rna-seq boston (23-25 june 2015) agenda

Overcome Transcriptome Complexity, Analyze & Interpret Transcriptome Data to Power Drug Discovery & Development

23-25 June 2015 Boston, USA

Tel: +1 212 531 5898 | Email: [email protected]

www.rna-seqsummit.com RESEARCHED & DEVELOPED BY:

DEEPAK RAJPALGSK

COLIN DEWEYUniversity of Wisconsin-Madison

BIN LITakeda

JOSHUA LEVINBroad Institute

COLE TRAPNELL, University of Washington

TED BURCZYNSKIBristol Myers Squibb

PROGRAM PARTNERS:

RNA-Seq Boston 2015 | 23-25 June 2015, USA

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

Genzyme

Tel: +1 212 531 5898 Email: [email protected]

www.rna-seqsummit.com @RNASeq_Summit RNA-Seq Forum


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BENEFITS OF ATTENDING

Interpret transcriptome analysis to optimize drug discovery and development Harness the latest analytical tools and protocols to unlock the potential of your RNA-Seq data and advance your discoveries

Following its inception in 2013, RNA-Seq Boston has taken significant steps towards providing a complete networking and learning solution for basic, translational and clinical researchers within the RNA-Seq Community. Unlocking the information within the transcriptome to leverage its knowledge for enhanced disease understanding and improve drug discovery and development.

RNA-Seq Boston 2015 will enable scientists to overcome the data bottleneck by applying the most appropriate bioinformatics tools and develop a unified, integrated approach for analysis and interpretation of huge data

sets, which in turn can positively impact therapeutic and clinical developments.

This is an opportunity for you to collaborate with other bioinformaticians and biologists to better understand the tools being applied to optimize RNA-Seq data analysis and the application of RNA-Seq in basic research, drug discovery and development.

Unravel your RNA-Seq data and unlock the potential of RNA Seq to excel your research.

Learn about the latest developments in RNA-Seq technology to optimize the integration of RNA-Seq data in your studies

Capture the tools being applied to optimize the analysis of single cell transcriptomic data

TOP 10 REASONS TO ATTEND RNA-SEQ BOSTON 2015:

Discover and validate analytical tools being utilized for enhanced transcriptome data interpretation

Enhance the transition and implementation of RNA-Seq technology in drug discovery and development

Understand the tools being applied for successful identification and quantification of isoforms

Explore and harness the application of RNA-Seq in biomarker discovery

Learn how combining multiple RNA-Seq platforms can optimize transcript assembly

Harness the protocols being utilized to process and integrate RNA-Seq data from public platforms and how they are being applied in large scale studies

Discover how to integrate large sequencing data sets to advance the interpretation of your transcriptome data

Understand how RNA-Seq technology is being implemented into late stage clinical trials




SPEAKERS

Some of the brightest minds and industry leaders in genomics for a series of illuminating seminars and beneficial meetings. We look forward to working with Hanson Wade in the near future. Bina Technologies

SEARCH GROUPS FOR: RNA-Seq Forum to join the online community.

Deepak RajpalDirector Computational Biology, R&D

Christopher MasonAssistant Professor, Weill Cornell Medical College

Katie CampbellInvestigator

Mark GersteinProfessor of Biomedical Informatics, Molecular Biophysics

Colin DeweyAssociate Professor Biostatistics & Medical Informatics

David SoongComputational Biologyinvestigator

Shaun GrosskurthSenior Scientist Oncology Bioinformatics

Michele ClampDirector of Informatics and Scientific Applications

Jay TiesmanResearch Fellow, Genomics Group Leader

Vishal ThaperSenior Bioinformatics Scientist

Julja BurchardAssociate Principal Scientist, Informatics & Analytics

Bin LiAssociate Director Computational Biology, Translational Medicine

Cole TrapnellAssistant Professor in Genome Sciences

Ted BurczynskiExecutive Director of Biomarker Technologies , Adjunct Professor of Pharmacology, University of Pennsylvania School of Medicine

Brian HaynesManager of Bioinformatics

Joshua LevinSenior Scientist I, Group Leader




WORKSHOP

• Overview of single-cell RNA-Seq protocols• Basic gene expression quantification in single cell RNA-Seq• Identifying cellular subpopulations and cell-state transitions using Monocle• Highlighting areas of future development

Cole Trapnell is an Assistant Professor in the Department of Genome Sciences at the University of Washington. His lab studies cell differentiation, reprogramming and cell-cell communication. The Trapnell lab also develops software to help identify genes that regulate these processes. Dr. Trapnell is the original developer of several widely used tools for RNA-Seq analysis, including TopHat and Cufflinks.

Workshop leaderCole TrapnellAssistant Professor in Genome SciencesUniversity of Washington

Single-Cell Transcriptome Analysis with RNA-SeqDate: 23rd June 2015 | Time: 9.00 – 12.00

NETWORKINGRNA-SEQ BOSTON 2015

SPEED NETWORKING

A structured networking session - run like speed dating- especially designed to facilitate quick introductions to the majority of attendees within the RNA-Seq field. Use the time wisely to meet new contacts, reconnect with old friends and identify those you want to spend more time with.

ROUND TABLE DISCUSSIONS

Take part in facilitated discussion sessions focused around specific, high priority issues surrounding RNA-Seq technology. Discuss your experiences and observations within focus groups then share your and the other groups’ finding with the main conference.

STRUCTURED NETWORKING BREAKS

In between the formal presentations the networking carries on. Use the multiple refreshment and lunch breaks to continue your discussions in an informal relaxed atmosphere. Move from scientific discoveries into meaningful collaborations.




Keynote Session Interactive Session Networking Session

8.00 Registration, Breakfast & Networking

9.00 Chair’s Opening Remarks

9.10 Enhancing the Applications of RNA-Seq - Where Are We At? Get an exclusive insight to the latest developments within the

RNA-Seq industry from one to one interviews with a panel of key opinion leaders, who are paving the way in implementing RNA-sequencing for drug discovery and development. The panel will discuss and answer the following questions:

• How can we make the whole process from technology to data analysis/interpretation more cost effective?

• Is the right technology in place to facilitate NGS applications in drug discovery and development?

• Are the right bioinformatic tools being developed and importantly utilized to get the best interpretation of transcriptomic data?

10.10 Going Beyond Standard RNA-Seq• Understand functional impact of genetic polymorphisms to

correctly identifying transcription start sites (TSSs) and splice isoforms

• What lab and computational approaches work best for TSS identification

• How to best combine Illumina, PacBio and Oxford Nanopore RNA-Seq for optimal transcript assembly

Joshua Levin, Senior Scientist I, Group Leader, Broad Institute

10.40 Morning Refreshments & Speed Networking

11.40 Enabling Translational Diagnostics through Discovery and Development Applications in RNA-Seq

• Whole transcriptome RNA-Seq can elucidate gene signatures and fusions from FFPE and FNA tumor biopsies

• Gene signatures can be efficiently migrated to a targeted RNA-Seq assay with high analytical fidelity

Brian Haynes, Manager of Bioinformatics, Asuragen, Inc

Latest Advances in RNA-Seq Data Analytical Tools

12.10 Transcriptome-Based Cellular Phenotyping

• A large amount of raw or heterogeneously-processed RNA-Seq data is accumulating in public databases

• Developing methods to uniformly process and bias-correct these data so that they be used in large cross-study analyses

• Using our uniformly processed RNA-Seq data to train statistical machine learning methods for classifying (phenotyping) cellular samples

Colin Dewey, Associate Professor, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison

12.40 Sponsored by Affymetrix RNA-Seq and Microarrays: Complementary Approaches to Understanding Gene Expression Profiling• RNA-Seq and microarrays provide data of similar quality

• Microarray studies are reliable and reproducible when designed and executed appropriately

• Microarrays exhibit throughput and cost advantages while

RNA-Seq provides advantages in dynamic range and potential for novel transcript discovery

Jay Tiesman, Research Fellow, Genomics Group Leader, The Procter & Gamble Company

1.10 Networking Lunch & Speaker Corner

2.10 Harnessing the RNA-Seq Platform for Differential Gene Expression Analysis • Overview of the challenges present in analyzing RNA-Seq

data

• Differential gene expression analysis from large scale sequencing studies

Michele Clamp, Director of Informatics and Scientific Applications, Harvard University

2.40 Mapping the Single Cell Non-Coding Landscape• Functional non-coding DNA sequences have important

biological functions in genome organization and transcriptional and translational regulation of coding sequences

• Non-coding DNA comprises structural elements including centromeres, telomeres and scaffold attachment regions (SARs), and give rise to a range of functional RNA products

• As part of our efforts to survey the landscape of cancer-associated noncoding RNA, we are trying to create methods to identify and annotate these regions in single cells

Vishal Thaper, Senior Bioinformatics Scientist, Massachusetts General Hospital

3.10 RNA Sequencing from Single Cells, to SEQC, to Space• To share a eight-platform comparison of RNA-sequencing

• To examine the in depth the effect of various protocol changes to RNA-Seq accuracy

• Harnessing targeted RNA sequencings (TREx) and nanopore RNA-Seq

Christopher Mason, Assistant Professor, Weill Cornell Medical College, Cornell University

3.40 Afternoon Refreshments & Poster Session

4.10 Round-table Session1. Isoform identification/quantification

2. Identifying the right statistical models for data analysis

3. Single cell RNA-Seq

4. Non-coding transcriptomics

5. Clinical implications of RNA-Seq


David Soong, Computational Biology investigator, GSK


Mark Gerstein, Professor of Biomedical Informatics, Molecular Biophysics, Yale University

5.00 Chair’s Closing Remarks

5.10 Close of Day 1

CONFERENCE DAY 1 – Wednesday 24th June 2015




Keynote Session Interactive Session Networking Session

8.00 Breakfast

9.00 Chair’s Opening Remarks RNA-Seq State of Address- What can we take forward from the discussions so far?

Application of RNA-Seq Technology in Drug Discovery and Development

9.10 Application of Genomics Approaches in Drug Discovery• Understanding the application of genomics based approaches

and applications in the drug discovery context

• Examples of RNA Seq studies that we employed in the drug discovery context

Deepak Rajpal, Director Computational Biology, R&D, GSK

9.40 Use of RNA-Seq for Uncovering Mechanism of Action of Combination Effect in Diffuse Large B-Cell Lymphoma

• Establishment of RNA-Seq pipeline to quantify gene expression for mechanistic study

• Utilization of gene set enrichment analyses and causal reasoning to elucidate pharmacological mechanism of action

• Validation of expression based hypotheses to strengthen mechanistic understanding

Shaun Grosskurth, Senior Scientist Oncology Bioinformatics, AstraZeneca

10.10 Identification and Quantification of Isoforms for Target and Pathway Validation

• How to identify and correctly predict isoforms from RNA-seq data

• Identifying and quantifying cancer-specific splicing isoforms

• Using isoform level information to reveal biological mechanisms for target validation


10.40 Morning Refreshments & Networking

11.10 Leveraging RNA-Seq in Drug Development to Ensure High Value Biomarker Work in Early Clinical Studies

• Utilizing the powerful tool RNA-Seq judiciously, in order to limit the bioinformatic resources required to analyze complex datasets

• Enhancing drug developers ability to conduct high value RNA-Seq experiments by setting translational biomarker strategies far in advance of a drug candidate entering human testing

• To identify biomarkers of disease pathophysiology, proof of mechanism, pharmacodynamic effect and patient stratification using properly designed and executed RNA-Seq experiments

Ted Burczynski, Executive Director of Biomarker Technologies, Bristol Myers Squibb, Adjunct Professor of Pharmacology, University of Pennsylvania School of Medicine

11.40 Systems Biology Approach to Analyzing and Integrating Large Data Sets• Establishing data analysis tools for large data sets

• Applying this approach for all aspects of drug discovery; from target identification and validation to clinical studies

Julja Burchard, Associate Principal Scientist, Informatics & Analytics, Merck & Co

12.10 Networking Lunch

Emerging Clinical Applications of RNA-Seq Technology

1.10 Application of Gene Expression Deconvolution to the Translation of Gene Expression Signatures from Pre-Clinical Models to the Clinic

• Heterogeneity of primary tissue samples can make translating gene expression signatures from cell line models difficult

• Methods for gene expression deconvolution can help elucidate this area

• Tested and developed deconvolution for primary tumor gene expression data

Katie Campbell, Investigator, Novartis Institutes for

Biomedical Research

1.40 Implementation of RNA-Seq Technology in Later Stage Clinical Trials• RNA-Seq method evaluation and pipeline building

• RNA-Seq quality control, process, and filtering for phase-III clinical trial samples

• Patient characterization using RNA-Seq data

Bin Li, Associate Director Computational Biology, Translational Medicine, Takeda

2.10 Afternoon refreshments

3.10 Unravel the Transcriptome Complexity This is a great chance for all the roundtable modulators to come together and feedback the discussions that took place and summarise their mine findings to everyone. This is also an opportunity to discuss future to developments and how the field needs to move forward to successfully utilise RNA-Sequencing in drug discovery and development.




Mark Gerstein, Professor of Biomedical Informatics, Molecular Biophysics, Yale University

4.10 Chairman’s closing remarks

4.20 Close of Congress

The speaker array and order was perfect and allowed me to take the maximal amount of knowledge back to the lab Novartis

CONFERENCE DAY 2 – Thursday 25th June 2015




SPONSORSRNA-Seq Boston is proud to partner with:

A pioneer in microarray technology and a leader in genomics analysis, Affymetrix now develops and provides innovative technologies that enable multiplex and parallel analysis of biological systems at the cell, protein, and gene level, facilitating the rapid translation of results into biology for a better world.

Our extensive portfolio of translational and clinical solutions enables scientists and clinicians to rapidly translate their research into understanding underlying disease mechanisms, identifying biomarkers for personalized medicine, creating novel molecular diagnostic tests, and improving genetic marker-assisted breeding programs in agriculture for human health and wellness.

www.affymetrix.com

PROGRAM PARTNER

Contact

Diane McKenna Commercial Director, GenomicsTel: +44 (0)203 141 8700 Email: [email protected]

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.

www.asuragen.com

PROGRAM PARTNER

As a result of the meeting we currently are involved in active negotiations with three companies we met there and are in question-answering stage with others. Almost too much interest for us to handle!! Thank you again and I look forward to seeing you soon MD, Director,Washington University School of Medicine



RNA-Seq Boston 2015 | 23-25 June 2015, USARNA-Seq Boston 2015 | 23-25 June 2015, USACode: 5165

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rna-seq boston (23-25 june 2015) agenda

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