1. REGISTER BY 31ST MAY 2012 AND RECEIVE A £300 DISCOUNTREGISTER BY 29TH JUNE 2012 AND RECIEVE A £100 DISCOUNT Next-Generation Sequencing A data interpretation and analytical perspective Monday 17th and Tuesday 18th September 2012 Copthorne Tara Hotel, London KEY SPEAKERS INCLUDE: Ben Sidders Patrik Kolar Principal Scientist, Bioinformatician, Head of Unit, Directorate-General for Neusentis Research Genomics and Systems Biology Pfizer European Commission Nicholas Murgolo Nicolas Fischer Fellow Head of Research Merck NovImmune Guy Cochrane Lachlan Coin Head of European Nucleotide Archive Senior Lecturer in Statistical Genomics European Bioinformatics Institute Imperial College London Michael Quail Alessandra Ferlini Sequencing R&D Team Leader Professor in Medical Genetics The Wellcome Trust Sanger Institute University of Ferrara Lisa Crossman Reiner Schulz Microbial Genomes Project Leader RCUK Research Fellow in Functional The Genome Analysis Centre Genomics Kings College London WHY YOU SHOULD ATTEND THIS CONFERENCE: • Generate longer nucleic acid and oligonucleotide sequences of higher quality • Increase consensus accuracy and genome coverage • Maximise the alignment and assembly of NGS reads with reference sequences • Enhance signal-to-noise measurements in real-time sequencing • Utilise exomics and deep sequencing to elucidate gene families implicated in disease and pharmacogenetic effects PLUS TWO INTERACTIVE POST–CONFERENCE WORKSHOPS Wednesday 19th September, 2012 A: RNA-sequencing – analytical challenges B: Challenges in bacterial genome sequence data and data interpretation interpretation Workshop Leader: Workshop Leader: John Marioni, Group Leader, European Bioinformatics Institute Lori Snyder, Reader in Biotechnology, Kingston University 8.30am - 12.40pm 1.30pm - 5.40pm To attend, contact Fateja Begum on Tel +44 (0) 20 7827 6184, Fax +44 (0) 20 7827 6185, email firstname.lastname@example.org or visit www.smi-online.co.uk/ts05.asp to register online
2. Next-Generation SequencingDay One | Monday, 17th September 2012 www.smi-online.co.uk/ts05.asp8.30 Registration and Coffee 1.25 Antibacterial mechanism discovery using next-generation sequencing9.00 Chairmans Opening Remarks • Strain comparison methods for target discovery Patrik Kolar, Head of Unit, Directorate-General for Research Genomics • Barcode strategy for simultaneous sequencing multiple samples and Systems Biology, European Commission • Genome coverage requirements for variant detection Methods, Interpretation and Analysis • Variant detection methods Nicholas Murgolo, Fellow, Merck9.10 OPENING ADDRESS Next-generation DNA sequencing techniques and applications 2.00 The role of NGS in the discovery of novel peptide antibiotics • Next-generation DNA sequencing techniques are opening • Peptide antibiotics are promising alternatives to conventional fascinating opportunities in the life sciences antibiotics • Commercially available DNA sequencing platforms • NGS has revolutionised progression of natural product screening • Single-molecule real-time methods, and conventional and graphene programmes where laborious reverse genetic approaches are now nanopore technologies being replaced by genome sequence determination • New techniques in development and biomedical applications Wilhelm Ansorge, Visiting Professor, École Polytechnique Fédérale • Innovative search tools now allow rapid in silico screening of de Lausanne bacterial genomes for potentially useful new antimicrobial peptides Mat Upton, Senior Lecturer in Medical Microbiology, University of9.45 Cutting edge developments in next-generation sequencing Manchester technologies • Improving our Illumina library-preparation methods 2. 35 Next-generation sequencing of mixed bacterial populations • Reducing contaminating human DNA in pathogen sequencing • Interpretation of complex data sets • Mapping transposon insertion sites • Identifying mixed populations in a pure culture • Direct strand-selective RNA sequencing • Understanding the mechanisms of genomic changes • A new protocol for long-insert (mate-pair) sequencing Michael Quail, Sequencing R&D Team Leader, The Wellcome Trust Lori Snyder, Reader in Biotechnology, Kingston University Sanger Institute 3.10 Afternoon Tea10.20 Making sense of next-generation sequencing data • Generating the species pan-genome 3.45 Scaling-up sequencing projects in the hunt for new antibiotics • Catalogue variation in populations and associating these with traits • Exploiting new environmental niches • Techniques for detecting and genotyping variation at the population • Technical challenges in next generation deep resequencing level, including copy number variation and indels • Genetics of antibiotic biosynthesis from fungus-farming ant- • Increasing sensitivity and decreasing false discovery rates associated species • Applications to polyploidy as well as diploid organisms Lachlan Coin, Senior Lecturer in Statistical Genomics, Imperial • High throughput genome scanning of Streptomyces College London Lisa C. Crossman, Microbial Genomes Project Leader, The Genome Analysis Centre10.55 Morning Coffee Panel Discussion11.15 Implementation of NGS in daily workflow: practical and analytical considerations 4.20 Next-generation sequencing- where are we and what are the • Complementarily of NGS with other genomics technologies prospects for the future? • Need of LIMS for tracking • Data analysis Panelists will discuss "user-friendly" interfaces for annotating and Patrick Descombes, Head of Functional Genomics Core, Nestlé analysing genome sequences, and exploiting this data in disease Institute of Health Sciences aetiology, diagnostic microbiology and drug discovery. Second and third generation technologies, library preparation, and assessing copy Antibiotic Drug Discovery and Development number and repeat variation on gene expression and disease susceptibility, will also be discussed.11.50 R&D of antibiotics- begin with the end in mind Nicholas Murgolo, Fellow, Merck • Identify targets and then identify druggable targets Michael Quail, Sequencing R&D Team Leader, The Wellcome Trust • Importance of whole cell assays and medicinal chemistry Sanger Institute • Outline toxicology and animal pharmacology • PK/PD predictors of outcome Roy Bicknell, Professor of Functional Genomics, University of • Importance of phase I and proof-of-concept studies Birmingham Richard Bax, Senior Partner, TranScrip Partners Richard Bax, Senior Partner, TranScrip Partners12.25 Networking Lunch 5.00 Chairmans Closing Remarks and Close of Day One To attend, contact Fateja Begum on Tel +44 (0) 20 7827 6184, Fax +44 (0) 20 7827 6185, email email@example.com or visit www.smi-online.co.uk/ts05.asp to register online Supported by
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Next-Generation Sequencing www.smi-online.co.uk/ts05.asp Day Two | Tuesday, 18th September 20128.30 Re-registration and Coffee 12.20 Identifying prognostic biomarker candidates in neuromuscular dystrophies using antibody suspension bead arrays9.00 Chairmans Opening Remarks • Disease progression in muscular dystrophies David Williams, Chief Executive Officer, Discuva • Protein profiling of plasma and serum using antibody-based suspension bead arrays Data Storage and Analysis • Identification of potential biomarkers for monitoring long-term disease progression Cristina Al-Khalili Szigyarto, Scientific Coordinator, Swedish Royal9.10 OPENING ADDRESS Institute of Technology Interpreting functional genomic data using integrative analyses and network models for drug target discovery Antiviral Targets • Moving beyond big datasets to uncover disease relevant biology • Benefits of using existing data and interpreting new data in that context 12.45 Networking lunch • Benefits of integrating disparate data into a single model • Strategies for target selection from such models 1.45 NGS revelations in shRNA maturation and siRNA mode of action Ben Sidders, Principal Scientist, Bioinformatician, Neusentis, Pfizer mechanisms targeting the hepatitis C virus (HCV) • How to implement NGS in shRNA maturation analysis and siRNA mode9.50 Public NGS data repositories: services and sustainability through data of action studies compression • Approaches to analysing and interpreting this type of NGS data • Data repositories operated by the European Bioinformatics Institute • Case study on a HCV-targeting siRNA therapeutic • Services provided by these repositories Sterghios Moschos, Reader in Industrial Biotechnology, University of • Development of sequence data compression under the CRAM Westminster framework 2.25 Minor variant detection in hepatitis C (HCV) and human • Choices to be made in lossy compression immunodeficiency (HIV) viral populations using 454 and Illumina Guy Cochrane, Head of European Nucleotide Archive, European sequencing technologies. Bioinformatics Institute • Comparison of mapping algorithms for deep sequencing applications • Error profiles of 454 and Illumina platforms10.30 Morning Coffee • Distinguishing sequencing errors from true low frequency variants • How deep can we reliably sequence using 454 and Illumina technologies?10.50 Next-generation sequencing in epigenetics: insights and challenges Joke Reumers, Bioinformatics Scientist, Janssen Infectious Diseases - • DNA methylation: a cornucopia of flavours Diagnostics • Complex cross-talk between DNA methylation , transcription and histone modifications 3.05 Afternoon Tea • Epigenetic variation and complex traits Reiner Schulz, RCUK Research Fellow in Functional Genomics, King’s Antibodies and Vaccines College London 3.25 Enhancing antibody discovery using next-generation sequencing • In vitro antibody discovery involves large collections of variants that can Duchenne Muscular Dystrophies be characterized by NGS • Classical antibody screening can be replaced or complemented by11.30 Genomic biomarkers discovery in Duchenne muscular dystrophies in silico antibody discovery using whole exome sequencing and targeted resequencing: a novel • Additional candidates missed during screening approaches can be approach based on candidate prioritised genes identified • Dystrophin • Dedicated software for antibody analysis has been developed • Susceptibility SNPS Nicolas Fischer, Head of Research, NovImmune • Candidate genes • Drug response 4.05 NGS sequencing of T and B cell repertoire: applications in biomarker • SNP grouping discovery, vaccine evaluation, and personalised treatment Alessandra Ferlini, Professor in Medical Genetics, University of Ferrara • Semi-quantitative and inclusive amplification of T and B cell repertoires from peripheral blood or other tissues11.55 Identifying genomic pre-clinical biomarkers in Duchenne muscular • Free online software developed for data clean-up, barcode separation dystrophy (DMD) patients trough whole exome sequencing (of pooled samples), CDR3 distribution, VDJ usage, and diversity index (D50) calculations • Genetic profiling of DMD patients to identify biomarkers, prediction of • Early studies show cancer patients associated with decreased diversity disease progression and improved therapeutics (lower D50 values) and also share some disease specific CDR3 • Genetic variants influencing differences in phenotype between DMD sequences patients • R10K (www.R10K.org): a non-profit, international collaboration, to • Whole exome sequencing and capture to identify variants underling sequence 10,000 samples and study 100 diseases. Initial results. disease variability Jian Han, Faculty Investigator, HudsonAlpha Institute for Biotechnology • Identification and validation of disease-progression-specific variants Irina Zaharieva, Research Associate, University College London 4.45 Chairman’s Closing Remarks and Close of Day Two To attend, contact Fateja Begum on Tel +44 (0) 20 7827 6184, Fax +44 (0) 20 7827 6185, email firstname.lastname@example.org or visit www.smi-online.co.uk/ts05.asp to register online Who should attend: SPONSORSHIP AND EXHIBITION OPPORTUNITIES Chief Executive Officers, Chief Operating Officers, Managing Directors, SMi offer sponsorship, exhibition, advertising and branding packages, Vice Presidents, Director, Partners, Heads and Managers in: uniquely tailored to complement your company’s marketing strategy. Prime networking opportunities exist to entertain, enhance and expand your client base within the context of an independent discussion specific to your industry. • Genomics • Molecular Medicine Should you wish to join the increasing number of companies benefiting from • Genome Sequencing • Oncology sponsoring our conferences please call: Alia Malick on +44 (0) 20 7827 6168 • Sequencing Technology • Clinical Research & Development or email: email@example.com • Bioinformatics • Translational Medicine • Computational Biology • Stratified Medicine / Personalised Want to know how you can get involved? Interested in • Medical Genetics Medicine promoting your pharmaceutical services to this market? • Clinical Genetics • Strategic Alliances Contact Margaret Mugema, SMi Marketing • Molecular Biology • Business Development on +44 (0) 207 827 6072, or email firstname.lastname@example.org
4. HALF DAY POST-CONFERENCE WORKSHOP Wednesday 19th September 2012 8.30am-12.40pm Copthorne Tara Hotel, London, UK A: RNA-sequencing – analyticalchallenges and data interpretation John Marioni, Group Leader, European Bioinformatics InstituteOverview of workshop:RNA-sequencing has revolutionised our ability to assay thetranscriptome. In the context of comparative genomics, it hasenabled the identification of changes in gene expression levelsthat might underlie phenotypic diversity, while in cancer it hasallowed fusion genes, which may play pivotal roles in cancerdevelopment, to be found. However, a common stumblingblock in utilizing RNA-sequencing to the fullest extent is theanalysis and interpretation of the data generated. In thisworkshop, we will begin by describing RNA-sequencing,before going on to explain how the data generated can beanalysed and describing how RNA-sequencing can be appliedin different contexts to obtain biological insights.What attendees can expect to gain from the workshop:• Insights into RNA-sequencing, one of the most popular next-generation sequencing techniques• An understanding of the challenges involved in measuring transcript expression from RNA-sequencing: read mapping, isoform identification and differential expression• Understanding how RNA-sequencing can be combined with other next-generation sequencing data to obtain knowledge about the regulation of gene expression levels• Techniques and skills learnt will be applicable in many contextsWorkshop format:8.30 Registration and coffee9.00 An overview of RNA-sequencing: analytical challenges and biological applications10.00 Coffee break10.20 Case study involving isoform identification and differentially expressed genes using RNA- sequencing data • From raw reads to the estimation of gene expression levels11.20 Coffee break11.40 Case study: using RNA-sequencing to understand gene regulation • Combining RNA-sequencing with other genetic information to interrogate gene expression regulation12.40 End of workshopAbout John Marioni: John Marioni has been a research group leader at the European Bioinformatics Institute (an outstation of the European Molecular Biology Laboratory) since late 2010. After completing his PhD in Computational Biology at the University of Cambridge in 2008, John moved to the University of Chicago as a post-doctoral scholarin the Department of Human Genetics. While in Chicago hepublished one of the first papers describing the analysis ofRNA-sequencing data and, since then, he has contributed tonumerous high-impact studies that have utilized next-generation sequencing to understand fundamental questionsin molecular biology and comparative genomics. His researchinterests focus on developing computational and statisticalmethods to answer pertinent questions in evolutionary biology.About European Bioinformatics Institute:The European Bioinformatics Institute (EBI) is an academicresearch institute located on the Wellcome Trust GenomeCampus in Hinxton near Cambridge (UK), part of the EuropeanMolecular Biology Laboratory (EMBL).The EBI’s mission is: (1.) To provide freely available data andbioinformatics services to all facets of the scientific communityin ways that promote scientific progress. (2.) To contribute tothe advancement of biology through basic investigator-drivenresearch in bioinformatics. (3.) To provide advancedbioinformatics training to scientists at all levels, from PhDstudents to independent investigators. (4.) To help disseminatecutting-edge technologies to industry
5. HALF DAY POST-CONFERENCE WORKSHOP Wednesday 19th September 2012 1.30am-5.40pm Copthorne Tara Hotel, London, UKB: Challenges in bacterial genome sequence data interpretation Workshop Leader: Lori Snyder, Reader in Biotechnology, Kingston UniversityOverview of workshop:This interactive workshop will explore the challenges presentedwhen analysing bacterial genome sequence data. While differentnext-generation sequencing platforms present their ownadvantages and challenges, there are common features to thedata generated. For bacterial genome sequence data, thesefeatures often relate to the biology of the organism. Being able tocorrectly identify and understand the information revealed in thesequence data is key to being able to use bacterial genomesequence data effectively. We will have a look at various aspectsof bacterial genome sequence data interpretation, includingcomparing read data, understanding variation, identifyinginversions and excisions, assessing the biological significance ofhomopolymeric tract changes, and homology based annotationof gene function.By the end of the workshop you will:• Be able to critically compare the advantages and disadvantages of different technologies in investigating bacterial genome sequences• Recognise how sequence features add complexity to genomic data analysis• Appreciate the range of variation in bacterial genome sequence data• Be familiar with how to identify complex sequence features in read data• Understand the potential pitfalls in annotated gene functionsProgramme1.30 Registration and coffee2.00 Introduction to interpretation challenges in bacterial genomics • Microbial genome diversity and horizontal gene transfer • Impact of sequencing platform technologies • Functional annotation3.00 Coffee break3.20 Case study problems for the group to discuss/work through • Sequence features in bacterial genome sequence data • Annotations in bacterial genome sequences4.20 Coffee break4.40 Solutions to overcome problems such as those presented in the case studies • Assessment of variation in read data • Discussion of partially aligned read data • Interpretation of annotation assignments5.40 End of workshopAbout Lori Snyder, Reader in Biotechnology, Kingston University: Dr. Snyder is a Reader at Kingston University where she is the Course Director for the Kingston University MSc in Biotechnology and leads the Kingston University Genome Sequencing Facility. Her research uses bacterial genome sequence data to conduct comparative analyses, revealing differences within and between strains and species. Dr.Snyder began genomic analyses during her PhD at EmoryUniversity, USA, with Prof. Bill Shafer, where she investigatedNeisseria gonorrhoeae and Neisseria meningitidis. Work onthese species continued during her post-doctoral research at theUniversity of Oxford. As a post-doctoral fellow at the University ofBirmingham, Dr. Snyder worked on the xBASE genomedatabase and its suite of analysis tools.About Kingston University:With more than 22,000 students, Kingston University is thelargest provider of higher education in South West London,offering an extensive range of undergraduate and postgraduateprogrammes both in the United Kingdom and overseas. TheUniversity is renowned for teaching excellence, has establisheditself as a growing force in research and is widely respected as apioneer in e-learning.
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