qPCR and Digital PCR Congress: USA · Sample preparation & quality control Detection, quantification and sequencing of RNA Precise quantification of nucleic acids Amplification curve

25-26 June 2015, San Diego, USA

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

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 American leg of our successful qPCR & Digital PCR series, which will be held on 25-26 June in San Diego, California at the Town and Country Resort Hotel.

Bringing together over 175 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, microfluidics 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 40-strong speaker faculty examining topics on four separate tracks covering:

Confirmed Speakers Include:

Keith Jerome Professor and Head, Virology Division, University of Washington/Fred Hutchinson Cancer Research Center

Mikael Kubista CEO, TATAA Biocenter & Head of Department, BTU, CAS

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

Conference Synopsis

Day 1 – Stream One

Digital PCR: Possibilities & Opportunities

Introduction, benefits, future development of dPCR

Converting to dPCR from qPCR

Oncology (rare variant detection, monitoring therapy response, early relapse detection, biomarkers for cancer detection etc.)

Verifying accuracy of dPCR data

Complimenting digital PCR with other technologies o NGS v dPCR – Advantages over NGS

Detection of patient-specific mutations

Multiplexing in digital PCR

Applications of precision medicine

Day 1 – Stream Two

qPCR: Strategies & Developments

MIQE guidelines & standardisation

qPCR/RT-PCR assay design, optimisation & validation

Sample preparation & quality control

Detection, quantification and sequencing of RNA

Precise quantification of nucleic acids

Amplification curve analysis/automated analysis of qPCR data/challenges & new solutions for data analysis

Bioanalytics

Single cell analysis

Day 2 - Stream One

qPCR & Digital PCR Case Studies

Clinical/Diagnostic applications

dPCR & its effect on patient care

qPCR/dPCR in diagnosis of neurological disorders

Molecular diagnostics

Micro RNA/ncRNA/siRNA applications

Infectious diseases/vaccines/environmental sampling

Non-invasive prenatal diagnostics

Gene expression

Microfluidics and Lab-on-a-Chip

Microfluidic design and flow control

Day 2 – Stream Two

Plant, Food and Environmental Case Studies

qPCR in plant research

Plant/ecology genomics

Detection and identification of plant and food pathogens

Gene expression analysis

qPCR in food research

GMO quantification in food

For more information please contact Nick Noakes, Marketing Director, Global Engage Ltd.

[email protected] +44 (0) 1865 849841

Confirmed Speakers

Keith Jerome Professor and Head, Virology Division, University of Washington/Fred Hutchinson Cancer Research Center Linda Starr-Spires Director, Nucleic Acid Methods Platform, Global Clinical Immunology Department, Sanofi-Pasteur

Hanlee Ji Director, Ji Research Group, Assistant Professor - Division of Oncology, Stanford University

Eva Redei Professor in Psychiatry & Behavioral Sciences and Physiology, Northwestern University

Mikael Kubista CEO, TATAA Biocenter & Head of Department, BTU, CAS

Tony Godfrey Associate Chair, Surgical Research, Associate Professor of Surgery, Boston University

Amanda Naaum Postdoctoral Fellow, Biodiversity Institute of Ontario, University of Guelph, Canada

Muhammed Murtaza Research Assistant Professor & Co-Leader, Center for Non-invasive Diagnostics, Translational Genomics Research Institute

Weian Zhao Assistant Professor, Department of Pharmaceutical Sciences, University of California, Irvine Adam Bell Institute of Infection, Immunity and Inflammation, University of Glasgow, UK

Lawrence Jennings Assistant Professor of Pathology; Director, Molecular Pathology, Northwestern University/Ann and Robert H. Lurie Children’s Hospital of Chicago

Andrew Brooks Chief Operating Officer, RUCDR Infinite Biologics and Director of the Bionomics Research and Technology Center, Rutgers University

Matthew McCall Assistant Professor, Department of Biostatistics and Computational Biology, University of Rochester Medical Center

Andrew Rhim Assistant Professor of Internal Medicine and Assistant Director for Translational Research, University of Michigan Medical School and Comprehensive Cancer Center

Emir Hodzic Director, Real-Time PCR Research & Diagnostic Core Facility, University of California, Davis Yuka Imamura Director, Penn State Hershey Genome Sciences Facility & Assistant Professor of Biochemistry and Molecular Biology and Pharmacology, Penn State College of Medicine

Rebecca Guy Research Scientist, Division of Science and Technology, Public Health Agency of Canada

Florian Schröper Leader Research Field: Innovative Detection Technologies and Assay Designs, Fraunhofer IME, Germany

Minnie Sarwal Professor of Surgery & Medical Director, University of California, San Francisco School of Medicine

John Griffith Principal Scientist & Coordinator of Molecular Technology, Southern California Coastal Water Research Project Flora Tassone Professor, Department of Biochemistry and Molecular Medicine, University of California, Davis

Carlotta Guiducci Assistant Professor, Laboratory of Life Sciences Electronics, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland

Matt Strain Assistant Professor, Dept. of Medicine & Associate Director, Genomics Core, University of California, San Diego Gary Lee Associate Director, Research, Sangamo Biosciences G. Mike Makrigiorgos Professor of Radiation Oncology, Dana Farber Cancer Institute and Harvard Medical School Xuelin Huang Professor, Department of Biostatistics, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center

Jose V. Die Visiting Scientist, Genetic Improvement of Fruits and Vegetables Laboratory, Agricultural Research Service, USDA

Alex Dobrovic Associate Professor & Head, Translational Genomics & Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Australia

Claire Davies Scientific Director, Genzyme, a Sanofi Company

Bertram Brenig Professor of Molecular Biology & Director of the Institute of Veterinary Medicine, University of Göttingen, Germany

Qingge Li Professor of Molecular Biology, Xiamen University, China

Elena Brin Principal Scientist, Polaris Pharmaceuticals [SESSION CHAIR] Vikash Bhardwaj Assistant Professor Biotechnology, Lovely Professional University, India

Also:

Senior Representative, Formulatrix

Senior Representative, Bio-Rad Laboratories

Jadwiga Bienkowska, Director, Computational Biology, Pfizer

Senior Representative, Integrated DNA Technologies

Senior Representative, RainDance Technologies

Senior Representative, Thermo Fisher Scientific

Alexander Urban, Assistant Professor, Psychiatry and Behavioral Sciences, Stanford University

Anton Bitner, Senior Scientist, Functional Genomics Lead, Janssen

qPCR & Digital PCR Congress: USA – June 25-26, San Diego, USA


[email protected] +44 (0) 1865 849841

P lat inum Sponsor P latinum Sponsor

Gold Sponsor Gold Sponsor

Gold Sponsor Gold Sponsor

Exhibitors and Content Sponsors

Media Partners

Venue

Town and Country Hotel 500 HOTEL CIRCLE NORTH SAN DIEGO, CA 92108 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.

Sponsors 2015


[email protected] +44 (0) 1865 849841

08.00-08.50 Registration & Coffee

08.50-09.00 Global Engage Welcome Address & Chairperson’s Opening Remarks Chairperson: TBC

09.00-09.35 Keynote Address: Digital PCR in the Clinical Virology Laboratory - Current Applications, and a Wish List for Next-Generation Instruments Digital PCR (dPCR) allows sensitive and accurate absolute quantitation of nucleic acid samples without the need for a standard curve. While dPCR is still mainly used in research settings, the characteristics of dPCR also make it attractive in the clinical laboratory. We will discuss applications of dPCR in the diagnostic virology laboratory, including ultraprecise cytomegalovirus monitoring, diagnosis of chromosomally integrated human herpesvirus 6, quantitation of latent HIV reservoirs, and virus detection from inhibition-prone samples. Despite the promise of dPCR, however, the current early generation instruments have substantially lower throughput than more mature qPCR platforms, and have limitations in the ability to multiplex assays. These limitations must be addressed before dPCR is likely to substantially replace qPCR as a major modality in clinical labs.

CONFIRMED:

Keith Jerome, Professor and Head, Virology Division, University of Washington/Fred Hutchinson Cancer Research Center

09.35-10.05 Solution Provider Presentation: Title To Be Confirmed

Platinum Sponsor

CONFIRMED:

Senior Representative, Bio Rad Laboratories

Solution Provider Presentation

For sponsorship opportunities please contact Steve Hambrook at [email protected]

Digital PCR Congress qPCR Congress

10.05-10.10 Stream Chair: TBC Stream Chair: Elena Brin, Principal Scientist, Polaris Pharmaceuticals

10.10-10.35 Title To Be Confirmed

RT-ddPCR to study HIV latency

CONFIRMED:

Matt Strain, Assistant Professor, Dept. of Medicine & Associate Director, Genomics Core, University of California, San Diego

PCR Applications for Personalized Medicine

CONFIRMED:

Minnie Sarwal, Professor of Surgery & Medical Director, University of California San Francisco School of Medicine

10.35-11.45 Morning Refreshments and Poster Presentation Session One-to-One Networking Meetings

11.45-12.10 Using Picodroplet PCR to Study Pancreatic Cancer

Here, we will discuss specific applications of picodroplet PCR technology to identify and study genetic and genomic events in pancreatic cancer progression.

CONFIRMED:

Andrew Rhim, Assistant Professor of Internal Medicine and Assistant Director for Translational Research, University of Michigan Medical School and Comprehensive Cancer Center

Analysis of Constitutional Methylation Using qPCR and Digital PCR Constitutional methylation refers to the presence of aberrant methylation (epimutation) of a given gene in normal tissues. We were the first to show that constitutional methylation of BRCA1 occurs in breast cancer (Snell et al 2008). This was the consequence of our focus on sensitive, reliable DNA methylation detection methodologies and our hypothesis that constitutional methylation of BRCA1 would lead to tumors resembling BRCA1 mutation-driven tumors. Methylation of BRCA1 was determined using MS-HRM and MethyLight. It is important to use quantitative assays as BRCA1 methylation occurs at low levels in the peripheral blood of at risk individuals. For this reason, the adoption of digital droplet PCR methodology is key to the diagnostic implementation of this study.

CONFIRMED: Alex Dobrovic, Associate Professor & Head, Translational Genomics & Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Australia

12.10-12.35 Title To Be Confirmed Digital PCR in Cancer

CONFIRMED:

Chief Operating Officer of RUCDR Infinite Biologics and Director of the Bionomics Research and Technology Center, Rutgers University

Today, Tomorrow and Down the Road: Developing, Validating and Maintaining Assay Relevance

CONFIRMED: Linda Starr-Spires, Director, Nucleic Acid Methods Platform, Global Clinical Immunology Department, Sanofi-Pasteur

Agenda: Day One – Thursday 25th June 2015


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mailto:[email protected]

12.35-13.00 The Right PCR in the Right Place: Tailored PCR Assays for Discoveries

I run a genomics core at Penn State University College of Medicine. We own both conventional real-time PCR (an LifeTech QuantStudio 12K Flex system with robotic plate handler) and digital PCR instrument (QuantStudio 3D digital PCR system). I would like to present some of our successful utilization of digital PCR and discuss about the “rightness” of the usage for particular projects. I would also like to present some cases that had benefited from using other type of PCR designs/instrumentations. A LifeTech QuantStudio 12K Flex system with robotic plate handler and QuantStudio 3D digital PCR system is available for qPCR gene expression and genotyping services.

CONFIRMED:

Yuka Imamura, Director, Penn State Hershey Genome Sciences Facility & Assistant Professor of Biochemistry and Molecular Biology and Pharmacology, Penn State College of Medicine

Development of Blood-based Transcriptomic Markers; from Animal Models to Clinical Studies Depression is one of the leading causes of disability in the United States and its prevalence is increasing steadily. A laboratory blood test, based on specific biomarkers, would increase diagnostic accuracy and initiation of treatment. We approached the identification of depression biomarkers via an integrative method of using animal models of both the genetic and the environmental/stress etiologies of depression. Examining genome-wide expression differences between each model and its control, in their brain and blood, we identified transcripts that show expression differences that are parallel in relevant brain regions and blood. Quantitative RT-PCR confirmation of these candidate biomarkers in the blood of the animal models and the identification of their human ortholoques led us to a panel of blood transcriptomic markers. These were analyzed quantitatively in the blood of 15-19 year old antidepressant-free adolescents with MDD and not depressed (ND) age, sex and race-matched controls. Transcript abundance of 11 blood markers differentiated subjects with early onset MDD from the ND group. In the second study, we assessed the blood-based biomarker panel in adult primary care patients with MDD and age, gender and race-matched non-depressed (ND) controls. Patients with MDD received cognitive behavioral therapy (CBT), clinical measures and blood RNA were obtained before and after 18 weeks of CBT. Blood transcript levels of nine markers differed significantly between subjects with MDD and ND controls at baseline. Co-expression patterns of transcripts differed between patients with different responses to treatment even before the onset of treatment. These results, therefore, suggest that quantitative transcriptomics across species is a fruitful approach for biomarker discovery and that qPCR-based blood markers can be developed even for illnesses traditionally

without a biological diagnosis.

CONFIRMED:

Eva Redei, Professor in Psychiatry and Behavioral Sciences and Physiology, Northwestern University


Gol d S po nso r

CONFIRMED:

Senior Representative, Formulatrix



13.30-14.30 Lunch

14.30-14.55 Detection of Circulating, Cell Free DNA in Plasma from Esophageal Adenocarcinoma Patients Using Digital PCR and NGS

Detection and quantification of mutated, circulating tumor DNA in plasma or serum of cancer patients has great potential as a biomarker for cancer detection, treatment selection and measuring response to therapy. We are using digital PCR and ultra-sensitive NGS to evaluate circulating tumor DNA for monitoring response to neoadjuvant therapy in patients with oesophageal adenocarcinoma. This talk will focus on technical challenges faced and how they are being overcome.

CONFIRMED:

Tony Godfrey, Associate Chair, Surgical Research, Associate Professor of Surgery, Boston University

Title To Be Confirmed

CONFIRMED: Anton Bittner, Senior Scientist, Functional Genomics Lead, Janssen

14.55-15.20 Reduction of HIV Reservoir Following Infusion of CCR5 Knockout T-cells Despite advances in anti-retroviral drugs that can effectively control viral replication, anti-retroviral treatment does not provide a cure for HIV. Currently the only documented HIV cure is a subject who received an allogeneic stem cell transplant from a donor with a homozygous defect for the CCR5 HIV co-receptor. Stem cell transplant is feasible in very few situations, however CCR5 can be genetically knocked out in T-cells or hematopoietic stem cells using novel genome editing technologies, thus rendering the modified cells resistant to HIV infection. We show that infusion of autologous CCR5 knockout T-cells is safe and provides immune reconstitution. Further, subjects treated with CCR5 knockout T-cells showed reduced HIV reservoir as measured by ddPCR. While quantification of the viral reservoir remains a challenge, ddPCR offers greatly improved precision and allows for evaluation of reservoir size in subjects over time.

CONFIRMED: Gary Lee, Associate Director, Research, Sangamo Biosciences

Modeling qPCR Non-Detects as Missing Data Quantitative real-time PCR (qPCR) remains one of the most widely used methods to measure gene expression. Despite extensive research in qPCR laboratory protocols, normalization and statistical analysis, little attention has been given to qPCR non-detects — those reactions failing to produce a minimum amount of signal. We show that the common methods of handling qPCR non-detects lead to biased inference. Furthermore, we show that non-detects do not represent data missing completely at random and likely represent missing data occurring not at random. We propose a model of the missing data mechanism and develop a method to directly model non-detects as missing data. Our approach results in a sizeable reduction in bias when estimating both absolute and differential gene expression.

CONFIRMED: Matthew McCall, Assistant Professor, Department of Biostatistics & Computational Biology and Department of Biomedical Genetics, University of Rochester Medical Center

Day One (cont.) – Thursday 25th June 2015


[email protected] +44 (0) 1865 849841


15.20-15.45 Digital Quantification of Biomarkers in Blood using the Integrated Comprehensive Droplet Digital Detection (IC 3D) System We will present a new platform technology that detects rare blood biomarkers including bacteria in blood stream infections, CTCs, miRNA and exosomes in cancer with extremely high sensitivity, specificity, and throughput. The technology relies on microencapsulated sensing systems that detect intracellular genetic markers, cell surface proteins or secreted markers.

CONFIRMED:

Weian Zhao, Assistant Professor, Department of Pharmaceutical Sciences, University of California, Irvine

A New Method for Quantitative Polymerase Chain Reaction Data Analysis Quantitative polymerase chain reaction (qPCR) is a sensitive gene expression measurement method that has been widely used in biomedical research and applications. There are two limitations in the current quantification methods. The first is the assumption that PCR amplification efficiencies are equal among different samples, which is known to be not true. The second is that an accurate determination of the background fluorescence level can hardly be achieved. The quantification results can be biased by incorrect background subtraction. We present a new method, the taking-difference method, to overcome these limitations. Briefly, for each two consecutive PCR cycles, we subtract the fluorescence in the former cycle from that in the later cycle and therefore transform the n-cycle raw data into new n-1 cycle data. Then linear regression is applied to the natural logarithm of the transformed data. Finally, PCR efficiency and the relative initial DNA amount are calculated for each reaction. Our data analysis results show that this taking-difference method is more accurate and reliable.

CONFRIMED:

Xuelin Huang, Professor, Department of Biostatistics, The University of Texas MD Anderson Cancer Center

15.45-16.15



Solution Provider Presentation: Implementing Quality Control and Performance Assessment of qPCR Instrumentation to Ensure Reliable Results The MIQE guidelines have made the ever growing qPCR community aware of the importance of robustness, reproducibility and quality assessment of qPCR measurements. This year regulatory bodies in Europe will start enforcing guidelines for the preanalytical process of molecular diagnostics developed by the European Standardizing Committee (CEN) and next year guidelines from the International Organization for Standardization (ISO) are expected. These guidelines help laboratories to assess the performance and quality of their analyses. This includes the performance of qPCR instruments, which shall be done on a regular basis to establish they meet vendors’ specifications and the laboratory’s internal quality requirements. Historically, performance specifications published by instrument vendors have not conformed to any particular standards and rarely have they been adequately documented in the product literature, making it hard for laboratories to use those important performance parameters as a basis for validating their assays and developing the associated quality control procedures. Here, we discuss the link between quality control routines and the emerging standards with novel and easily implementable approaches for the assessment of qPCR instrument performance using the IntelliQube platform from Douglas Scientific. Go l d S po nso r

CONFIRMED:

Mikael Kubista, CEO, TATAA Biocenter & Head of Department, BTU, CAS

16.15-17.05 Afternoon Refreshments and Poster Presentation Session One-to-One Networking Meetings

17.05-17.20 Young Investigator’s Presentation: Title To Be Confirmed

Invite to:

Young Investigator’s Presentation: Parallel DNA Polymerase Chain Reaction (PD-PCR) Conventionally in a PCR reaction a template DNA is amplified as it is but we have developed a novel PD-PCR (Parallel DNA- PCR) technique by which we were able to amplify a single stranded DNA into another DNA. I will discuss importance of it and the ways it can be used in future development of PCR.

CONFIRMED:

Vikash Bhardwaj, Assistant Professor Biotechnology, Lovely Professional University, India


Reserved:

Alexander Urban, Assistant Professor, Psychiatry and Behavioral Sciences, Stanford University

Title To Be Confirmed

CONFIRMED:

Carlotta Guiducci, Assistant Professor, Laboratory of Life Sciences Electronics, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland

17.45 Day 1 Close

17.45-18.45 Drinks Reception

Day One (cont.) – Thursday 25th June 2015


[email protected] +44 (0) 1865 849841


08.15-08.55 Coffee & Networking Meetings

08.55-09.00 Stream Chair Welcome Address

09.00-09.35 Keynote Address: Quantum-Scale Digital Genetics for Precision Medicine With digital genetic technologies that partition small number of discrete DNA molecules, one can achieve high sensitivity that borders on single molecule detection. The measurement of genetic variation at near single molecule resolution provides opportunities and challenges for translational studies and clinical diagnostics. Two different approaches that consider low and high molecular weight DNA analysis at single molecule resolution will be discussed. Their clinical implications will be considered.

CONFIRMED:

Hanlee Ji, Director, Ji Research Group, Assistant Professor - Division of Oncology, Stanford University

09.35-10.00 COLD-PCR and Digital COLD-PCR for Ultra-Sensitive Detection and Sequencing of Low-Level Resistance Mutations in Tumors and Bio-Fluids As applied, droplet digital PCR can only be used to detect known mutations at single sequence positions, e.g. 'hotspot' mutations in oncogenes. We present novel forms of ddPCR that, when combined with COLD-PCR or DiSSECT technologies enable mutation scanning over multiple sequence positions. A single dd-COLD-PCR reaction now interrogates numerous mutations within an amplicon, and replaces multiple individual digital-PCR reactions. Identification of type and position of mutations is performed via highly sensitive COLD-PCR combined with next generation sequencing. We describe examples of detecting resistance-associated mutations in EGFR and multiple TP53 mutations, using lung-adenocarcinoma DNA and plasma circulating DNA.

CONFIRMED:

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

10.00-10.30



Solution Provider Presentation: Zen Double Quenched Probes for Optimized Detection in qPCR and dPCR

Platinum Sponsor

CONFIRMED:

Senior Representative, Integrated DNA Technologies

10.30-11.20 Morning Refreshments and Poster Presentation Sessions One-to-One Networking Meetings

qPCR & Digital PCR Case Studies Plant, Food and Environmental Case Studies

11.20-11.50

Solution Provider Presentation: Title To Be Confirmed

Gold Sponsor

CONFIRMED:

Senior Representative, RainDance Technologies



11.50-12.15 Genotyping of Pathogens based on qPCR Platform Pathogen genotyping is crucial for tracking of those severe infectious diseases. A key feature of a genotyping approach is that it should be able to provide transferable digital genotyping data, which can be stored into a database with internationally recognized genotypes. Ideally, the genotyping method should be easy, rapid, reliable, and can be used in a sentinel laboratory. We describe hereby our efforts in the development of a novel melting curve-based multilocus sequencing typing, McMLST, on a qPCR platform. It utilized probe-based melting curve analysis to interrogate resolution optimized SNP sites derived from the MLST database. The Tm values generated were transformed into 0/1 codes, which are correspondent with absence or presence of the alleles of SNPs. The sequence type (ST) in MLST was thus replaced by a melting type (MT) that consists of a series of 0/1 codes. As models, two pathogens, Staphylococcus aureus and Vibrio parahaemolyticus, were chosen to evaluate the method. The results showed that McMLST is highly concordant with MLST and features increased rapidness, ease of use, and throughput when compared with MLST.

CONFIRMED:

Qingge Li, Professor of Molecular Biology, Xiamen University, China

Pooling of Fecal and Environmental Samples for the Detection of Salmonella spp. by qPCR Several studies have evaluated the use of qPCR for the detection of Salmonella spp. in fecal and environmental samples. The purpose of this study was to evaluate the pooling of feces and environmental samples following a selective enrichment culture step for the detection of Salmonella spp. by qPCR. Equine fecal and environmental samples were collected at veterinary hospitals, inoculated into selenite broth and incubated overnight, then processed for DNA purification. Salmonella spp. qPCR assay targeting the invasion A gene was performed. The pooling strategy of collected samples incubated in selective enrichment broth was able to detect all culture and individual PCR positive samples. This strategy appears to be cost- and time-effective in a hospital environment with a low prevalence for Salmonella spp.

CONFIRMED:

Emir Hodzic, Director, Real-Time PCR Research & Diagnostic Core Facility, University of California, Davis

Agenda: Day Two – Friday 26th June 2015


[email protected] +44 (0) 1865 849841




CONFIRMED:

Lawrence Jennings, Assistant Professor of Pathology; Director, Molecular Pathology, Northwestern University/Ann and Robert H. Lurie Children's Hospital of Chicago

qPCR Quantification of a Bacterial Pathogen, Campylobacter, in Recreational Lake Water. QPCR is gaining acceptance for use in monitoring water quality as evidenced by the United States Environmental Protection Agency (USEPA) approval of its use for quantification of a fecal indicator bacteria, Enterococcus, in fresh and marine waters. We have applied qPCR to quantification of Campylobacter, the major cause of bacterial gastroenteritis worldwide. Our aim was to better understand the potential risks to humans of acquiring Campylobacter infection through use of recreational lake water. We applied qPCR on DNA extracted directly from 20 fresh water lakes in Quebec, Canada, over 3 summers. Due to variability in estimates of DNA standards we employed dPCR to correct the standard curves for quantification. The approaches used in qPCR optimisation and general findings of the study will be presented.

CONFIRMED:

Rebecca Guy, Research Scientist, Division of Science and Technology, Public Health Agency of Canada

12.40-12.55 Young Investigator’s Presentation: Title To Be Confirmed

Invite to:

Young Investigator’s Presentation: Making use of the Barcode of Life Data System for Real-time PCR to Identify Species DNA barcoding is being used to catalogue biodiversity, and has been shown to be a useful tool for species identification, but has limitations for certain applications. However, the Barcode of Life Data System (BOLD) is an excellent source of sequences for developing qPCR assays, which may be more suitable in cases where rapid, portable testing is necessary, or where testing of mixtures is required. This talk will focus on expanding the use of BOLD beyond DNA barcoding and discuss case studies where qPCR assays based on DNA barcode sequences have been developed and applied for species identification in food and agriculture applications.

CONFIRMED:

Amanda M. Naaum, Postdoctoral Fellow, Biodiversity Institute of Ontario, University of Guelph, Canada


Gold Sponsor

CONFIRMED:

Senior Representative, Thermo Fisher Scientific



13.25-14.25 Lunch

14.25-14.50 Developing PCR Assays for a QC environment: QbD, Regulations and Risk Based Approaches Examples of qPCR limit tests, quantitative assays using multiplex reactions, integration of innovation controls, and perhaps different PCR endpoints e.g. CE for restriction enzyme digestion

CONFIRMED:

Claire Davies, Scientific Director, Genzyme, a Sanofi Company

Exploring the Potential of ddPCR as a Tool for Environmental Monitoring

Despite wide acceptance for clinical applications, molecular technology has only recently found its way into the field of environmental monitoring. US EPA published an approved qPCR method microbial recreational water quality monitoring in 2012, but technical and and logistical obstacles have prevented agencies for adopting it. This presentation will focus on the the potential of ddPCR to reduce or ameliorate the technical obstacles associated with the current EPA-approved qPCR method for recreational water quality monitoring and how this may lead to more widespread adoption of molecular approaches to environmental monitoring.

CONFIRMED:

John Griffith, Principal Scientist, Department of Microbiology, Southern California Coastal Water Research Project

Agenda: Day Two (cont.) – Friday 26th June 2015


[email protected] +44 (0) 1865 849841


14.50-15.15 Droplet Digital PCR as a Screening Tool for 22q Deletion Syndrome 22q11.2 Deletion Syndrome is the most common chromosomal deletion characterized by a complex display of sub-phenotypes, comprising heart defects, recurrent infections, immunological anomalies, behavioral disorders and learning disabilities. It is due to a 1.5 or 3 Mb deletion in the 22q11 deletion region. A delayed diagnosis of 22q11DS can lead to life-long health issues that could be potentially ameliorated with early intervention and treatment. Thus, we have developed a new genetic screen for 22q11DS, PCR-based, namely droplet digital PCR (ddPCR), a rapid, cost-effective and easily used methodology. Our data demonstrates the utility of multiplex ddPCR for large-scale population screening studies, including newborn screening for 22q11DS, and potentially for other microdeletion syndromes, where early detection can positively impact clinical outcome for those affected.

CONFIRMED:

Flora Tassone, Professor, Department of Biochemistry and Molecular Medicine, University of California, Davis

Novel Approaches in Plant Breeding by Utilizing qPCR and Next Generation Sequencing for High Throughput Trait and Zygosity Determination. Novel smart breeding approaches aim to determine certain loci within the plant genome associated to desired phenotypic traits. Additionally identifying the zygosity state for such traits is an important criteria for the generation of new plant lines. Currently there are no methods available enabling the detection of quantitative trait loci in combination with their zygosity. Established techniques for zygosity determination are time consuming and error-prone. To overcome these limitations we have developed a novel qPCR based approach to facilitate trait analysis coupled with zygosity determination. This innovative qPCR approach was enhanced for high throughput analysis by utilizing next generation sequencing. Thus we are now able to screen hundreds of individual plant samples and identify different conventional as well as transgenic traits and predict their zygosity.

CONFIRMED: Florian Schröper, Leader Research Field: Innovative Detection Technologies and Assay Designs, Fraunhofer IME, Germany

15.15-15.40 Quality Assessment of Circulating Cell-free DNA using Multiplexed ddPCR

Analysis of circulating cell-free tumor-specific DNA in plasma allows monitoring of metastatic cancer burden and evolution. However, standardization of pre-analytical factors such as sample processing is needed to establish analytical and clinical validity of these assays. I will describe early progress in quality assessment of circulating cell-free DNA using multiplexed droplet-digital PCR.

CONFIRMED:

Muhammed Murtaza, Research Assistant Professor, Co-Leader, Center for Non-invasive Diagnostics, Translational Genomics Research Institute

Identification and Quantification of Species in Meat and Meat Products Using Droplet Digital PCR Species fraud and product mislabeling in processed food, albeit not being a direct health issue, often results in consumer distrust. Therefore methods for quantification of undeclared species are needed. Targeting mitochondrial DNA is unsuitable, due to a five-fold inter-tissue variation in mtDNA content per cell resulting in either an under- or overestimation of species DNA contents. We present a reliable two-step droplet digital PCR assay targeting the nuclear F2 gene for precise quantification of cattle, horse, and pig in processed meat products. The ddPCR assay is advantageous over qPCR showing a limit of quantification and detection in different meat products of 0.01% and 0.001%, respectively. Hence, determining F2 in food by ddPCR can be recommended for quality assurance and control in production systems.

CONFIRMED: Bertram Brenig, Professor of Molecular Biology & Director of the Institute of Veterinary Medicine, University of Göttingen, Germany


CONFIRMED:

Jadwiga Bienkowska, Director, Computational Biology, Pfizer

Quality Control and Technical Variance in plant qPCR analysis Rather than the ‘gold standard technology’ often used to describe it, the RT-qPCR suffers from considerable pitfalls during the general workflow. While sensitive and precise, one major drawback of the technique is the numerous critical steps required throughout the entire workflow that may influence the accuracy and reliability of results and contribute substantially to the overall error. In this talk I shall focus on RNA quality and reference genes-based normalization and its influence on qPCR performance as well as the errors that are introduced into measurements by the qPCR steps. An optimal experiment design that minimizes the technical noise will also be discussed.

CONFIRMED:

Jose V. Die, Visiting Scientist, Genetic Improvement of Fruits and Vegetables Laboratory, Agricultural Research Service, USDA

16.05-16.35 Afternoon Refreshments and Poster Presentation Sessions

16.35 Chairperson’s Closing Remarks & Conference Close

Also coming in 2015… the 3rd qPCR & Digital PCR Congress: Europe 20-21 October 2015. London, UK

Following on from last year’s sell-out event, and co-located with the 2nd Synthetic Biology Congress, this meeting will bring

together over 300 industry and academic experts to look at advances, strategies and innovative applications in both qPCR and

Digital PCR. Further information including highlights from last year’s meeting can be found at:

www.globalengage.co.uk/qpcr.html

Agenda: Day Two (cont.) – Friday 26th June 2015


[email protected] +44 (0) 1865 849841

http://www.globalengage.co.uk/qpcr.html

Workshop Organiser

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

Additional 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: Town and Country Resort Hotel, 500 HOTEL CIRCLE NORTH. SAN DIEGO, CA 92108 Academic: $799

Date: 23-24 June 2015 Industry: $999

Course Leader: Mikael Kubista, CEO, TATAA Biocenter & Head of Department,

BTU, CAS

- 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

Dr Kubista is the head of the department of gene expression at the institute of Biotechnology of the Czech Academy

of Sciences, and founder and CEO of the TATAA Biocenter (www.tataa.com). He was one of the pioneers contributing

to the development of quantitative real-time PCR (qPCR) and introduced qPCR for single cell expression profiling. He

led the development of reagents for high throughput single cell expression profiling and quality control at TATAA. He

also developed qPCR tomography for intracellular expression profiling. Kubista co-authored the Minimum Information

for Publication of Quantitative. Real-Time PCR Experiments (MIQE) guidelines, was partner of the SPIDIA project, and

is member of the CEN and ISO workgroups drafting the forthcoming guidelines on pre-analytics.

http://www.tataa.com/

The conference will also host a range of poster presentations for you to study and to discuss with the presenters during designated sessions.

Here are a few examples of already approved abstract titles:

Title Principal Author(s) Affiliation

A direct qPCR method for residual DNA quantification in monoclonal antibody drugs produced in CHO cells

Musaddeq Hussain Merck Research Laboratories

Molecular genotyping of canine parvovirus occurring in Sulaimani/Iraq and phylogenetic sequence analysis for partial VP2 gene

Mohammed Omar Baba sheikh, Peshnyar Muhammad Atta, Ari Salahadin Marouf, Zhino Hussen Raheem, Manjunath S and Sarath Chandra Janga

Indiana University Purdue University Indiana

Directed evolution for the development of an inhibitor resistant DNA polymerase for improved target amplification and quantification of crude samples with real-time PCR

Wolfgang Schäfer, Ziningi Madonsela, Martmari Botha, Penny Smorenburg, Charles Joseph, Kerry Gordon, Gavin Rush

Kapa Biosystems, 200 Ballardvale Street, Suite 350, Wilmington, MA 01887

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 all abstracts in full. 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 forum you need to be registered as a delegate. Please note that there is limited space available and posters space is assigned on a first come first served basis (subject to checks and successful registration). For further information on submission, approval and the technical poster spec, please contact: [email protected] or go to www.globalengage.co.uk/qpcr/usa/posters.html

Poster Presentations


[email protected] +44 (0) 1865 849841


http://www.globalengage.co.uk/qpcr/usa/posters.html

Documents

qPCR and Digital PCR Congress: USA · Sample preparation & quality control Detection, quantification and sequencing of RNA Precise quantification of nucleic acids Amplification curve