"16th-17th November 2009, London INTRODUCTION TO THE 2009 ME"
th th 16 -17 November 2009, London INTRODUCTION TO THE 2009 MEETING th th Oxford Global Conferences is proud to present Next Generation Sequencing (NGS)Congress, which is to be held on the 16 & 17 November 2009 in London. The congress is held in conjunction with qPCR Congress( www.qpcr-congress.com). Next-generation sequencing technologies are revolutionizing biology by allowing for genome-wide transcription factor binding-site profiling, transcriptome sequencing, and more recently, whole-genome resequencing. These technologies will provide a genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. Over the 2 days, the conference provides an overview of the current options of next-generation sequencing platforms, technologies, applications and the newest computational tools for the analysis of next-generation sequencing data. The event will attract over 120 senior-level decision makers working in bioinformatics & data management, next generation sequencing, discovery, RNA profiling, molecular genomics, and clinical & diagnostics development from the UK, Europe and US. This prestigious event provides a forum for practitioners and researchers to learn more about key solutions being provided to their industry, network with their peers, and address key industry concerns through a series of cutting edge conference presentations in a professional yet relaxed environment. THE EVENT In keeping with Oxford Global’s highly successful life sciences series, an expert panel of 25 speakers will present a full conference programme covering the following key topics include: th Day 1 – 16 November • Next Generation Sequencing – High Throughput Sequencing Platforms: Implementation and Technology Considerations Sequencing Applications Considerations • Applying Next-Generation Sequencing to Cancer and Medical Genetics and Discovery Research th Day 2 – 17 November • Next Generation Sequencing Technologies and Bioinformatic Analysis Tools • Data Analysis • Data Management and Storage Strategies WHO ATTENDS? Delegates are pre-qualified dependent on budget, responsibility and seniority. Delegates are senior-level decision makers, from major pharmaceutical, biotech companies and research institutions based in Europe and typically include VPs, Directors, Managers and Heads of: Drug Discovery High throughput Technologies Bioinformatics Data Management Principal Investigation Molecular Profiling/Diagnostics Clinical Development Genetics Next Generation Computational Biology Biostatistics Genomics Sequencing YOUR NETWORKING OPPORTUNITIES Meet face-to-face with leading solution providers and senior-level industry peers through a series of formal and informal networking opportunities. Using our online appointment system, you are able to view the full profiles of all solution provides before the event. In addition you have the chance to pre-arrange one-to-one meetings with them, giving you the opportunity to discuss technologies, services and solutions that address your key business needs. Categories of solution providers include: Next Generation Sequencing Platforms NGS technologies Screening Technologies High Throughput Sequencing Data Management Methods Bioinformatics/Biostatistics Solutions CONFIRMED SPEAKERS 2009: • Dr Chen Wei, Head of Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck- Center for Molecular Medicine, Berlin, Germany • Dr David Dow, Group Leader, Molecular and Cellular Technologies, Glaxo SmithKline • Dr James Brown, Manager Computational Biology for Infectious Diseases, Glaxo SmithKline • Dr David Taylor, Discovery Platform Manager, Microbiology, Unilever R&D • Dr. Karol Kozak, Database Implementation, High Content Screening; RISC, Eth Zurich • Professor Peter Donnelly, Principal Investigator, Director, Wellcome Trust Centre for Human Genetics (WTCHG) • Dr Kalim Mir, Research Fellow/ Principal Investigator, The Wellcome Trust Centre for Human Genetics, University of Oxford • Dr Mark Blaxter, Principal Investigator, MRC- Scottish Hub, University of Edinburgh • Professor Neil Hall, Principal Investigator, MRC- North England Hub, University of Liverpool • Dr Chris Lord, Senior Staff Scientist, The Institute of Cancer Research, UK • Dr. Dan Turner, Head of Sequencing Technology Development, Wellcome Trust Sanger Institute • Dr Ann Curtis, Northern Genetics Service, Newcastle Hospitals NHS Foundation Trust • Dr Jonathan Coxhead, Institute of Human Genetics, Newcastle University • Dr Joaquin Dopazo, Head of the Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe • Dr Pawel Herzyk, DNA, Arrays, Bioinformatics, Sir Henry Wellcome Functional Genomics Facility, University of Glasgow • Dr. Eric Kemen, Post Doctoral Researcher, Sainsbury Laboratory Dr Francesca Ciccarelli, European Oncology Institute, Milan, Italy • Dr Niek de Vries, Team Leader, Dept. Clinical Immunology & Rheumatology FOCIS & EULAR Center of Excellence, AMC • Dr Matthew Eldridge, Head, Computational Biology Core at Cancer Research UK (Cambridge Research Institute), Cambridge UK • Dr Aaron Golden, Lecturer, Bioinformatics Research Group, Enabling Technologies, National Centre for Biomedical Engineering Science, NUI, Galway • Dr Jenny Taylor, Programme Director, Genetics and Pathology Theme, Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics Oxford • Dr. Lori Snyder, Senior Lecturer in Biotechnology, Kingston University • Dr Paul J. Hurd, Lecturer in Molecular Biology & Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London • Dr Hendrik Marks, Post Doctoral Researcher, Radboud University • Dr Robert Nutter, Sr. Staff Applications Scientist, SOLiD Transcriptomic Applications, Applied Biosystems • Dr Stephanie Brooking, European Segment Manager, Sequencing, Regional Marketing-Europe, Illumina • Niels Kruize, Sales Director, KBiosciences Ltd • Dr Laura Clarke, Scientific Programmer, EBI • Dr William E. Jack, Research Director, New England Biolabs • Senior Representative, Fluidigm • Senior Representative, Quantum • Senior Representative, HP • Dr. Marcus Droege, Global Marketing Director Genome Sequencing, Roche Applied Science Sponsored by: Day 1 –16th November 2009 08.10 REGISTRATION & COFFEE 08.30 Chairman’s Opening Address Robert Nutter, Sr. Staff Applications Scientist, SOLiD Transcriptomic Applications, Applied Biosystems 08.40 Keynote Address Next Generation Sequencing: Its Role in Infectious Disease Drug Discovery • Rapid DNA sequencing now allow whole genome approaches to study novel, multi-gene, drug resistance pathways in pathogenic bacteria and viruses • Old methods of drug discovery, such as whole cell screening, can be re-invented by using whole genomic sequences to reveal mechanisms of drug/target action • Finally, next generation DNA sequencing technology will help us understand more fully, the diversity of viral and bacterial pathogens in clinical settings CONFIRMED: James Brown, Manager Computational Biology for Infectious Diseases, GSK Next Generation Sequencing – High Throughput Sequencing Platforms, Technologies and Sequence based Research Next generation sequencing (NGS) platforms are currently being utilized for targeted sequencing of candidate genes or genomic intervals to perform sequence based research The increased throughput and ability to scan whole genome or global gene expression profiles will have broad implications across drug development industry. This stream looks at the different options and platforms available and technological considerations 9.10 Solution Provider Presentation Using Ultrahigh Throughput Sequencing to Revolutionize our understanding of RNA structure and Function • Sequencing is unsurpassed for discovery of novel RNA structures. • The discoveries made thus far already are changing our understanding of the role RNA plays in gene expression. • Improved bioinformatic tools will now be needed to take full advantage of this technology. CONFIRMED: Robert Nutter, Sr. Staff Applications Scientist, SOLiD Transcriptomic Applications, Applied Biosystems Sponsored by: 9.40 Solution Provider Presentation Re-sequencing of the Human Genome on the 454 Genome Sequencer FLX System The Genome Sequencer FLX System (GS FLX), powered by 454 Sequencing, is a next-generation DNA sequencing technology featuring a unique mix of long reads, exceptional accuracy, and ultra-high throughput. It has been proven to be the most versatile of all currently available next-generation sequencing technologies, supporting many high profile studies in over 7 applications categories. GS FLX users have pursued innovative research in de novo sequencing, re-sequencing of whole genomes and target DNA regions, metagenomics, and RNA analysis. 454 Sequencing is a powerful tool for human genetics research, having recently re-sequenced the genome of an individual human, currently re- sequencing the complete human exome and targeted genomic regions using the NimbleGen sequence capture process, and detected low frequency somatic mutations linked to cancer. This presentation will provide a short overview about the 454 Sequencing technology, and will focus on applications possible to address with the Genome Sequencer FLX system, with special emphasis on human re-sequencing. It will also provide information on the newest product developments, including the 2010 launch of kits allowing to generate read lengths of >800 - 1000 bases on the today’s FLX instrument. CONFIRMED: Marcus Droege, Global Marketing Director Genome Sequencing, Roche Applied Science Sponsored by: 10.10 PANEL DISCUSSION Fitting the Requirements of Drug Discovery Process A new generation of sequencing technologies will increase the speed and lower the cost of sequencing, and promises to expand the utility of sequencing in drug discovery and development. The panellists are invited to share their experiences in development of next generation sequencing applications in the drug discovery process, the state of the technology and the issues and challenges facing its application. Moderator: Dr Robert Nutter, Sr. Staff Applications Scientist, SOLiD Transcriptomic Applications, Applied Biosystems Panellists: CONFIRMED: David Dow, Group Leader, Molecular and Cellular Technologies, GSK David Taylor, Discovery Platform Manager, Microbiology, Unilever James Brown, Manager Computational Biology for Infectious Diseases, GSK 10.35 MORNING REFRESHMENTS 11.05 Solution Provider Presentation Illumina Genome Analyzer System - The Most Widely Adopted Next Generation Sequencing System Whether you need to sequence an entire genome or a large candidate region, the Illumina Genome Analyzer is today’s most productive and economical sequencing tool. The Genome Analyzer delivers unprecedented volumes of high-quality data rapidly and economically, with a simple workflow and minimal sample input.. • Leverage single or paired-end reads for a wide range of genome sequencing applications. -Discover and confirm SNPs -Identify chromosomal rearrangements, including Copy Number Variations (CNVs) -Map break points -Detect rare variants • The Genome Analyzer can generate highly accurate results in under a week, with the fastest and least labor-intensive workflow of any sequencing technology. • DNA sequencing with the Genome Analyzer delivers: -superior accuracy - more accurate reads per run than any other massively-parallel sequencing method -highest throughput - gigabases of data per run with the smallest amount of starting material and the lowest cost per base compared to other technologies -simplest workflow - single-operator driven process and walk-away automation with minimal hands-on time per run CONFIRMED: Stephanie Brooking, European Segment Manager, Sequencing, Regional Marketing-Europe, Illumina 11.35 Pushing the Limits of Next Generation Sequencing CONFIRMED: Dr Dan Turner, Head of Sequencing Technology Development, Wellcome Trust Sanger Institute 12.00 High-throughput small RNA sequencing in acute myeloid leukaemia (AML) • Distribution of microRNAs and small non-coding (snc)RNAs in AML • Dysregulation of microRNAs (miRNAs) in acute myeloid leukaemia AML • Discovery of novel species of microRNAs and other sncRNAs CONFIRMED: Dr. Silvana Debernardi, Senior Postdoctoral Research Fellow, Medical Oncology Centre, Barts & The London School Of Medicine 12.25 Solution Provider Presentation “Scalable DNA Fragmentation using Novel Nuclease Digestion” • NEBNExt™ dsDNA Fragmentase™ is an enzyme-based solution to generating random, representative DNA fragmentation. A unique blend of engineered nucleases promotes scalable fragmentation from a variety of sample sources • A root level examination of the kinetics of nucleotide incorporation by DNA polymerases has illuminated the mechanism for accurately copying a DNA template. Further studies of modified polymerases and nucleotides have provided additional insight into determinants of fidelity, and have guided engineering of the essential components of DNA sequencing platforms. Examples of insights obtained by kinetic studies will be presented CONFIRMED: Dr William E. Jack, Research Director, New England Biolabs Sponsored by: 12.55 LUNCH 13.50 Solution Provider Presentation Update on Tools for NextGen DNA shearing (Covaris), Advances in Emulsion PCR and Cost Efficient, High Throughput In-silico & In- situ SNP Assays for NextGen SNP Validation • Advances in NextGen DNA shearing using Covaris Adaptive Focussed Acoustics (AFA) • Advances in Emulsion PCR, HydroCycler and emulsion bag/MTP formats • Advances in Cost Efficient, High Throughput In-silico & In-situ SNP Assays for NextGen SNP Validation using KBiosciences KASP technology CONFIRMED: Niels Kruize, Sales Director, KBiosciences Ltd Sponsored by: 14.20 Case Study: High Throughput Sequencing Platforms CONFIRMED: Dr Kalim Mir, Research Fellow/ Principal Investigator, The Wellcome Trust Centre for Human Genetics, University of Oxford 14.45 Exploring the Potential Applications of Next Generation Sequencing in Molecular Genetic Diagnostics CONFIRMED: Dr Ann Curtis, Northern Genetics Service, Newcastle Hospitals NHS Foundation Trust CONFIRMED: Dr Jonathan Coxhead, Institute of Human Genetics, Newcastle University 15.15 Solution Provider Presentation Next Gen Sequencing Applications: 15.45 Highly Sensitive Detection of Genomic Instability using Next-Generation Sequencing • Genomic instability and cancer • Ultradeep sequencing of cancer genome • Statistical treatment and error control CONFIRMED: Dr Francesca Ciccarelli, Group Leader, European Oncology Institute, Milan, Italy 16.10 AFTERNOON REFRESHMENTS 16.35 Panel Discussion & Presentation Implementation of HighThroughput Next Generation Sequencing DNA Research in the UK • Overview of the Medical Research Council project • Technology Considerations Moderator: CONFIRMED: Stephanie Brooking, European Segment Manager, Sequencing, Regional Marketing-Europe, Illumina CONFIRMED: Scottish Hub- Dr Mark Blaxter, Principal Investigator, University of Edinburgh, Gene Pool North England Hub- Professor Neil Hall, Principal Investigator, University of Liverpool West England Hub- Professor Peter Donnelly, Principal Investigator, Director, Wellcome Trust Centre for Human Genetics (WTCHG) 17.05 Comparison of Solexa High Throughput Sequencing and Affymetrix Microarrays in Transcriptomics Study of Drosophila Melanogaster • The FlyAtlas project • Comparison of gene expression results from microarrays and sequencing data • Investigating gene structure and alternative splicing CONFIRMED: Dr Pawel Herzyk, DNA, Arrays, Bioinformatics, Sir Henry Wellcome Functional Genomics Facility, University of Glasgow 17.30 Next-Generation Sequencing in Epigenetic Research • Advantages of NGS in epigenetic research • ChIP-Seq delivers data-rich epigenomic maps • The landscape of histone tri-methylation in the human genome CONFIRMED: Dr Paul J. Hurd, Lecturer in Molecular Biology & Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London 17.55 CLOSE OF CONFERENCE Day 2- 17th November 2009 REGISTRATION & COFFEE Applications, Bioinformatics and Data Analysis 08.25 Interactive Workshop Seminar Maximize the Potential of Next-generation Sequencing in Genomic Research 20 minutes Presentation - Data Management & Storage • Strategies for data storage, quality control and analysis CONFIRMED: Workshop leaders- Senior Representatives, Quantum and HP 20 minutes – Industry Client Case Study 20 minutes Interactive Panel Discussion- Moderator Quantum and HP 9.20 Chairman’s Opening Address CONFIRMED: Marcus Droege, Global Marketing Director Genome Sequencing, Roche Applied Science Coping with ‘Le Deluge’ - Boosting ChIPseq Analysis using Self Organising Maps • ‘De novo’ motif finding using Self-Organising Maps • Filtering ChIPseq datasets for high signal-to-noise reads • From Clouds to Cards: the computational options CONFIRMED: Dr Aaron Golden, Lecturer, College of Engineering and Informatics, Enabling Technologies, National Centre for Biomedical Engineering Science, NUI, Galway 9.45 Bioinformatics Support for Next Generation Sequencing: A Core Facility Perspective • Automated data processing supported by LIMS and high performance computing • Secondary analysis pipelines for short-read data • Managing projects and workload CONFIRMED: Dr Matthew Eldridge, Head, Computational Biology Core, Cancer Research UK (Cambridge Research Institute), Cambridge UK 10.10 Clinical Applications of Next Generation Sequencing CONFIRMED: Dr Jenny Taylor, Programme Director, Genetics and Pathology Theme, Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics Oxford 10.35 Morning Refreshments 11.05 Next-Generation Sequencing in Pipeline Style – Open Source Alternative for Data Analysis and Management • Sequence data workflow management • Sequence database and data management • Multiparametric classification CONFIRMED: Dr Karol Kozak, Database Implementation, High Content Screening; RISC, Eth Zurich 11.30 Solution Provider Presentation The Agilent Technologies SureSelect™ Platform for Target Enrichment • Enables you to focus your sequencing efforts on a subset of the genome • Uses long oligonucleotides to capture genomic material of interest • Protocols available for both Illumina and Solid workflows CONFIRMED: Dr Ruth Burton, Applications Specialist, Agilent Sponsored by: 12.00 Developments in RNA-seq and in SNP Characterization in Resequencing • Calling SNPs in RNAseq and in resequencing gene enriched genomes (“exomes”) • Coding and non-coding SNPs with functional effect • Predicting functional SNPs within gene sequences CONFIRMED: Joaquin Dopazo, Head of the Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe 12.25 Next Generation Sequencing of B- and T-cell Receptor Rearrangements • Amplification protocols for quantitative analysis of rearrangements • Bioinformatic workflow of BCR and TCR analysis • Results of sequencing BCR and TCR in human and mouse samples CONFIRMED: Dr Niek de Vries, Team Leader, Dept. Clinical Immunology & Rheumatology FOCIS & EULAR Center of Excellence, University Hospital Amsterdam, The Netherlands 12.50 LUNCH 13.50 Next-Generation Sequencing of Bacteria- Bugs to Data to Discoveries • Application of NGS to bacteria • How far to go with assembly, closure, finishing, annotation...? • Discoveries made and those to come CONFIRMED: Dr. Lori Snyder, Senior Lecturer in Biotechnology, Kingston University 14.15 De Novo Sequencing and Transcriptomics Analysis of an Obligate Biotrophic Plant Pathogen, Albugo candida Illumina sequencing, cDNA sequencing, expression profiling, genome sequencing, de-novo assemblies, genome annotation, quality controls, synteny analyses, detection of SNPs, heterozygosity CONFIRMED: Dr. Eric Kemen, Post Doctoral Researcher, Sainsbury Laboratory 14.40 The 1000 Genomes Project, a Large Data Problem CONFIRMED: Laura Clarke, Scientific Programmer, EBI 15.10 Afternoon Refreshments 15.35 ChIP-Seq: How to Analyze Epigenetic Profiles to Address Fundamental Biological Questions • The experimental and bioinformatic workflow of ChIP-Seq • Publicly available software tools for ChIP-Seq applications • Studying X inactivation in mouse embryonic stem cells using ChIP-Seq CONFIRMED: Dr Hendrik Marks, Post Doctoral Researcher, Radboud University 16.00 Separating Wheat from Chaff –Molecular Elucidation of Genetic Factors Underlying Mental Retardation by Genome Partitioning and Large Scale Next-Generation Sequencing The recent introduction of massive parallel sequencing technology has revolutionized genomic research. These so-called next-generation sequencing platform can sequencing DNA orders of magnitude faster and at much lower cost than traditional Sanger method. However, even with the dramatically improved efficiency, presently available instruments do not allow to resequence the complete genome from a large number of human patients in economically realistic manner. Therefore, robust methods to isolate relevant genomic regions fro targeted sequencing are required. In this study, we evaluated different genome partitioning strategies including droplet-based PCR from RainDance Technologies, solution hybrid selection from Agilent Technologies and chromosome sorting. With different strengths, they are eventually combined to identify genetic factors underlying mental retardation. CONFIRMED: Dr Chen Wei, Head of Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany 16.25 CLOSE OF CONFERENCE qPCR and Next Generation Sequencing Congress - Poster Presentations Organisation Title and Authors AstraZeneca Evaluation of Methods for the Accurate Determination of Gene Copy Number in Human DNA and Tumour Cell Lines Principal Principal Author: R. M. Hampson, R&D Genetics, Astrazeneca. Other Authors: V. Williams, M. J. McLoughlin, E. Donald, T. Pinel, R. M. Lawrance & J.E.N. Morten Islamic Azad University of SYBR Green1 as a Biomarker for Schizophrenia Tonekabon Principal Author: Mehdi Rahmati, Islamic Azad University of Tonekabon Other Authors: Davood Zaeifi, Vahab Piranfar Islamic Azad University of D1- D5 dopamine Receptors Expression in Paranoid Schizophrenia Patients Tonekabon Principal Author: Davood Zaeifi, Islamic Azad University of Tonekabon Other Authors: Mehdi Rahmati, Vahab Piranfar Faculty Hospital Brno, Expression Profiling of Glioblastoma Tumors Masaryk University, Faculty of Petr Vanhara, Faculty Hospital, Brno Science Other Authors: Jiri Smejkal, Sabina Sevcikova, Jan Smarda, Marek Sova, Martin Smrcka, Leos Kren, Jaroslav Michalek European Bioinformatics Institute Author: Peter Rice The Institute of Animal Health qPCR to investigate effect of vaccination on replication and shedding of virulent Marek’s disease virus Principal Author: Lydia B. Kgosana (Institute for Animal Health) Other Authors: Susan J. Baigent (Institute for Animal Health), Lorraine P. Smith (Institute for Animal Health) Venugopal K. Nair (Institute for Animal Health), Andrew F. Read (Penn State University) The GenePool, University of Author: Karim Gharbi Edinburgh Food and Environment Research Next Generation Sequencing as a Tool for the Characterisation of Diseases of Unknown Aetiology Agency Principal Author: Ian Adams Other Authors: Rachel Glover, Jennifer Hodgetts, Richard Thwaites, Ben Barrett, Rick Mumford & Neil Boonham University Medical Centre Hamburg- Development of a RQ-PCR Assay for Quantitative Detection of Dental Pathogens like Strepococcus Eppendorf, Department of Operative Mutans and Preventive Dentistry, Centre of Principal Author: Torben Heinsohn Dental and Oral Medicine, Martinistr. Other Authors: Ulrich Schiffner 52, 20246 Hamburg Albert-Schweitzer Grammar School, Hamburg, Germany