This document provides an agenda for the RNA-Seq 2014 conference held in Boston, MA from June 17th-19th 2014. It outlines the various sessions to be held over the two day period focusing on RNA sequencing technologies, applications in clinical trials and drug development, and management of RNA sequencing data. The conference featured over 25 expert speakers from companies such as Roche, Pfizer, Broad Institute, and Johnson & Johnson and provided attendees opportunities to learn about the latest developments and applications of RNA sequencing through panel discussions and workshops.

1. June 17th – 19th 2014
BOSTON, MA
25 EXPERT SPEAKERS INCLUDING:
Lore Gruenbaum
Lead, Global Biomarkers &
Experimental Medicine
Roche
David von Schack
Associate Research
Fellow
Pfizer
Joshua Levin
Senior Scientist,
Group Leader
Broad Institute
Qingqin Li
Scientific Director
Johnson & Johnson
Integrate the Technology
Manage the Data
Interpret the Results
PROGRAM PARTNERS:
Produced by Hanson Wade
www.rna-seqsummit.com
Yihong Yao
Director, Head of
Pharmacogenomics
MedImmune
SPOTLIGHT PARTNERS:
Maarten Leerkes
Genome Analysis
Specialist
NIH

2. RNA-Seq 2014 | A Hanson Wade Event
Master RNA-Sequencing to Crack the
Transcriptome
RNA-Seq 2014 will showcase the very latest pre-clinical, clinical
and drug discovery case studies that are revolutionizing the
field. Gain first hand knowledge of how RNA-sequencing is
revealing the, previously untold, therapeutic potential hidden in
the transcriptome.
This meeting brings you together with the industry’s leaders
to dissect the latest advancements in RNA-Sequencing.
Critically evaluate, with the biggest players in the field, which
technologies and software packages are proving successful,
and which hold the most promise for you.
As the only meeting solely dedicated to RNA-Sequencing,
RNA-Seq is the annual meeting for the entire industry, attracting
academia, pharma and research institutions alike. Discover
how they are managing and analyzing RNA-sequencing data to
generate results with exquisite speed and efficiency.
Submerse yourself amongst those who feel confined by the
same challenges as you, and those that have overcome them.
Discuss, debate and decide your solution. Leave brimming with
new ideas to maximize your RNA-Seq projects.
Blueprint your complete RNA-Seq workflow and strategy
demonstrated by Merck, Pfizer and Gilead Sciences
Roche and Johnson & Johnson reveal how you can overcome the
main RNA-Seq challenges for development of new therapies
Maximize pre-clinical and clinical outcomes - discover how NIH
and MedImmune store and manage RNA-Seq data
Get ahead of the game and find out which RNA-Seq technologies
and software packages are coming out on top in direct
comparative studies at The Dana-Farber Cancer Institute and
Infinity Pharmaceuticals
Understand how RNA-Seq has been essential in a global multi-
institute research project as demonstrated in the Genome Tissue
Expression Project (GTEx)
Top Benefits of Attending Testimonials
1
2
4
3
5
I thought that the conference
was well organized, sessions were
well planned and we had a good mix
of academic & pharma speakers.
Conference was a great success.
GSK
This is the best conference I
have ever gone to. It’s a very good
conference for bioinformatician. I
have already recommended people
in my group to go next year.
AVEO Oncology
Hanson Wade continued their
excellent organization skills, and the
focus towards making innovative fields
and technologies more and more
visible.
Baylor College of Medicine
Search groups for RNA-Seq Forum to
join the online community
Follow us on Twitter
#RNASeq2014
RNA-Seq 2014 Boston | www.rna-seqsummit.com
Email: info@hansonwade.com | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898

3. RNA-Seq 2014 | A Hanson Wade Event
EXPERT SPEAKERS:
Qingqin Li
Scientific Director
Yaoyu Wang
Associate Director
Gary Schroth
Distinguished Scientist
Jianchao Yao
Senior Scientist
Seth Crosby
Director, Partnerships &
Alliances
Alisa Jackson
Senior Marketing Manager,
Automation & Genomics
Thomas Tibbitts
Research Director
David DeLuca
Computational Biologist
Yihong Yao
Director, Head of
Pharmacogenomics
Todd Lowe
Chief Scientific Officer
Maarten Leerkes
Genome Analysis Specialist
Joshua Levin
Senior Scientist, Group Leader
Dongliang Ge
Director, Bioinformatics
David von Schack
Associate Research Fellow
Lore Gruenbaum
Lead, Global Biomarkers &
Experimental Medicine
Steve Kain
Director of Product Management
Qichao Zhu
Principal Scientist
Alexander Seitz
CEO
Brian Haynes
Senior Scientist
Monica Wang
Lead System Engineer,
Project and Program
Manager
Ted Burckzynski
Executive Director
Biomarker Technologies
Todd Richmond
Director, Research Informatics
Kelli Bramlett
R&D Scientist
John Tan
Senior Scientist
I thought the RNA-Seq conference was a huge success.
Definitely learned more than I expected in just two days.
Genzyme
Boris Umylny
CEO
RNA-Seq 2014 Boston | www.rna-seqsummit.com
Email: info@hansonwade.com | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898

4. RNA-Seq 2014 | A Hanson Wade Event
CONFERENCE DAY ONE - Wednesday June 18th 2014
Panel Session Interactive Session Networking Session
8.00 Registration & Breakfast
8.50 Chairman’s Opening Remarks
Maarten Leerkes, Genome Analysis Specialist, NIH
RNA-Seq: Spearheading the Genomic Revolution
9.00 Setting the Scene: An Overview of the RNA-Seq Field & a
Brief Look at New Technologies
• The basics of RNA-Seq
• What have been the key breakthroughs in the field?
Joshua Levin, Senior Scientist, Group Leader, Broad Institute
9.30 RNA-Seq Sample Preparation: Solutions for Challenging
Samples
• Sample prep for total RNA from human whole blood, FFPE
samples, samples with just 10pg total and single cell lysates
• Application of NuGEN’s lnDA-C technology for targeted
depletion of virtually any unwanted transcript types
Steve Kain, Director of Product Management,
NuGEN Technologies
10.00 RNA-Seq Strategies in Precision Medicine
• Efficiently manage and analyse data at different levels of
precision to ensure a seamless workflow
• How to design and execute clinical trials more effectively
Dongliang Ge, Director of Bioinformatics, Gilead Sciences
10.30 RNA-Seq Sample Prep Does Not Need to be Complicated
• Simplicity, reproducibility, and strandedness make SENSE
for RNA-Seq
• Introducing QuantSeq library prep: Gene expression
profiling by simply counting 3’ ends
Alexander Seitz, CEO, Lexogen
11.00 Speed Networking & Morning Refreshments
Implementation & Comparison of RNA-Seq Technologies
12.00 Increased Visibility to Low-Abundance Transcripts & Related
Variants via a Novel RNA-Seq Target Enrichment Method
• Novel target enrichment workflow that overcomes low
abundance transcripts and increases sequencing efficiency
• How this is applied to uncover novel exons, rare splicing
transcripts, mutations, gene fusions and expression profiling
John Tan, Senior Scientist, Roche NimbleGen
12.30 Total Solutions for RNA-Seq Within the Illumina Ecosystem
Gary Schroth, Distinguished Scientist, Illumina
1.00 Panel Discussion: Where are we with RNA-Seq Technologies?
• What can some platforms offer that others cannot?
• How do you decide what is best for you?
Ted Burczynski, Executive Director, Bristol-Myers Squibb
Gary Schroth, Distinguished Scientist, Illumina
Yaoyu Wang, Associate Director, Dana-Farber Cancer Institute
Kelli Bramlett, R&D Scientist, Life Technologies
John Tan, Senior Scientist, Roche NimbleGen
Todd Richmond, Director, Roche Nimblegen
1.30 Networking Lunch & Poster Session
2.30 An Unbiased Comparison of RNA-Seq Technologies
• RNA-Seq technologies in comparative experiments
• How do these technologies tie in with each other?
Yaoyu Wang, Associate Director, Dana-Farber
Cost-Effectively Managing the Integration of RNA-Seq
3.00 An Automated RNA-Seq Pipeline for Developing & Executing
Workflows on the Cluster
• How this pipeline has been built and what it encompasses
• The applications of this pipeline to Merck’s internal projects
Jianchao Yao, Senior Scientist, Merck
3.30 RNA-Seq vs Microarrays: A Precise Comparison as to Which
Approach is Most Cost-Effective for Which Situation
• Compare identical samples run on microarrays and RNA-Seq
• How the results were analyzed and what this means for the
relationship between these technologies
Seth Crosby, Director, Partnerships & Alliances,
Washington University School of Medicine
4.00 Introduction to Automated Solutions That Generate Highly
Reproducible Technical Replicate RNASeq Libraries for
Improved Transcriptome Analysis
• How increased sample quality improves sequencing and
how pre-programmed methods enable quick
implementation
• Increasing throughput to meet demand of high-capacity
sequencers
Alisa C. Jackson, Senior Marketing Manager, Automation &
Genomics, Beckman Coulter
4.15 Afternoon Refreshments & Networking
RNA-Seq in Action
4.45 Roundtable Session: The Breakdown of RNA-Seq
Crowd-source solutions and share opinions to debate best
practice in pre-assigned topic areas:
Technologies - What are you going to use?
Software - Which are you going to apply?
Moderator: Monica Wang, Lead System Engineer, Takeda
Data - How are you going to store and manage it?
Moderator: Maarten Leerkes, Genome Analysis Specialist,
NIH
Clinical Applications - Where to focus your efforts?
Moderator: David von Schack, Associate Research Fellow,
Pfizer
5.45 Chairman’s Closing Remarks
RNA-Seq 2014 Boston | www.rna-seqsummit.com
Email: info@hansonwade.com | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898

5. RNA-Seq 2014 | A Hanson Wade Event
CONFERENCE DAY TWO - Thursday June 19th 2014
8.00 Breakfast
8.50 Chairman’s Opening Remarks
Maarten Leerkes, Genome Analysis Specialist, NIH
The Data: What are Your Options?
9.00 Comparison of RNA-Seq Data Analysis Parameters Using
Multiple Datasets
• Case study: From alignment to differential expression when
a gene has been knocked out
• Data management and computation infrastructure
Qingqin Li, Scientific Director, Johnson & Johnson
9.30 RNA-Seq of FFPE Specimen for Biomarker Discovery &
Development
• The effects of RNA input mass and sample quality on
expression quantitation
• A case study in applying RNA-Seq to profile archived thyroid
tumor samples for diagnostic biomarker discovery
Brian Haynes, Senior Scientist, Asuragen
10.00 Panel Discussion: Dealing With the Data: What Approaches
are Out There?
• Comparison between managing in-house and outsourcing
• What other options do you have at your disposal?
• How do you get the best return on your investment?
Maarten Leerkes, Genome Analysis Specialist, NIH
Thomas Tibbitts, Research Director, Infinity Pharmaceuticals
Monica Wang, Lead System Engineer, Takeda
Dr Boris Umylny, CEO, Lumenogix
10.30 Beyond Known microRNAs: Exploring the Rest of the Small
RNA Transcriptome
• MaverixAnalytic Platform: Pre-configured RNA-Seq
analysis pipelines to explore small RNAs
• Cloud-based analytical platforms and examples of where
small RNA’s have been utilized
Todd Lowe, Chief Scientific Officer, Maverix Biomics Inc
10.45 Morning Refreshments & Networking
11.15 Exploring Scalable Options for Processing & Storing RNA-
Seq Data
• Molecular characterization of patient samples from clinical
trials and investigation of new cloud-based approaches
• Implementation and comparison of open-source and
commercial tools for scalable data processing and storage
Thomas Tibbitts, Research Director, Infinity Pharmaceuticals
Pre-clinical, Clinical & Drug Discovery Applications
11.45 RNA-Seq Expression Analysis: a Step-by-Step Guide
• Detailed “how-to” expression analysis process with
comparison of the 3 popular RNA-Seq expression analysis
algorithms as well as quantification algorithms with
replicates or no replicates
Dr Boris Umylny, CEO, Lumenogix
12.00 RNA-Seq & Exploratory Biomarker Analyses in Clinical Trials
• Logistics and operational aspects in and out of Pfizer
and how to incorporate RNA-Seq data analysis workflows
in exploratory biomarker analysis
• Examples of RNA-Seq based analyses, what Pfizer have
learnt and where are they going with RNA-Seq?
David von Schack, Associate Research Fellow, Pfizer
12.30 Using RNA-Seq to Characterize Animal Models of Chronic
Viral Infection
• How Roche have overcome the main challenges for
development of new therapies for chronic Hepatitis B
• How RNA-Seq is used to generate biomarker hypotheses
that can be tested in clinical studies
Lore Gruenbaum, Lead, Global Biomarkers & Experimental
Medicine, Roche
1.00 Networking Lunch
2.00 Genotype Tissue Expression (GTEx) Project
• How RNA-Seq has been fundamental in the GTEx project
• How RNA-Seq has leveraged detailed insight into the
transcriptome in multiple human tissues
David DeLuca, Computational Biologist, Broad Institute
2.30 Incorporating RNA-Seq into Drug Development
• Novel biomarker identification and how this links to
personalized medicine
• This big picture: Where does RNA-Seq tie into drug
development?
Yihong Yao, Director, Head of Pharmacogenomics,
MedImmune
Maximizing the Potential of RNA-Seq
3.00 The Power of RNA-Seq: What’s Next?
• RNA-Seq technologies and their future perspective
• Where are we going with data analysis?
• Case study of RNA-Seq applications in drug development
Qichao Zhu, Principal Scientist, Boehringer-Ingelheim
3.30 Afternoon Refreshments & Networking
4.00 Mastermind Groups and Open Q&A: What are the Lessons
Learned from the Day 1 Roundtable Sessions?
Roundtable moderators will feedback the key intelligence from
interactive debates on day 1
What are the Next Moves with RNA Seq?
• Discussion as to where best to invest in the RNA-Seq field
and where the hottest areas of research are
• How to implement what you have learnt at RNA-Seq 2014
• How will the field progress and what do you want to be
discussing at RNA-Seq 2015?
4.45 Close of Conference
Panel Session Interactive Session Networking Session
RNA-Seq 2014 Boston | www.rna-seqsummit.com
Email: info@hansonwade.com | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898

6. RNA-Seq 2014 | A Hanson Wade Event
RNA-Seq 2014 Boston | www.rna-seqsummit.com
Email: info@hansonwade.com | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898
Workshop A
Workshop B
A practical introduction for those at the start of the journey and what’s
new for those who have already set off.
Whether or not you are new to the field, this all-encompassing workshop
will give detailed insight, in an interactive format, across the entire
RNA-Seq landscape. RNA sources and preparation, the myriad library
construction options, sequencing: to pair or not to pair, and the world
of analysis – all will be covered and discussed in this complete learning
experience.
Leave this workshop with:
• A comprehensive understanding of the RNA-Seq landscape
• Further development of the questions to ask when considering
RNA-Seq
• A review of the bench and informatic technologies that are
right for your specific research needs
Transcriptomic and proteogenomic annotation using cross-omics
approaches by integrating datasets from genomics, transcriptomics and
proteomics aids in putting together alternative splicing fingerprints. The
concerted usage of post-genomic applications enhances gene model
reconstruction when different omics technologies are used in genomic
and transcriptomic annotation initiatives.
This workshop gives a hands-on experience with the use of these
automated transcriptomic annotation pipelines that allow you to use RNA-
Seq data as well as peptide data from proteomic mass-spectrometry. By
following this workshop, you’ll get a unique insight into innovative ways of
bridging technology gaps in this new era of “big data”. You will also find
ways of annotating the splicing transcriptome and use this information in
downstream functional analysis.
Leave this workshop with:
• A comprehensive understanding of the innovative ways of bridging
technology gaps in the new era of big data
• Up-to-date perspective of the latest advancements in this area and
what is just around the corner
• A better understanding of how alternative splicing is key in
fingerprinting the transcriptome
Seth has been at Washington
University for nearly 12 years. During
that time he directed the Genome
Technology Access Center during its
first 2 years. Prior to that he was the
Director of Translational Research
at the Genome Center (now the
Genome Institute). Prior to his tenure
at Washington University, Dr. Crosby
worked in the field of genomics and
drug discovery at Abbott Laboratories,
Pfizer and Pharmacia.
Workshop leader
Seth Crosby
Director Partnerships
& Alliances
Washington University
School of Medicine
RNA-Seq: A Fundamental Guide to the Field
Date: June 17th 2014 | Time: 9.00 – 12.00
A Cross-Omics Approach to Annotation of Human
Splicing Transcriptomes
Date: June 17th 2014 | Time: 1.00 – 4.00
Workshop leader
Maarten Leerkes
Genome Analysis Specialist
NIH
In his role of a Genome Analysis
Specialist and Computational Biology
Specialist, Maarten collaborates
with NIAID scientists to statistically
design, analyze, manage, interpret,
visualize, and illustrate genomic-scale
experiments. His specialities include
using primarily next-generation
sequencing technologies, de novo
sequence assembly, whole-genome
and exome variant analysis, RNA-
Seq, strand-specific sequencing
analysis, ChIP-Seq, ChIP-exo, and
meta-genomics, as well as microarray
technologies (SNP, miRNA, protein,
and/or standard expression arrays).
Conference Workshops
RNA-Seq 2014 delivers more than just a 2 day learning and networking experience. In the constantly developing field of
next generation sequencing, these two conference workshops enable you to get to the heart of some of the most pressing
issues in the field. This is facilitated through an interactive learning environment and peer-to-peer discussion to deepen
your knowledge and become inspired by new ideas.

7. RNA-Seq 2014 | A Hanson Wade Event
SPONSORS
PROGRAM PARTNERS:
Illumina is a leading developer, manufacturer, and
marketer of life science tools and integrated systems for
the analysis of genetic variation and function. We provide
innovative sequencing and array-based solutions for
genotyping, copy number variation analysis, methylation
studies, gene expression profiling, and low-multiplex
analysis of DNA, RNA, and protein. We also provide tools
and services that are fueling advances in consumer
genomics and diagnostics. Our technology and products
accelerate genetic analysis research and its application,
paving the way for molecular medicine and ultimately
transforming health care.
Lexogen is an Austrian biotech start-up located at the
Campus Vienna Biocenter. It was founded in 2007 and
currently employs 27 scientists and staff. The company’s
mission is already reflected in its name: Lexogen
literally means “word of gene”. We are focused on the
development of unique technologies enabling complete
transcriptome sequencing. Lexogen‘s SENSE mRNA-Seq
library preparation kit is a fast, all-in-one protocol which
generates rRNA free libraries with exceptional strand-
specificity from low amounts of total RNA. Lexogen‘s
SQUARE technology subdivides the transcriptome and
enables the detection and quantification of unique splice
variants as well as exact start- and end-sites, allowing
the complete profiling of all transcript isoforms present in
an RNA sample.
Since the company was founded in 2000, NuGEN has
been a leader in the development of novel genomic
sample preparation solutions for microarray, qPCR and
NGS analysis. Through the use of innovative technologies
employed in rapid and simple workflows, NuGEN enables
accurate representation of biology with no compromise in
data quality for a broad range of samples. NuGEN’s RNA-
Seq portfolio offers sample preparation solutions for the
most challenging samples with the flexibility of a broad
range of inputs down to a single cell. For DNA analysis,
NuGEN offers low input and PCR free library preparation
products in addition to a novel target enrichment
technology using single primer extension for rapid, single
tube workflows and easy custom design capability.
Asuragen is a molecular diagnostics company using
genomics to drive better patient management through
best-in-class clinical testing solutions. With a pioneering
position in miRNA, Asuragen has assembled cutting edge
technologies to discover, develop and commercialize
diagnostic products and clinical testing services. Our
experienced team utilizes these capabilities to operate
with efficiency and flexibility with our internal R&D
programs as well as with our companion diagnostic
partners. Building on the company’s heritage, Asuragen
has developed a reputation as a world class molecular
diagnostics company and has created a culture driven by
nimble, innovative and determined teams of scientists and
professionals inspired to improve patient management
through molecular diagnostics.
Roche NimbleGen: Roche Sequencing is a business
unit of Roche dedicated to the development of break-
through sequencing technologies in the life science and
translational research fields. Current products include
a full line of target enrichment solutions marketed
under the Roche NimbleGen brand as well as Next Gen
Sequencing systems under the 454 brand.
RNA-Seq 2014 Boston | www.rna-seqsummit.com
Email: info@hansonwade.com | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898

8. RNA-Seq 2014 | A Hanson Wade Event
GET IN TOUCH
If your organization needs to raise profile, promote products and services or develop new
partnership opportunities in the RNA-Seq sector then contact us now to find out more.
Diane McKenna, Commercial Director, Genomics
Hanson Wade
Tel: +44 20 3141 8700
Email: sponsor@hansonwade.com
SPONSORS CONTINUED
SPOTLIGHT PARTNERS:
Beckman Coulter Life Sciences’ global leadership and
world-class service and support delivers instrument
systems, reagents and services to improve workflow and
outcomes for researchers in academic and commercial
life sciences laboratories, enabling discoveries in
biology-based research and development, and solutions
for bioprocessing. A leader in centrifugation and
flow cytometry, Beckman Coulter also has brought
to market innovations in capillary electrophoresis,
particle characterization and liquid handling laboratory
automation. Its products are used to further important
areas of scientific investigation, including genomics and
proteomics.
Maverix provides life sciences researchers direct
interaction with a secure, cloud-based platform to
manage, explore, and visualize genomic data generated
via high throughput sequencing. Integrating best-in-
class open-source software, scientists are empowered
to ask new questions; build collaborative “communities
of discovery” to share data, methods, and results; and
integrate their data in context with the latest public and
private biomic information for viral, bacterial, vertebrate,
and plant genomes. The Maverix Analytic Platform is also
optimized to discover previously unknown roles of small
RNA in every aspect of cell regulation.
Lumenogix is built on the principle that researchers in the
life sciences should be able to analyze and understand
their own next-generation sequence data. For many
scientists, high-throughput sequencing has just moved
the research bottleneck from data generation to data
analysis, with frustrating delays caused by dependence
on specialized analysts. In contrast, we believe that the
computer should be viewed as a laboratory instrument
used in the pursuit of research. Our product, Lumenogix
NGS, is offered in three configurations to cover all possible
customer requirements: as a hosted solution on a private
cloud, as a hardware appliance, configured and ready to
run in your office or lab, and as full installation in your
data center.
Life Technologies™ instruments, everyday essentials,
and services help life science researchers harness
the power of science to transform lives. As a brand of
Thermo Fisher Scientific, Life Technologies believes in the
power of science to transform lives. To support scientists
worldwide, we offer high-quality, innovative life science
solutions—from everyday essentials to instruments—for
every lab, every application.
RNA-Seq 2014 Boston | www.rna-seqsummit.com
Email: info@hansonwade.com | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898

9. RNA-Seq 2014 | A Hanson Wade Event
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