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Next-Gen Sequencing Informatics 

Final Agenda

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 LeachMartin Leach, Ph.D., CIO, Broad Institute of MIT and Harvard

Jill MesirovJill P. Mesirov, Ph.D., Associate Director and Chief Informatics Officer; Director, Computational Biology and Bioinformatics, Broad Institute of MIT and Harvard



Hitachi Data Systems5:00 - 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 PerakslisEric 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

Cycle Computing small9:45 Coffee Break in the Exhibit Hall with Poster Viewing



Organizational Approaches to NGS Informatics 

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

Complete Genomics - small logo12:00 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.

Omixon logo small12:15 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.

Life_Technologies 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

Panelists:

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

Quantum 125px2:45 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. 

gd3:00 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



Cloud Computing & Collaborative Technologies 

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.

Illumnia logo4:45 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


Translating Genomic Data and Research into Clinical Practice 

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

Data Direct Networks9:45 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.

Ingenuity10:00 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


Sequencing Data Analysis and Applications 

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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