Overview | Day 1 | Day 2 | Day 3 | Download Brochure | Breakout Discussions

FRIDAY, FEBRUARY 27

INTEGRATING GENOMIC DATA

8:30 Chairperson’s Remarks

8:35 The Genomic Data Pipeline: Collecting, Cleaning, Analyzing, Integrating, Sharing
Jeanette Papp, Ph.D., Associate Professor, Human Genetics, University of California, Los Angeles
A tour of the Genomic Information Superhighway - from historical perspective to current challenges and solutions, with a glimpse into the future. I will cover the evolution of genomic data management and integration systems and outline some of our own solutions in data collection and management, data merging and integration, statistical and network analysis, and data sharing. List why this paper should be considered?: I can give a comprehensive perspective on the history, current state of the art, and future challenges of genomic data integration. My group has been involved in genomic analysis from the early days of the Human Genome Project. We developed some of the earliest statistical genetics methods and software, built some early genetic LIMS/databases to hold genetic data when data sets numbered in the thousands of data points, and have evolved those systems over the years to accommodate whole genome association data and next generation sequencing data of tens of millions of data points. We are now extending our web-based data systems that integrate multiple data types, querying tools, analysis methods, and data sharing capabilities. 

9:05 Surviving the Data Deluge: Informatics for Next Generation Sequencing
Toby Bloom, Ph.D, Director of Informatics, Genome Sequencing Platform, The Broad Institute

9:35 Integrating Public Genomics Data into Pharmaceutical R&D
Hans-Martin Will, Ph.D., Senior Director, Genomics R&D, Rosetta Biosoftware
Over the past few years, more and more comprehensive genomics data sets have been generated by academic and publicly-funded consortia and made accessible-notable examples are the Framingham Heart Study and the data released by the Wellcome Trust Case Control Consortium. This abundance of data is creating a new reality for pharmaceutical R&D, whereby a large number of data sets relevant to internal R&D projects are generated from publicly-funded, academic and governmental organizations. With this insight, many organizations are in the process of devising strategies for making best use of these data, and implementing approaches for effectively bringing the data sets in-house and integrating them into the context of their on-going scientific research efforts. In this talk, we will discuss the various types of challenges pharmaceutical R&D organizations are facing when bringing in public data sets. Starting with mundane data formatting problems, unknown data quality and varying taxonomies, we will conclude our discussion with a brief survey of approaches and opportunities for mining these data.

10:05 Search Strategies for Correlating Combined Public and Internal Large-Scale Studies Ilya Kupershmidt, Cofounder and Vice President Products, NextBio NextBio specializes in the discovery and testing of hypotheses within the growing body of the world’s high-throughput data. To enable real time search NextBio pre-computes billions of findings within highly heterogeneous data. These findings are based on the global meta-analysis across thousands of genomic, genotyping and other large-scale “omics” studies.

Sponsored by

10:20 Coffee Break

11:00 Platform for the FDA Genetic Data Submission and Review Process 
Weida Tong, Ph.D., Director, Center for Toxicoinformatics, National Center for Toxicological Research, U.S. Food and Drug Administration
Rapidly developing technologies for genetic analysis are driving the emergence of the new research fields of personalized medicine and targeted therapeutics. In order to guide effective development and regulation of pharmacogenomics and medical devices resulting from this research, the expertise, tools, and processes for utilizing genetic data are needed in the FDA. To this end, the FDA’s Critical Path Initiative created the Voluntary eXploratory Data Submission (VXDS) mechanism to provide a collaborative environment in which the research community, sponsors and the FDA can work together on data management, analysis and interpretation outside normal regulatory interactions. With the increasing number of submissions based on genetic data, a parallel informatics platform has been conceived. This talk will introduce this new initiative, SNPTrack, being undertaken by the NCTR/FDA in collaboration with Rosetta Biosoftware, for development of FDA regulatory capability for analyzing VXDS and formal submissions of genotyping data. The goal is a system which enables FDA reviewers to reconstruct sponsor analysis of genetic variation data, explore alternative analysis methodologies and respond to the sponsor with the agency’s understanding and recommendations. It is envisioned that the outcome of this initiative will drive adoption of industry best practices and standards for formal data submissions. 

11:30 Speaker to be Announced

12:00 pm Luncheon Presentation (Sponsorship Available) or Lunch on Your Own

DATA INTEGRATION AND MANAGEMENT FOR EARLY AND LATE CHEMISTRY

1:00 Chairperson’s Remarks

1:05 Lilly’s Transition from Paper to Electronic Lab Notebooks
Keith DeVries, Ph.D., Director, Chemical Product, R&D, Eli Lilly and Company, Lilly Research Labs 
Lilly began evaluating electronic lab notebooks in 2003.  By 2005, the Process Chemistry group had fully implemented a paper-less system. The planned deployment of a single electronic lab notebook solution across the entire company will be described, as well as various challenges related to quality and legal concerns and end-user uptake.  The benefits to Lilly derived from a shift from paper to electronic lab notebooks will be shared, in addition to our recent efforts to transition our third party partners to electronic lab notebooks. 

1:35 Integration of Chemical Genomics and Structural Biology Informatics: Novel Insights into the Kinase Gene Family?
Stephan Schürer, Ph.D., Department of Pharmacology, Miller School of Medicine & Center for Computational Science, University of Miami
We developed integrated data analysis pipelines to quantify similarity relationships among the protein kinase complement of the human genome (the “kinome”) from different perspectives: domain sequences, small molecule kinase activity data, and structure-based physicochemical properties of the ATP binding sites.  While we gain insight into differences and synergies of chemogenomics- and structural biology-informatics based approaches to identify and utilize gene-family-wide similarity relationships we also investigate the differences of active and inactive kinase conformations in the same context.  Integrating large chemical genomics data sets and high-quality experimental and modeled structures covering almost the entire Kinome we developed discovery pipelines allowing receptor-site information and small molecule activity data from entire target families to be used in the rational design of compounds with desirable selectivity profiles.

2:05 Techniques for Effective Integrated Access to Large Compound-oriented Drug Discovery Databases
Michael, Lajiness, Ph.D., Research Scientist, Structural and Computational Sciences, Eli Lilly & Company 

2:35 Closing Remarks and Wrap-up: Integrated R&D Informatics 
Moderator: Joseph A. Cerro, President & Founder, Schooner Group LLC

3:05 Close of Conference

Overview | Day 1 | Day 2 | Day 3 | Download Brochure | Breakout Discussions

For questions or suggestions about the meeting, please contact:
Edel O'Regan
Cambridge Healthtech Institute
250 First Avenue, Suite #300
Needham, MA 02494
Tel: 781-972-5423
Fax: 781-972-5425
email: eoregan@healthtech.com 

For sales information, contact:
Carol Dinerstein
Tel: 781-972-5471 
email: Dinerstein@healthtech.com 
OR
Jon Stroup
Tel: 781-972-5483
email: jstroup@healthtech.com