

- Background about the MIQE guidelines

o What are the MIQE guidelines?

o Why are they important?

- What to think about when doing experimental design

- How to do nucleic acid extraction and quality control of extracts

o Different approaches for nucleic acid extraction

o How can we check the quality of extracted samples?

o How do we identify inhibitory samples?

- The Reverse Transcription reaction

o Different priming strategies for reverse transcription

o Pros and cons for different strategies

- How to do primer and probe design

o How to search for gene sequences

o Which are the factors that affect design?

o How do we avoid primer dimer formation?

o Other important considerations for primer design

o How to design hydrolysis probes

o Practical exercises in primer design

Key Information Cost:

Location: Hilton Philadelphia City Avenue Hotel, 4200 City Avenue, Philadelphia, PA 19131 Academic: $499

Date: 13th-14th July 2016 Industry: $699

- How to optimize qPCR assays

o Which factors affect the PCR?

o Which factors can be optimized?

- How to validate qPCR assays, LOD and LOQ

o How to determine LOD and LOQ

o Precision estimation

o Which controls to use

- Data analysis

o How does qPCR software process the data?

o How to evaluate curves and set threshold

- Normalization

o Different ways to normalize

o How to find stable reference genes

- How to do relative quantification

o Quantification methods and equations

o How to interplate calibration

- Absolute quantification strategies

o What is a suitable standard?

o How to do absolute quantification

Additional 2 Day Course: MIQE – How to get Good Quality Control in qPCR

Course Leader: Robert Sjöback, R&D Manager and Vice President, TATAA Biocenter

Robert Sjöback is currently working as RnD Manager and Vice President at TATAA Biocenter. He received his PhD

degree in Physical Chemistry from Chalmers University of Technology where he studied the fluorescent properties of

DNA binding dyes and contributed to the development of the LightUp probes. Sjöback worked several years with

research and product development of both PCR and ELISA based kits for food diagnostics. Since 2005 Sjöback has

worked at TATAA Biocenter being responsible for the company research and product development, and the application

and coordination of the company’s externally financed research projects, including EU projects within FP6, FP7 and

Horizon H2020 programs, as well as being lead instructor in the company training course program.