2nd RNA-Seq, Boston, MA 17-19 June 2014 updated brochure

June 17th – 19th 2014 BOSTON, MA

25 EXPERT SPEAKERS INCLUDING:

Lore GruenbaumLead, Global Biomarkers & Experimental Medicine Roche

David von SchackAssociate Research Fellow Pfizer

Joshua LevinSenior Scientist, Group Leader Broad Institute

Qingqin LiScientific Director Johnson & Johnson

Integrate the TechnologyManage the DataInterpret the Results

PROGRAM PARTNERS:

Produced by Hanson Wade

www.rna-seqsummit.com

Yihong YaoDirector, Head of Pharmacogenomics MedImmune

SPOTLIGHT PARTNERS:

Maarten LeerkesGenome Analysis Specialist NIH

RNA-Seq 2014 | A Hanson Wade Event

Master RNA-Sequencing to Crack the TranscriptomeRNA-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

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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 MedicineSearch groups for RNA-Seq Forum to join the online community

Follow us on Twitter #RNASeq2014

RnA-seq 2014 Boston | www.rna-seqsummit.com Email: [email protected] | Tel: +1 (212) 357 5898 | Fax: +1 (212) 357 5898


eXpeRT SPEAKERS:

Qingqin LiScientific Director

Yaoyu WangAssociate Director

Gary SchrothDistinguished Scientist

Jianchao YaoSenior Scientist

Seth CrosbyDirector, Partnerships & Alliances

Alisa JacksonSenior Marketing Manager, Automation & Genomics

Thomas TibbittsResearch Director

David DeLucaComputational Biologist

Yihong YaoDirector, Head of Pharmacogenomics

Todd LoweChief Scientific Officer

Maarten LeerkesGenome Analysis Specialist

Joshua LevinSenior Scientist, Group Leader

Dongliang GeDirector, Bioinformatics

David von SchackAssociate Research Fellow

Lore GruenbaumLead, Global Biomarkers & Experimental Medicine

Steve KainDirector of Product Management

Qichao ZhuPrincipal Scientist

Alexander SeitzCEO

Brian Haynes Senior Scientist

Monica Wang Lead System Engineer, Project and Program Manager

Ted Burckzynski Executive Director Biomarker Technologies

Todd RichmondDirector, Research Informatics

Kelli BramlettR&D Scientist

John TanSenior Scientist

I thought the RNA-Seq conference was a huge success. Definitely learned more than I expected in just two days.

Genzyme

Boris UmylnyCEO



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



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




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 leaderSeth CrosbyDirector Partnerships & AlliancesWashington University School of Medicine

RNA-Seq: A Fundamental Guide to the FieldDate: June 17th 2014 | Time: 9.00 – 12.00

A Cross-Omics Approach to Annotation of Human Splicing TranscriptomesDate: June 17th 2014 | Time: 1.00 – 4.00

Workshop leaderMaarten LeerkesGenome Analysis SpecialistNIH

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 WoRkshopsRNA-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.


sponsoRsPROGRAM 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.



geT in TOUCHIf 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: [email protected]

sponsoRs ConTinUedSPOTLIGHT 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.



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* All discount offers (including team discounts) require payment at the time of registration to receive any discount. ‘Early Bird’ discounts require payment at time of registration and on or before the cut-off date to receive any discount. All discount offers cannot be combined with any other offer. The conference fee includes lunch, refreshments and course documentation. The fee does not include travel or hotel accommodation.

Full payment is due on registration. Cancellation and Substitution Policy: Cancellations must be received in writing. If the cancellation is received more than 14 days before the conference attendees will receive a full credit to a future conference. Cancellations received 14 days or less (including the fourteenth day) prior to the conference will be liable for the full fee. A substitution from the same organiza-tion can be made at any time.

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Event code: 4439

Venue: Courtyard Boston Downtown 275 Tremont Street Boston , Massachusetts 02116,USA

www.marriott.co.uk

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GOLD PACKAGE: Conference + 2 Workshops $3497 (Save $400)

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