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Next-Generation Sequencing
17 September - 18 September 2012
Next-Generation Sequencing

Identifying potential therapeutic drug targets and validating their suitability is a complex process involving numerous experimental platforms, including DNA sequence analysis. Since its introduction in 2005 next-generation sequencing (NGS) has fundamentally altered genomics research. Large knowledge-gaining experiments are in progress that were financially unjustifiable or even impossible five years ago. These include metagenomics to compare different disease states or patient variablility, genome sequencing of model and pathogenic species or ELT compound library screening techniques.

NGS is now successfully utilised by biopharmaceutical companies from the earliest stages of drug discovery to provide detailed genomic data and clinical applications are now emerging. These range from investigating the molecular basis of drug resistance and planning antimicrobial regimens, to vaccine development and disease diagnostics. In the rapidly growing field of personalised medicine, eight percent of medicines now have a biomarker or stratified element as compared to just a few percent five years ago.

As sequencing costs continue to fall, the future will see even faster identification of responders and non-responders, benefiting patients, prescribers and payors.

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FEATURED SPEAKERS

Ben Sidders

Ben Sidders

Principal Scientist, Bioinformatician, Pfizer Ltd
Guy Cochrane

Guy Cochrane

Head of European Nucleotide Archive, European Bioinformatics Institute
Joke Reumers

Joke Reumers

Bioinformatics Scientist, Janssen Infectious Diseases - Diagnostics
Lisa Crossman

Lisa Crossman

Microbial Genomes Project Leader, The Genome Analysis Centre
Matthias  Prucha

Matthias Prucha

Business Development Manager Europe, Partek Inc
Michael Quail

Michael Quail

Team Leader, The Wellcome Trust Sanger Institute
Nicholas Murgolo

Nicholas Murgolo

Lead, Infectious Diseases, Merck Research Laboratories

Alessandra Ferlini

Associate Professor, University of Ferrara
Alessandra Ferlini

Ben Sidders

Principal Scientist, Bioinformatician, Pfizer Ltd
Ben Sidders

Cristina Al-Khalili Szigyarto

Scientific Coordinator, Royal Institute of Technology
Cristina Al-Khalili Szigyarto

David Williams

Chief Executive Officer, Discuva
David Williams

Elia Stupka

Co-Director and Head of Unit, San Raffaele Scientific Institute
Elia Stupka

Gerard Didelot

Research Scientist, Novimmune
Gerard  Didelot

Guy Cochrane

Head of European Nucleotide Archive, European Bioinformatics Institute
Guy Cochrane

Irina Zaharieva

Research Associate, UCL Institute of Child Health
Irina Zaharieva

Jian Han

Faculty Investigator, HudsonAlpha Institute for Biotechnology
Jian Han

Joke Reumers

Bioinformatics Scientist, Janssen Infectious Diseases - Diagnostics
Joke Reumers

Lachlan Coin

Senior Lecturer in Statistical Genomics, Imperial College
Lachlan Coin

Lisa Crossman

Microbial Genomes Project Leader, The Genome Analysis Centre
Lisa Crossman

Lori Snyder

Reader in Biotechnology, Kingston University
Lori Snyder

Mat Upton

Senior Lecturer In Medical Microbiology, Manchester University
Mat Upton

Matthias Prucha

Business Development Manager Europe, Partek Inc
Matthias  Prucha

Michael Quail

Team Leader, The Wellcome Trust Sanger Institute
Michael Quail

Nicholas Murgolo

Lead, Infectious Diseases, Merck Research Laboratories
Nicholas Murgolo

Patrik Kolar

Head of Unit – Personalised Medicine, Directorate-General for Research and Innovation , European Commission
Patrik Kolar

Richard Bax

Senior Partner, TranScrip Partners
Richard Bax

Roy Bicknell

Professor of Cancer Biology and Genomics, University of Birmingham
Roy Bicknell

Sterghios Moschos

Reader in Industrial Biotechnology, University of Westminster
Sterghios Moschos

Wilhelm Ansorge

Visiting Professor, École Polytechnique Fédérale de Lausanne
Wilhelm Ansorge

Conference agenda

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8:30

Registration & Coffee

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9:00

An overview of RNA-sequencing: analytical challenges and biological applications

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10:00

Morning Coffee

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10:20

Case study involving isoform identification and differentially expressed genes using RNA-sequencing data

  • From raw reads to the estimation of gene expression levels
     
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    11:20

    Late-Morning Coffee

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    11:40

    Case study: using RNA-sequencing to understand gene regulation

  • Combining RNA-sequencing with other genetic information to interrogate gene expression regulation
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    12:40

    End of workshop

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    13:30

    Registration & Coffee

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    14:00

    Introduction to interpretation challenges in bacterial genomics

  • Microbial genome diversity and horizontal gene transfer
  • Impact of sequencing platform technologies
  • Functional annotation
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    15:00

    Afternoon Tea

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    15:20

    Case study problems for the group to discuss/work through

  • Sequence features in bacterial genome sequence data
  • Annotations in bacterial genome sequences
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    16:20

    Afternoon Tea

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    16:40

    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 assignments
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    17:40

    End of workshop

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    8:30

    Registration & Coffee

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    9:00

    Chairman's Opening Remarks

    Patrik Kolar

    Patrik Kolar, Head of Unit – Personalised Medicine, Directorate-General for Research and Innovation , European Commission

    David Williams

    David Williams, Chief Executive Officer, Discuva

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    9:10

    Next-generation DNA sequencing techniques and applications

    Wilhelm Ansorge

    Wilhelm Ansorge, Visiting Professor, École Polytechnique Fédérale de Lausanne

  • Next-generation DNA sequencing techniques are opening fascinating opportunities in the life sciences
  • Commercially available DNA sequencing platforms
  • Single-molecule real-time methods, and conventional and graphene nanopore technologies
  • New techniques in development and biomedical applications
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    9:45

    Cutting edge developments in next-generation sequencing technologies

    Michael Quail

    Michael Quail, Team Leader, The Wellcome Trust Sanger Institute

  • Improving our Illumina library-preparation methods
  • Reducing contaminating human DNA in pathogen sequencing
  • Mapping transposon insertion sites
  • Direct strand-selective RNA sequencing
  • A new protocol for long-insert (mate-pair) sequencing
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    10:20

    Making sense of next-generation sequencing data

    Lachlan Coin

    Lachlan Coin, Senior Lecturer in Statistical Genomics, Imperial College

  • Generating the species pan-genome
  • Catalogue variation in populations and associating these with traits
  • Techniques for detecting and genotyping variation at the population level, including copy number variation and indels
  • Increasing sensitivity and decreasing false discovery rates
  • Applications to polyploidy  as well as diploid organisms
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    10:55

    Morning Coffee

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    11:15

    Overcoming common challenges of RNA-Seq data analysis

    Matthias  Prucha

    Matthias Prucha, Business Development Manager Europe, Partek Inc

  • Manage the huge data
  • Use powerful and flexible analysis tools
  • Apply statistics to get most from your data
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    11:30

    Use of next generation sequencing for the identification of novel cancer targets

    Roy Bicknell

    Roy Bicknell, Professor of Cancer Biology and Genomics, University of Birmingham

  • Complementarity of NGS with other genomics technologies
  • Current limitations of NGS in the context of target identification
  • Impact of results from NGS on the direction of cancer research
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    12:05

    R&D of antibiotics- begin with the end in mind

    Richard Bax

    Richard Bax, Senior Partner, TranScrip Partners

  • Identify targets and then identify druggable targets
  • Importance of whole cell assays and medicinal chemistry
  • Outline toxicology and animal pharmacology
  • PK/PD predictors of outcome
  • Importance of phase I and proof-of-concept studies
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    12:40

    Networking Lunch

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    13:40

    Antibacterial mechanism discovery using next-generation sequencing

    Nicholas Murgolo

    Nicholas Murgolo, Lead, Infectious Diseases, Merck Research Laboratories

  • Strain comparison methods for target discovery
  • Barcode strategy for simultaneous sequencing multiple samples
  • Genome coverage requirements for variant detection
  • Variant detection methods
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    14:15

    The role of NGS in the discovery of novel peptide antibiotics

    Mat Upton

    Mat Upton, Senior Lecturer In Medical Microbiology, Manchester University

  • Peptide antibiotics are promising alternatives to conventional antibiotics
  • NGS has revolutionised progression of natural product screening programmes where laborious reverse genetic approaches are now being replaced by genome sequence determination
  • Innovative search tools now allow rapid in silico screening of bacterial genomes for potentially useful new antimicrobial peptides
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    14:50

    Next-generation sequencing of mixed bacterial populations

    Lori Snyder

    Lori Snyder, Reader in Biotechnology, Kingston University

  • Interpretation of complex data sets
  • Identifying mixed populations in a pure culture
  • Understanding the mechanisms of genomic changes
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    15:25

    Afternoon Tea

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    15:45

    Scaling-up sequencing projects in the hunt for new antibiotics

    Lisa Crossman

    Lisa Crossman, Microbial Genomes Project Leader, The Genome Analysis Centre

  • Exploiting new environmental niches
  • Technical challenges in next generation deep re-sequencing
  • Genetics of antibiotic biosynthesis from fungus-farming ant-associated species
  • High throughput genome scanning of Streptomyces
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    16:20

    Panel discussion: Next-generation sequencing- where are we and what are the prospects for the future?

    Panelists will discuss "user-friendly" interfaces for annotating and analysing genome sequences, and exploiting this data in disease aetiology, diagnostic microbiology and drug discovery.  Second and third generation technologies, library preparation, and assessing copy number and repeat variation on gene expression and disease susceptibility, will also be discussed.

    Nicholas Murgolo

    Nicholas Murgolo, Lead, Infectious Diseases, Merck Research Laboratories

    Michael Quail

    Michael Quail, Team Leader, The Wellcome Trust Sanger Institute

    Guy Barker

    Guy Barker, Director, Genomics Resource Centre, University of Warwick

    Roy Bicknell

    Roy Bicknell, Professor of Cancer Biology and Genomics, University of Birmingham

    Richard Bax

    Richard Bax, Senior Partner, TranScrip Partners

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    16:55

    Chairman’s Closing Remarks and Close of Day One

    Patrik Kolar

    Patrik Kolar, Head of Unit – Personalised Medicine, Directorate-General for Research and Innovation , European Commission

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    8:30

    Registration & Coffee

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    9:00

    Chairman's Opening Remarks

    Elia Stupka

    Elia Stupka, Co-Director and Head of Unit, San Raffaele Scientific Institute

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    9:10

    Interpreting functional genomic data using integrative analyses and network models for drug target discovery

    Ben Sidders

    Ben Sidders, Principal Scientist, Bioinformatician, Pfizer Ltd

  • Moving beyond big datasets to uncover disease relevant biology
  • Benefits of using existing data and interpreting new data in that context
  • Benefits of integrating disparate data into a single model
  • Strategies for target selection from such models
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    9:50

    Public NGS data repositories: services and sustainability through data compression

    Guy Cochrane

    Guy Cochrane, Head of European Nucleotide Archive, European Bioinformatics Institute

  • Data repositories operated by the European Bioinformatics Institute
  • Services provided by these repositories
  • Development of sequence data compression under the CRAM framework
  • Choices to be made in lossy compression
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    10:30

    Morning Coffee

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    10:50

    Do we understand enough about genomes to build next generation molecular networks of disease?

    Elia Stupka

    Elia Stupka, Co-Director and Head of Unit, San Raffaele Scientific Institute

  • Using genomics to unravel the predisposition and progression of pathologies
  • Limitations of GWAS and SNP microarrays in understanding the heritability of disease
  • NGS  offers a unified view of molecular networks underlying disease states
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    11:30

    Genomic biomarkers discovery in Duchenne muscular dystrophies using whole exome sequencing and targeted resequencing: a novel approach based on candidate prioritised genes

    Alessandra Ferlini

    Alessandra Ferlini, Associate Professor, University of Ferrara

  • Dystrophin
  • Susceptibility SNPs
  • Candidate genes
  • Drug response
  • SNP grouping
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    11:55

    Identifying genomic pre-clinical biomarkers in Duchenne muscular dystrophy (DMD) patients trough whole exome sequencing

    Irina Zaharieva

    Irina Zaharieva, Research Associate, UCL Institute of Child Health

  • Genetic profiling of DMD patients to identify biomarkers, prediction of disease progression and improved therapeutics
  • Genetic variants influencing differences in phenotype between DMD patients
  • Whole exome sequencing and capture to identify variants underling disease variability
  • Identification and validation of disease-progression-specific variants
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    12:20

    Identifying prognostic biomarker candidates in neuromuscular dystrophies using antibody suspension bead arrays

    Cristina Al-Khalili Szigyarto

    Cristina Al-Khalili Szigyarto, Scientific Coordinator, Royal Institute of Technology

  • Disease progression in muscular dystrophies
  • Protein profiling of plasma and serum using antibody-based suspension bead arrays
  • Identification of potential biomarkers for monitoring long-term disease progression
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    12:45

    Networking Lunch

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    13:45

    NGS revelations in shRNA maturation and siRNA mode of action mechanisms targeting the hepatitis C virus (HCV)

    Sterghios Moschos

    Sterghios Moschos, Reader in Industrial Biotechnology, University of Westminster

  • How to implement NGS in shRNA maturation analysis and siRNA mode of action studies
  • Approaches to analysing and interpreting this type of NGS data
  • Case study on a HCV-targeting siRNA therapeutic
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    14:25

    Minor variant detection in hepatitis C (HCV) and human immunodeficiency (HIV) viral populations using 454 and Illumina sequencing technologies

    Joke Reumers

    Joke Reumers, Bioinformatics Scientist, Janssen Infectious Diseases - Diagnostics

  • Comparison of mapping algorithms for deep sequencing applications
  • Error profiles of 454 and Illumina platforms
  • Distinguishing sequencing errors from true low frequency variants
  • How deep can we reliably sequence using 454 and Illumina technologies?
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    15:05

    Afternoon Tea

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    15:25

    Enhancing antibody discovery using next-generation sequencing

    Gerard  Didelot

    Gerard Didelot, Research Scientist, Novimmune

    In vitro antibody discovery involves large collections of variants that can be characterized by NGS
    Classical antibody screening can be replaced or complemented by in silico antibody discovery
    Additional candidates missed during screening approaches can be identified
    Dedicated software for antibody analysis has been developed

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    16:05

    NGS sequencing of T and B cell repertoire: applications in biomarker discovery, vaccine evaluation, and personalised treatment

    Jian Han

    Jian Han, Faculty Investigator, HudsonAlpha Institute for Biotechnology

  • Semi-quantitative and inclusive amplification of T and B cell repertoires from peripheral blood or other tissues
  • Free online software developed for data clean-up, barcode separation (of pooled samples), CDR3 distribution, VDJ usage, and diversity index (D50) calculations
  • Early studies show cancer patients associated with decreased diversity (lower D50 values) and also share some disease specific CDR3 sequences
  • R10K (www.R10K.org): a non-profit, international collaboration, to sequence 10,000 samples and study 100 diseases.  Initial results
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    16:45

    Chairman’s Closing Remarks and Close of Day Two


    Research Associate
    UCL Institute of Child Health
    Reader in Industrial Biotechnology
    University of Westminster
    Principal Scientist, Bioinformatician
    Pfizer Ltd
    Lead, Infectious Diseases
    Merck Research Laboratories
    Associate Professor
    University of Ferrara
    Senior Lecturer In Medical Microbiology
    Manchester University
    Professor of Cancer Biology and Genomics
    University of Birmingham
    Faculty Investigator
    HudsonAlpha Institute for Biotechnology
    Team Leader
    The Wellcome Trust Sanger Institute
    Research Scientist
    Novimmune
    Visiting Professor
    École Polytechnique Fédérale de Lausanne
    Scientific Coordinator
    Royal Institute of Technology
    Bioinformatics Scientist
    Janssen Infectious Diseases - Diagnostics
    Business Development Manager Europe
    Partek Inc
    Co-Director and Head of Unit
    San Raffaele Scientific Institute
    Senior Partner
    TranScrip Partners
    Head of Unit – Personalised Medicine, Directorate-General for Research and Innovation
    European Commission
    Microbial Genomes Project Leader
    The Genome Analysis Centre
    Chief Executive Officer
    Discuva
    Senior Lecturer in Statistical Genomics
    Imperial College
    Head of European Nucleotide Archive
    European Bioinformatics Institute
    Reader in Biotechnology
    Kingston University

    Workshops

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    Copthorne Tara Hotel

    The Copthorne Tara Hotel London Kensington is an elegant contemporary four-star hotel in prestigious Kensington, located just a two minutes walk from High Street Kensington underground station, making exploring easy. The hotel offers well-appointed and comfortable guest rooms combining Standard, Superior and Club accommodation. Club rooms offer iconic views over the city and include Club Lounge access for complimentary breakfast and refreshments. Guests can sample the authentic Singaporean, Malaysian and Chinese cuisine at Bugis Street, traditional pub fare at the Brasserie Restaurant & Bar or relax with a delicious drink at West8 Cocktail Lounge & Bar.

    The Copthorne Tara Hotel boasts 745 square meters of flexible meeting space, consisting of the Shannon Suite and the Liffey Suite, ideal for hosting conferences, weddings and social events. Facilities include access to the business centre 24 hours a day, fully equipped fitness room, gift shop, theatre desk and Bureau de Change. With ample onsite parking outside the London congestion charge zone and excellent transport links via Heathrow Airport, the hotel is the perfect location for business or leisure stays. The hotel is within close proximity to the shops of High Street Kensington, Knightsbridge and Westfield London, Olympia Conference Centre, Royal Albert Hall, Kensington Palace and Hyde Park.

     

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    WHAT IS CPD?

    CPD stands for Continuing Professional Development’. It is essentially a philosophy, which maintains that in order to be effective, learning should be organised and structured. The most common definition is:

    ‘A commitment to structured skills and knowledge enhancement for Personal or Professional competence’

    CPD is a common requirement of individual membership with professional bodies and Institutes. Increasingly, employers also expect their staff to undertake regular CPD activities.

    Undertaken over a period of time, CPD ensures that educational qualifications do not become obsolete, and allows for best practice and professional standards to be upheld.

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    For some institutes undertaking CPD is mandatory e.g. accountancy and law, and linked to a licence to practice, for others it’s obligatory. By ensuring that their members undertake CPD, the professional bodies seek to ensure that professional standards, legislative awareness and ethical practices are maintained.

    CPD Schemes often run over the period of a year and the institutes generally provide online tools for their members to record and reflect on their CPD activities.

    TYPICAL CPD SCHEMES AND RECORDING OF CPD (CPD points and hours)

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    As a formal provider of CPD certified activities, SAE Media Group can provide an indication of the learning benefit gained and the typical completion. However, it is ultimately the responsibility of the delegate to evaluate their learning, and record it correctly in line with their professional body’s or employers requirements.

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