TUESDAY, APRIL 24
7:00 am Workshop Registration and Morning Coffee
8:00 am - 4:00 pm Pre-Conference Workshops*
- Leveraging SaaS for Next-Gen Sequencing: Case Study with the Galaxy Community
- Cloud Computing
*Separate Registration Required
2:00 - 7:00 pm Main Conference Registration
4:00 Event Chairperson’s Opening Remarks
Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute
4:05 Keynote Introduction
Sanjay Joshi, Solutions Architect, Life Sciences, EMC Isilon Storage Division
4:15 PLENARY KEYNOTES
Martin Leach, Ph.D., CIO, Broad Institute of MIT and Harvard
Jill P. Mesirov, Ph.D., Associate Director and Chief Informatics Officer; Director, Computational Biology and Bioinformatics, Broad Institute of MIT and Harvard
5:00 - 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing
Drop off a business card at the CHI Sales booth for a chance to win 1 of 2 iPod touches® or 1 of 2 Xbox 360s®*!
*Apple® is not a sponsor or participant in this program
WEDNESDAY, APRIL 25
7:00 am Registration and Morning Coffee
7:55 Chairperson’s Opening Remarks
Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute
8:00 Keynote Introduction
Bas Burger, President, Global Commerce, BT Global Services
8:15 PLENARY KEYNOTE
Eric D. Perakslis, Ph.D., CIO and Chief Scientist of Informatics, U.S. Food and Drug Administration
8:45 Benjamin Franklin Award & Laureate Presentation
9:10 Best Practices Award Program
9:45 Coffee Break in the Exhibit Hall with Poster Viewing
10:50 Chairperson’s RemarksKevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
11:00 Washington University Approach to NGS Informatics
David J. Dooling, Ph.D., Assistant Director, The Genome Institute, Washington University, St. Louis
11:30 Broad Approach to NGS Informatics
Toby Bloom, Ph.D., Director, Informatics, Genome Sequencing, Broad Institute
12:00 pm The Informatics of Whole Human Genome Sequencing
Jason M. Laramie, Ph.D., Principal Application Scientist, Complete Genomics, Inc.
In the last three years, there has been a deluge of data generated from the advancement of a variety of sequencing technologies. This massive amount of data has created a number of unique informatics challenges. Through numerous examples, this talk will cover the informatics challenges of sequencing over five hundred whole human genomes per month.
12:15 Blind Validation of Omixon Software for Diagnostic Applications: Oncogenes and HLA
Attila Berces, Ph.D., CEO, Omixon
Omixon presents clinical grade analysis using NGS data for target-specific variants of oncogenes and HLA/MCH genes. The studies are based on Illumina, Ion Torrent and Roche 454 data, and validated by capillary Sanger sequence comparisons. Omixon software correctly identified challenging variants such as indels up to 62 bp. The HLA analysis was validated in collaboration with the Hungarian Blood Services and serves in companion diagnostics development in the clinical trials of Genetic Immunity.
12:30 Luncheon Presentation
Ion Torrent: Open, Accessible, Enabling
Matt Dyer, Ph.D., Associate Director, Bioinformatics & Community, Ion Torrent, Part of Life Technologies
Ion Torrent has pioneered an entirely new approach to sequencing that enables a direct connection between chemical and digital information and leverage decades of semiconductor technology advances. The result is the first commercial sequencing technology that does not use light, and as a result delivers unprecedented speed, scalability, accuracy, and low cost. In just the first year the Ion Torrent Personal Genome Machine (TM) has become the fastest selling sequencing platform. The throughput scaled 100X, from 10Mb to 1Gb, in just the first year and will scale another 100X in the next year with the new Proton (TM) sequencer, which will enable the single day $1000 human genome. Automated data analysis is driven by Torrent Suite, an open-source software suite that provides a simple and intuitive interface to streamline data analysis and provide results in minutes to hours, not days. Built on top of Torrent Suite is a flexible SDK that allows users to expand the analysis capabilities through the development and utilization of plugins and APIs.
1:40 Chairperson’s Remarks
Rick Friedman, Vice President, Marketing & Product Management, Terascala, Inc.
1:45 NGS Informatics - Surnames Leakage, Hacking and Genetic PrivacyYaniv Erlich, Ph.D., Principal Investigator, Whitehead Fellow, Whitehead Institute for Biomedical Research
2:15 Panel Discussion: Organizational Approaches to NGS Informatics and Privacy
David J. Dooling, Ph.D., Assistant Director, The Genome Center, Washington University, St. Louis
Toby Bloom, Ph.D., Director, Informatics, Genome Sequencing, Broad Institute
Yaniv Erlich, Ph.D., Principal Investigator, Whitehead Fellow, Whitehead Institute for Biomedical Research
2:45 Using Tiered Archives to Reduce Storage Costs for Next Gen Instrument Data
Will McGrath, Manager, Business Development, Quantum
Next generation genomic sequencers and other instruments are becoming smarter in how they generate data off-instrument, but still data storage requirements grow. Some suggest the cost of managing and analyzing this data will outpace the cost to actually sequence. Research institutions and bio-informatics firms have more aggressively begun to set up tiered storage environments to deal with increasing power and cooling costs and shrinking data center footprint of storing and protecting all this big data. This sponsor session will highlight strategies certain life science customers are using for long-term data tiering, archival, and data protection for handling next gen instrument data using solutions like Quantum’s StorNext software and appliances.
3:00 Next Generation Software for Next Generation Sequencing Data
Tamas Rujan, Product Manager, Genedata Expressionist
Experimental designs of molecular profiling studies in life sciences are becoming more complex and sample sizes are growing:
-Genedata Expressionist – data management, processing, and analysis in one powerful enterprise solution
-Data visualization – more than just a nice to have
-Integrative data analysis – better insight into biological systems and superior biomarkers
-No limitations on data size – remove one of the major bottlenecks for NGS
3:15 Refreshment Break in the Exhibit Hall with Poster Viewing
3:45 NGS Pipelines in the Cloud
Peter J. Tonellato, Ph.D., Visiting Professor, Senior Research Scientist, Pathology, BIDMC & Center for Biomedical Informatics, Harvard Medical School
4:15 Transparent and Public Genomics
Alexander Wait Zaranek, Ph.D., Director, Informatics, Harvard Personal Genome Project, Genetics, Harvard Medical School
At the Personal Genome Project, we are building a transparent and public resource consisting of genomes, detailed phenotypes, as well as cell-lines and other tissue samples for more than 100,000 individuals. With inspiration from the open source and free knowledge movements, we will discuss new ways to benefit from the breathtaking improvements in genomic technologies.
4:45 BaseSpace: A Scalable Cloud Platform for Research and Clinical Sequencing Informatics
Alex Dickinson, Senior Vice President, Cloud Genomics, Illumina, Inc.
The rapid migration of sequencing from the core lab, to the researcher desktop, to the clinical lab has major implications for bioinformatics. In particular, these new users are looking for solutions that provide ease of use, require no investment in IT infrastructure, and are compliant with the appropriate regulations. Illumina has developed BaseSpace, a cloud computing platform that meets these needs by seamlessly linking on-instrument, local cloud, and public cloud bioinformatics.
5:15 Best of Show Awards Reception in the Exhibit Hall
6:15 Exhibit Hall Closes
THURSDAY, APRIL 26
8:40 Chairperson’s Opening Remarks
Gholson J. Lyon, M.D., Ph.D., Assistant Professor in Human Genetics, Cold Spring Harbor Laboratory; Research Scientist, Utah Foundation for Biomedical Research
8:45 The Gene Partnership
Isaac Samuel Kohane, M.D., Ph.D., Henderson Professor of Health Sciences and Technology, Children’s Hospital and Harvard Medical School; Director, Countway Library of Medicine; Director, i2b2 National Center for Biomedical Computing; Co-Director, HMS Center for Biomedical Informatics
9:15 Carpe Novo & Clinical Genome Sequencing
Elizabeth Worthey, Ph.D., Assistant Professor, Human and Molecular Genetics Center, Department of Pediatrics, Bioinformatics Program, Medical College of Wisconsin
9:45 Embedded NGS Processing with iRODS in DDN SFA Storage Controllers
Jan Jitze Krol, Solutions Architect, Life Sciences, DataDirect Networks, Inc.
NGS pipelines produce vast amounts of data. It has becomes a challenge to manage and process these large data sets. The SFA10KE and SFA12KE line of storage controllers offers the unique capability to embed user processes inside the controller, giving those processes the fastest access to the data. These platforms can facilitate pipeline automation, and reduce the overall time to results.
10:00 Rapid Biological Interpretation of Human NGS Data via Ingenuity® Variant Analysis™
Sandeep Sanga, Ph.D., Bioinformatics Product Development Scientist, Ingenuity Systems
Biological interpretation of thousands of potentially causal variants is a bottleneck in extracting valuable insights from NGS studies, often requiring months of effort after completion of read alignment and variant calling steps. Here we demonstrate Ingenuity® Variant Analysis™ (www.ingenuity.com) as a tool for empowering clinical researchers to quickly zero in on the few variants that are most compelling for follow-up.
10:15 Coffee Break in the Exhibit Hall and Poster Competition
10:45 Plenary Keynote Panel Chairperson’s Remarks
Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
10:50 Plenary Keynote Panel Introduction
Geoffrey Noer, Senior Director, Product Marketing, Panasas
11:00 Plenary Keynote Panel:
A special plenary session featuring trends and challenges in cancer research:
- Julian Adams, Ph.D., President, Research and Development, Infinity Pharmaceuticals, Inc.
- Jose Baselga, M.D., Ph.D., Chief and Bruce A. Chabner Chair, Division of Hematology/Oncology, Massachusetts General Hospital; Associate Director, Massachusetts General Hospital Cancer Center; Professor of Medicine, Harvard Medical School
- Sir John Burn, MD, FMedSci, Professor of Clinical Genetics, Institute of Genetic Medicine, Newcastle University, UK; Genetics Lead, National Institute of Health Research, UK; Medical Director, QuantuMDx Ltd
- John Quackenbush, Ph.D., Professor, Biostatistics and Computational Biology, Cancer Biology Center for Cancer Computational Biology, Dana-Farber Cancer Institute
12:15 Luncheon in the Exhibit Hall with Poster Viewing
1:55 Chairperson’s RemarksDawn Van Dam, General Manager, Cambridge Healthtech Associates
2:00 Speaker to be Announced
2:30 Measurement of T Cell Repertoire Diversity in the Peripheral Blood by Novel Multiplex PCR and Next-Generation Sequencing Methods
Jian Han, Ph.D., Faculty Investigator, Hudson Alpha Institute for Biotechnology
This presentation describes the Repertoire 10K or R10K project – a new method for analysis of the immune repertoire by high-throughput sequencing and informatics, and a new index for measurement of health status and disease prognosis. This method is based on semi-quantitative and comprehensive analysis of the T cell receptor beta CDR3 sequences present in peripheral blood.
3:00 Assess and Minimize False SNVs from RNA-Seq Analysis
Wenming Xiao, Ph.D., Staff Scientist, Division of Computational Biology, Center for Information Technology, National Institutes of Health
RNA-Seq analysis is widely used to discover SNVs in cancer samples. However, many people are struggling with the false results due to software error or mis-mapping of reads. The methodology and process we developed would help researchers to discover SNVs with great accuracy and thus minimize the risk of wasted effect due to analysis error.
3:30 Closing Featured Speaker Introduction
Jonathan Sheldon, Ph.D., Global Senior Director, Translational Medicine, Oracle Health Sciences
3:40 Closing Featured Speaker:
GeneStack — Universal Platform for Genomics Application Development
Misha Kapushesky, CEO GeneStack Ltd.
4:00 Conference Adjourns
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