This document provides information about a two-day conference on next-generation sequencing taking place on September 17-18, 2012 in London. The conference will feature talks from industry leaders on topics such as sequencing technologies, data analysis and interpretation, antibiotic drug discovery, and applications in disease research. Attendees can gain insights into RNA sequencing, variant detection, antimicrobial discovery, and epigenetics. Interactive workshops on RNA sequencing and bacterial genome analysis will also be offered on the third day. Registration discounts are available before May 31st and June 29th.

1. REGISTER BY 31ST MAY 2012 AND RECEIVE A £300 DISCOUNT
REGISTER 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
King's 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 fbegum@smi-online.co.uk
or visit www.smi-online.co.uk/ts05.asp to register online

2. Next-Generation Sequencing
Day One | Monday, 17th September 2012 www.smi-online.co.uk/ts05.asp
8.30 Registration and Coffee 1.25 Antibacterial mechanism discovery using next-generation
sequencing
9.00 Chairman's 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, Merck
9.10 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 of
9.45 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 Tea
10.20 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 Centre
10.55 Morning Coffee
Panel Discussion
11.15 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 Partners
12.25 Networking Lunch 5.00 Chairman's 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 fbegum@smi-online.co.uk or visit www.smi-online.co.uk/ts05.asp to register online
Supported by

3. Next-Generation Sequencing
www.smi-online.co.uk/ts05.asp Day Two | Tuesday, 18th September 2012
8.30 Re-registration and Coffee 12.20 Identifying prognostic biomarker candidates in neuromuscular
dystrophies using antibody suspension bead arrays
9.00 Chairman's 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 Royal
9.10 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 mode
9.50 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 platforms
10.30 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 by
11.30 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 tissues
11.55 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 fbegum@smi-online.co.uk 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: amalick@smi-online.co.uk
• 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 mmugema@smi-online.co.uk

4. HALF DAY POST-CONFERENCE WORKSHOP
Wednesday 19th September 2012
8.30am-12.40pm
Copthorne Tara Hotel, London, UK
A: RNA-sequencing – analytical
challenges and data interpretation
John Marioni, Group Leader, European
Bioinformatics Institute
Overview of workshop:
RNA-sequencing has revolutionised our ability to assay the
transcriptome. In the context of comparative genomics, it has
enabled the identification of changes in gene expression levels
that might underlie phenotypic diversity, while in cancer it has
allowed fusion genes, which may play pivotal roles in cancer
development, to be found. However, a common stumbling
block in utilizing RNA-sequencing to the fullest extent is the
analysis and interpretation of the data generated. In this
workshop, we will begin by describing RNA-sequencing,
before going on to explain how the data generated can be
analysed and describing how RNA-sequencing can be applied
in 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
contexts
Workshop format:
8.30 Registration and coffee
9.00 An overview of RNA-sequencing: analytical
challenges and biological applications
10.00 Coffee break
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
11.20 Coffee break
11.40 Case study: using RNA-sequencing to
understand gene regulation
• Combining RNA-sequencing with other genetic
information to interrogate gene expression
regulation
12.40 End of workshop
About 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 scholar
in the Department of Human Genetics. While in Chicago he
published one of the first papers describing the analysis of
RNA-sequencing data and, since then, he has contributed to
numerous high-impact studies that have utilized next-
generation sequencing to understand fundamental questions
in molecular biology and comparative genomics. His research
interests focus on developing computational and statistical
methods to answer pertinent questions in evolutionary biology.
About European Bioinformatics Institute:
The European Bioinformatics Institute (EBI) is an academic
research institute located on the Wellcome Trust Genome
Campus in Hinxton near Cambridge (UK), part of the European
Molecular Biology Laboratory (EMBL).
The EBI’s mission is: (1.) To provide freely available data and
bioinformatics services to all facets of the scientific community
in ways that promote scientific progress. (2.) To contribute to
the advancement of biology through basic investigator-driven
research in bioinformatics. (3.) To provide advanced
bioinformatics training to scientists at all levels, from PhD
students to independent investigators. (4.) To help disseminate
cutting-edge technologies to industry

5. HALF DAY POST-CONFERENCE WORKSHOP
Wednesday 19th September 2012
1.30am-5.40pm
Copthorne Tara Hotel, London, UK
B: Challenges in bacterial genome
sequence data interpretation
Workshop Leader: Lori Snyder, Reader in
Biotechnology, Kingston University
Overview of workshop:
This interactive workshop will explore the challenges presented
when analysing bacterial genome sequence data. While different
next-generation sequencing platforms present their own
advantages and challenges, there are common features to the
data generated. For bacterial genome sequence data, these
features often relate to the biology of the organism. Being able to
correctly identify and understand the information revealed in the
sequence data is key to being able to use bacterial genome
sequence data effectively. We will have a look at various aspects
of bacterial genome sequence data interpretation, including
comparing read data, understanding variation, identifying
inversions and excisions, assessing the biological significance of
homopolymeric tract changes, and homology based annotation
of 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 functions
Programme
1.30 Registration and coffee
2.00 Introduction to interpretation challenges in
bacterial genomics
• Microbial genome diversity and horizontal gene
transfer
• Impact of sequencing platform technologies
• Functional annotation
3.00 Coffee break
3.20 Case study problems for the group to
discuss/work through
• Sequence features in bacterial genome sequence
data
• Annotations in bacterial genome sequences
4.20 Coffee break
4.40 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
5.40 End of workshop
About 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 Emory
University, USA, with Prof. Bill Shafer, where she investigated
Neisseria gonorrhoeae and Neisseria meningitidis. Work on
these species continued during her post-doctoral research at the
University of Oxford. As a post-doctoral fellow at the University of
Birmingham, Dr. Snyder worked on the xBASE genome
database and its suite of analysis tools.
About Kingston University:
With more than 22,000 students, Kingston University is the
largest provider of higher education in South West London,
offering an extensive range of undergraduate and postgraduate
programmes both in the United Kingdom and overseas. The
University is renowned for teaching excellence, has established
itself as a growing force in research and is widely respected as a
pioneer in e-learning.

6. NEXT-GENERATION SEQUENCING
Conference: Monday 17th and Tuesday 18th September 2012, Copthorne Tara Hotel, London Workshops: Wednesday 19th September 2012, London
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