Themes covered in this Track include the handling of next-generation sequencing data, combining markers/tests for usage in personal genomics, GWAS, genotyping, Gene ID, biological databases, and microarrays.

TUESDAY, APRIL 20

2:00 - 6:00 pm Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

Cindy Crowninshield, Conference Director, Cambridge Healthtech Institute

Presented by
4:05  Keynote Introduction: Ronald Ranauro, Chief Executive Officer, GenomeQuest, Inc. 

4:15 PLENARY KEYNOTE: Drug Discovery Opportunities and Challenges -- VC, Biotech and Pharma Perspectives Christoph Westphal, M.D., Ph.D., CEO, Sitris Pharmaceuticals; Senior Vice President, Center of Excellence for External Drug Discovery, GlaxoSmithKline

 

5:00 - 7:00 pm Welcome Reception in the Exhibit Hall

***Drop off your business card at the CHI Sales Booth for a chance to win an Apple® - iPod nano®!
** 2 Winners will be announced at 6:45pm in the Exhibit Hall

 

WEDNESDAY, APRIL 21

7:30 am Registration and Morning Coffee

Sponsored by
 8:15 Event Chairperson’s Opening Remarks

Phillips Kuhl, Co-founder and President, Cambridge Healthtech Institute

Keynote Introduction: Jamie Wyatt, Vice President and General Manager Health and Life Sciences, Netezza

8:20 PLENARY KEYNOTE: Impact of HIT Stimulus on Novel Sources of Data for Research John Halamka, M.D., M.S., CIO, Harvard Medical School           9:00 Keynote Presentation & 2010 Benjamin Franklin Award  Alex Bateman, Ph.D., Senior Investigator, Pfam Database Project, Wellcome Trust Sanger Institute

 

Sponsored by
 9:30 Coffee Break, Poster and Exhibit Viewing
***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®)

 

DRIVING BIOMARKER DISCOVERY AND
TRANSLATIONAL RESEARCH THROUGH
EMERGING GENOMICS TECHNOLOGIES

10:50 Track Chairperson’s Remarks
Chris Duffy, Product Marketing Manager, Quantum

11:00 Leverage Emerging Technologies to Manage Genomic and Clinical Data

Stephen Friend, M.D., Ph.D., President, Sage Bionetworks

Why are we blindly assuming linear data sets and pathways will be sufficient to navigate the coming onslaught of genomic and clinical data? Many remain pleased with narrative approaches to diseases where like in the middle ages their favorite gene must be at the center of the universe. This is likely to prove insufficient. Many also are assuming GWAS data sets will provide the treasure maps to understanding disease risks. Further, those starting efforts in collecting clinical data are wooed by the scale and scope of the data. All evidence from more mature “big science” efforts in other sciences like Physics would say “hold on- wait a minute.” This lecture will frame four tenets on which we will need to operate if we are going to leverage the emerging genomics technologies coupled to robust clinical datasets.

11:30 Enabling Translational Research and Biomarker Discovery through Informatics and Genomics

Jacob de Vlieg, Ph.D., Global Head Molecular Design & Informatics & Professor Computational Drug Discovery, MSD

Genomics and bioinformatics are well-established scientific disciplines in pharmaceutical research. Vast amounts of structural information on targets and target-ligand complexes and the availability of complete genome sequences have stimulated tremendous efforts to rationalize the drug design process. While it’s believed that ‘omics’ and informatics may create opportunities to speed up the process and provide novel design processes, a concern of low productivity and high late stage attrition will continue to challenge the industry. This talk will explore how R&D approaches and genomics-based methods can be integrated efficiently to address these concerns. Advances in bioinformatics, cheminformatics, and genomics technologies in drug discovery and development will be discussed.

Sponsored by
12:00 pm Pipelining Your NGS Data

Nancy Miller Latimer, M.S., Senior Product Manager, Biological Sciences and Analytics, Accelrys

Has data pipelining become the darling of next-generation sequencing (NGS) analysis challenges? We present a web-based NGS workbench for variation detection on reads data generated from 3 different NGS platforms, Illumina, SOLiD, and 454, that caters to the novice but also has the flexibility required for the expert. We will look underneath the covers at a popular common pipelining software application that drives the workbench. We also discuss a model for deployment of the workbench to the cloud environment.

Sponsored by
12:15 RISe: An Approach to Combine Online Transaction Processing and Semantic Information in a Research Informatics Platform

Ajay Shah, Ph.D., MBA, PMP, Director of Research Informatics, Elan Pharmaceuticals Inc.
Elan and Infosys are building an integrated research data integration platform called RISe (Research Informatics System at élan). RISe enables integration of diverse experimental, computational, in-house and external data for registration, inventory tracking, workflow and analysis.  RISe enables research analytics dashboards, collaboration and knowledge management to enhance research productivity.  RISe utilizes a unique software architecture that combines multiple approaches to database schemas to achieve the integration.  Flexibility of the definition of biological entities is accommodated via Entity-Attribute-Value model, efficiency-prioritized OLTP schema is used for inventory management and RDF schema is used for semantic data integration.  RISe utilizes a workflow driven, multi-tiered, SOA based architecture built on the Microsoft.NET platform and SharePoint client.

12:30 Luncheon Presentation Sponsored by  
Empowering Researchers with Hypothesis-Driven Data Exploration
Jian Wang, Ph.D., CEO, BioFortis Inc.
A significant bottleneck on productivity in translational research is the inability for researchers to directly interrogate data by themselves.  Instead, the standard workflow is often to rely heavily on informatics specialists to answer questions, which has limitations in many ways. As a repeatable, best-practice measure, we present a novel process & case study to demonstrate how, with the right tools, translational researchers can be more self-sufficient, efficient and productive, while enabling informatics specialists to focus more on higher value contributions instead of mundane ad hoc data manipulations.

 

DATA MANAGEMENT AND
INTEGRATION STRATEGIES

1:40 Chairperson’s Remarks

Richard Golob, President and Chief Executive Officer, GGA Software Services, LLC

1:45 CASTOR QC - A Database Approach for Handling Large Genomic Data Sets

Marc Bouffard, M.Sc., Senior Bioninformatician, Montreal Heart Institute and Genome Quebec Pharmacogenomics Center

Current genetic analysis solutions are overwhelmed by the large volume of data produced by current generation sequencing and genotyping technologies. Next generation sequencing is significantly increasing the amount of data produced. New solutions must be developed to transform this data into useful knowledge. The CASTOR QC (Comprehensive Analysis and STORage) project uses a novel database-centric approach to leverage both data structures and database technologies to enable rapid analysis of genotypic and phenotypic data. Attendees will learn about data and data processing, how data converts into knowledge, and what steps can be taken in order to transform this data into a storage and analysis friendly format.

2:15 Success Strategies in Translational Medicine: The Best Decisions Are Made with the Best Information

Jonathan Usuka, Ph.D., M.B.A., Director, Research & Development, Celgene Corporation

In this discussion, we will examine specific commercial successes in translational research for the inflammation and oncology therapy areas. We will review the ingredients for success as indicated in the underlying strategies - emerging criteria for a successful biomarker effort, such as diagnostic partnering, clinical sample repositories, patient consent, and increased reimbursement for increased efficacy or safety. The economic effects of a fragmented market resulting from personalized therapy will be examined in the context of the declining blockbuster model.

Presented by
2:45 Featured Presentation

The BIG Idea: Strategies to Achieve a Rapid-Learning Health System

(Joint Talk with Tracks 2, 3, 4, 6, and 7)

Ken Buetow, Ph.D., Associate Director, Bioinformatics and Information Technology, National Cancer Institute

Considerable momentum has been building in government, academe and the commercial sector towards implementation of a “rapid-learning health system”. In this approach to biomedicine, research and clinical care are seamlessly linked in a virtuous circle that enables the collection and analysis of information on clinical outcomes of large populations. This talk will outline the requisite components of such a system—including a mega-community called the BIG Health Consortium™ encompassing the various sectors of biomedicine and electronic interoperability that enables the liquidity of information—and will showcase this new model in action.

3:15 Refreshment Break, Poster and Exhibit Viewing
***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®)  Winners will be announced at 3:30pm in the Exhibit Hall

3:45 Cancer Pharmacogenomics Data Integration: Challenges, Promises and its Application to Cancer Drug Discovery

Lihua Yu, Ph.D., Principal Scientist II, Cancer Discovery, AstraZeneca R&D

AstraZeneca Cancer has developed a cancer pharmacogenomics data integration system. The system manages multi-dimensional data (compound profiling data across cancer cell lines, gene expression, aCGH and mutation data of cancer cell lines) and is widely used across cancer drug discovery. We will discuss the system’s design principles and key functionalities, drug discovery projects where this system has been used, and challenges & lessons learned.

4:15 Engineering Hope: Conducting Successful Translational Medicine in Oncology and Immunology Biopharmaceutical Development

Eric Perakslis, Ph.D., Vice President, R&D Informatics, Johnson & Johnson Pharmaceutical R&D

Delivering successfully on the promise of translational medicine and science, the Johnson & Johnson Pharmaceutical group has reinvented the approach to informatics. By centralizing the function and bringing all data into scope for a single team, significant strides have been made in systems, processes and value delivery. One technical outcome is the tranSMART data warehouse and analytics system, enabling superior decision support across the R&D process. The process, social engineering and systems methodology approaches will be detailed in this talk.

Sponsored by
4:45 NGS: The Bioinformatics Bottleneck
Richard Resnick, Vice President, Software and Professional Services, GenomeQuest, Inc.
Next-generation sequencing instruments are being placed by the hundreds while their throughput increases every quarter. Massive disk arrays, hundreds of thousands of cores of processing power, and tens of new mapping algorithms have been introduced to keep up. And yet the vast majority of researchers still wait months after their sequencing runs to get analyses to drive their science forward, while bioinformaticians scurry to keep pace. We will briefly present a free online NGS sequence data management (SDM) platform on the cloud produces interactive, mineable, shareable NGS analyses on not one but thousands of genomes, with an open API to allow bioinformaticians to develop and publish their own workflows for some or all to use.

5:15 – 6:15 2010 Best of Show Awards in the Exhibit Hall

6:15 Exhibit Hall Closes

Sponsored by
6:30 – 10:00 2010 Best Practices Awards Reception & Dinner

 

 

 

 

 

THURSDAY, APRIL 22

8:00 am Registration and Morning Coffee

Sponsored by
8:45 Event Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Keynote Introduction:  Eric Blatte, Vice President of Sales, Commercial & Public Sector, Imprivata

8:50 PLENARY KEYNOTE: There is No Magic, There is Only Awesome: Scientific Computing with Amazon Web Services Deepak Singh, Ph.D., Business Development Manager, Amazon Web Services   Presentation delivered via a live, interactive videoconferencing platform.       9:30 KEYNOTE PANEL The Future of Personal Genomics A special plenary panel discussion featuring: James Heywood, Co-founder and Chairman, PatientsLikeMe Dan Vorhaus, J.D., M.A., Attorney, Robinson, Bradshaw & Hinson; Editor, Genomics Law Report Dietrich Stephan, Ph.D., President & CEO, Ignite Institute Kári Stefánsson, MD, Dr Med, Executive Chairman and President of Research, deCODE genetics Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

 

10:30 Coffee Break, Poster Competition, Vendor Theater Presentations and Exhibit Viewing
***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®)

Application Of Data

10:55 Chairperson’s Remarks 

Richard Resnick, Vice President, Software and Professional Services, GenomeQuest, Inc.

11:00 Unbiased Prioritization of Mutations in Cancer Genomes

David Dooling, Ph.D., Director, Analysis Developers, Laboratory Information Management Systems (LIMS), and the Information Systems Groups, The Genome Center at Washington University in St. Louis School of Medicine

With the advent of massively-parallel sequencing technologies, the rate of discovery of mutations in cancer genomics far outstrips our ability to attribute functional significance to the mutations. Short of a breakthrough in functional genomics, other methods will be needed to, at the very least, narrow down the massive number of potentially important mutations into a more manageable set of mutations that are clinically relevant, i.e., so-called driver mutations. Using massive data sets on dozens of tumors and matched normals, a highly-scalable information management system, and machine learning algorithms, we have developed a system that can integrate sequence reads, array data, clinical information, phenotypic data, genomic annotation, and cellular pathway databases to assign significance scores to the millions of mutations found in cancer genomes.

11:30 Combining Multiple Signals to Identify the Causal Variant within Regions Under Positive Natural Selection

Pardis Sabeti, M.D., D.Phil., M.Sc., Assistant Professor, Center for Systems Biology and Department of Organismic and Evolutionary Biology, Harvard University

The genomes of humans and other species contain hundreds of regions with evidence of recent positive natural selection, yet, for all but a handful of cases, the underlying advantageous mutation remains unknown. This talk illustrates the Composite of Multiple Signals (CMS), a novel method developed and validated, that combines tests for multiple signals of selection and provides 10-100x better positional resolution than any individual signal.

Sponsored by
12:00 pm Integrative Biological Analysis of Public and Proprietary Microarray, GWAS and Nextgen Sequencing Data

Ilya Kupershmidt, Cofounder and VP Products, NextBio

Ability to integrate and mine public and proprietary datasets from microarray and next-gen technologies is central to modern day biology. In this talk I will describe the latest evolution of NextBio platform to support integrative biological analysis and correlation of data from gene expression, DNA copy-number, resequencing, epigenetic and genotyping studies in order to explore gene function and mechanisms of disease development. Meta-analysis techniques combining these diverse data types within the context of genome structure and pathway information will be explored.

 

12:15  Sponsored by
  
Highly Efficient Bioinformatics Solutions on Amazon Web Services offered by Omixon Biocomputing Solutions
Attila Berces, Ph.D., Chief Executive Officer, Omixon
Omixon offers computationally and cost efficient NGS analysis web services such as a highly sensitive short read gapped alignment application called Crema. BAYGEN Research Institute used this tool to analyze genome sequences from 14 P. acnes isolates sequenced by ABI SOLiD V3.5 sequencer. The attendees will learn how this tool is used to find SNPs, insertions and deletions, in a number of genes encoding putative virulence factors. We present a comparative study  to align 135 million reads from Ciona savigny with Crema as well.
Omixon aims to provide the most cost efficient solutions for the most computationally intensive problems.

 

12:30 Luncheon in the Exhibit Hall
***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®)  Winners will be announced at 1:45pm in the Exhibit Hall

2:00 Exhibit Hall Closes

1:55 Track Chairperson’s Remarks

2:00 Pharma Informatics: Looking Beyond Our Walls
(Joint with Tracks 2 and 3)

Martin D. Leach, Ph.D., Executive Director, MRL IT for Discovery & Preclinical Sciences, Merck & Co.

Matteo di Tommas, Vice President, Research Informatics, Pfizer, Inc.

The pharmaceutical industry is under increasing pressure to increase the output from research pipelines in an environment of increasing regulatory oversight, and need for significant cost-containment. Across pharma R&D IT the trend is to focus on greater business value and partnership and lower cost.   Both Pfizer & Merck are increasingly looking outside our walls to leverage expertise and develop capabilities for R&D scientists.  Our joint presentation will highlight lessons learned and innovative approaches to meeting the challenge of delivering better outcomes at lower costs by changes in governance, sourcing, collaboration and architecture.

2:30 What is Still Required for Semantic Linked Data to Advance Biomedical & Pharmaceutical R&D?

Eric Neumann, Ph.D., Director, Clinical Semantics Group; Former Chair, W3C Healthcare and Life Sciences Interest Group

Linked Data standards have been quite successful in some areas recently (UK public data), and many powerful demonstrations have been compiled around Linked Open Data (LOD). However, for them to be practical and powerful in scientific and enterprise R&D, some additional features and capabilities need to be developed and utilized. They will also need to align with existing installed technologies in order to provide a way forwards and to gain vendor acceptance. These issues will be further elaborated on and proposed solutions to help realize the vision of semantic integration through Linked Data will be offered.

 

3:00 Toward Meaningful Whole-Genome Interpretation with Open Access Tools from the Genome Commons

Reece Hart, Ph.D., Chief Scientist, Genome Commons, UC Berkeley QB3 and Center for Computational Biology

The widespread availability of personal genomic data is imminent, yet we are ill-prepared to reap the full personal, scientific, clinical, and social benefits from these data. Among the many barriers to holistic genome interpretation, four are prominent: 1) isolation of genotype and phenotype data; 2) lack of tools that are easily interoperable; 3) insufficient scientific methods for the analysis of variants; and 4) unsettled ethical and social policy issues. The Genome Commons is a nascent collaboration among faculty from UC Berkeley and UC San Francisco that will provide freely accessible databases, analytical tools, and scientific methods for the interpretation of human genomic data. Our collaborators bring expertise in computational biology, computer science, statistics, clinical genetics, and ethics. While scientific utility is our immediate goal, we envision that the Genome Commons will provide a foundation for clinical tools and a repository for studies of human variation. In this talk, I will introduce the Genome Commons, describe our preliminary results, and present the outlook for this project.

4:00 Conference Adjourns

Apple® - iPod touch®,  Nano®, Nintendo® Wii™, are  not sponsors or participants in this program.