Track 5 is dedicated to advances in analysis and intepretation of next-gen data. Topics to be covered include analysis of sequence variants related to cancer research from NGS data, instruments facilitate a cloud approach for NGS, analysis tools and workflows, and network biology/network medicine.

Final Agenda

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TUESDAY, APRIL 9

7:00 am Workshop Registration and Morning Coffee

8:00 Pre-Conference Workshops*

*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

Kevin Brode, Senior Director, Health & Life Sciences, Americas Hitachi Data Systems

5:00 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 iPads® or 1 of 2 Kindle Fires®!*

*Apple® is not a sponsor or participant in this program

WEDNESDAY, APRIL 10

7:00 am Registration and Morning Coffee

8:00 Chairperson’s Opening Remarks

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

8:05 Keynote Introduction

Sanjay Joshi, CTO, Life Sciences, EMC Isilon

8:55 Benjamin Franklin Award & Laureate Presentation

9:15 Best Practices Award Program

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

Best Practices for Genomic Data Interpretation & Analysis 

10:50 Chairperson’s Remarks

Steve Dickman, Founder & CEO, CBT Advisors, Inc. 

11:00 CLARITY Challenge

Shamil Sunyaev, Ph.D., Associate Professor, Division of Genetics, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School

11:30 HLA and KIR Typing from NGS Reads with Omixon Target

Attila Berces, Ph.D., CEO, Omixon

HLA is the most polymorphic region of the human genome with several segmental duplications and its analysis is a computational challenge. In this presentation I will show examples including validation studies of HLA typing from various sources of genomic data: whole genome, whole exome, targeted amplicon sequencing with Illumina, Ion Torrent and Roche sequencer.

11:45 Comparison of Genome Analysis Tools 

Jason Wang, Co-founder & CTO, Arpeggi, Inc.

A major impediment to clinical sequencing is the paucity of analysis standards and comparison metrics. We present our progress towards developing analysis standards, as well an open-access collaborative tool that enables anyone to define comparison metrics and compare tool performance. We hope that in making available this resource we can help fuel a community-driven solution for standardizing genome analysis pipelines.
 

12:00 Case Study: Sequencing Informatics System to Profile Genetic Changes in Tumors

Long Phi Le, M.D., Ph.D., Department of Pathology, Massachusetts General Hospital

This presentation will discuss the development of a sequencing informatics system to profile genetic changes in tumors that is in collaboration between PerkinElmer with Massachusetts General Hospital. This system, based on PerkinElmer’s Geospiza platforms, will allow genotype analysis to define key targets.

12:30 Luncheon Presentation: Ion Torrent Informatics Enables Semiconductor Sequencing

Darryl León , Ph.D., Associate Director, Product Management, Ion Torrent, Life Technologies

Data generated by the Ion Torrent Personal Genome Machine Sequencer or the Ion Torrent Proton Sequencer are analyzed by Torrent Suite Software.  An overview of the data analysis steps will be provided.  Torrent Suite offers a flexible plug-in system allowing software developers the ability to deliver custom analysis solutions using the compute resources associated with the local Torrent Server.  For researchers with need for either rich annotations or controlled data analysis, the Ion Reporter Software offers a streamlined data analysis and decision engine for use with amplicons, exomes, or genomes.

1:40 Chairperson’s Remarks

Jeffrey Rosenfeld, Ph.D., Assistant Professor of Medicine, IST/High Performance & Research Computing, New Jersey Medical School (UMDNJ)  

1:45 Data Intensive Academic Grid (DIAG): A Free Computational Cloud Infrastructure Designed for Bioinformatics Analysis

Anup Mahurkar, Executive Director, Software Engineering and IT, Institute for Genome Sciences, University of Maryland School of Medicine

We have deployed the NSF funded Data Intensive Academic Grid (DIAG), a free computational cloud designed to meet the analytical needs of the bioinformatics community. DIAG has 200+ registered users from 130 institutions worldwide who conduct large-scale genomics, transcriptomics, and metagenomics data analysis. Learn about the grid’s architecture, how to access this free resource, and success stories.

2:15 Performance Comparison of Variant Detection Tools for Next Generation Sequencing (NGS) Data: An Assessment Using a Pedigree-Based NGS Dataset and SNP Array

Ming Yi, Ph.D. IT Manager, Functional Genomic Group, Advanced Biomedical Computing Center, SAIC-Frederick at Frederick National Laboratory for Cancer Research (formerly National Cancer Institute)

There is an urgent need for the NGS community to be able to make the right choice out of a large collection of available SNP detection tools. Our methodology offers a great example of comparing SNP discovery tools and paving a way to expand such methods in more global scope for comparison.  

 2:45 Informatics in the Cloud  

Karan Bhatia, Ph.D., Solutions Architect, Amazon Web Services

Learn about how to easily create sophisticated, scalable, secure pipelines to accelerate life science research with Amazon Web Services. In this presentation, you will learn how to drive scale out, tightly coupled and Hadoop based workflows on Amazon EC2, a utility computing platform that provides a perfect fit for data management and collaboration. 

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing 

Gene Mapping & Expression 

3:45 InSilico DB Genomic Datasets Hub: An Efficient Starting Point for Managing and Analyzing Genomewide Studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor

David Weiss, Ph.D., CEO, InSilico Genomics

Alain Coletta, Ph.D., Co-Founder and CTO, InSilico Genomics

The InSilico DB platform is a powerful collaborative environment, with advanced capabilities for biocuration, datasets subsetting and combination, and datasets sharing. InSIlico DB solution architecture will be presented along with a live demo of the InSilico DB online platform. Learn how more than 1000 users from top academic and research institutions are using InSilico DB in their daily research.

4:15 Constructing a Comprehensive Map for Molecules Implicated in Obesity and Its Induced Disorders

Kamal Rawal, Ph.D., Faculty, Biotechnology and Bioinformatics, Jaypee Institute of Information Technology

We have constructed a comprehensive map of all the molecules (genes, proteins, and metabolites) reported to be implicated in obesity. This map paves the way to understanding the pathophysiology of obesity and identify drug targets and off-targets for existing drugs. This talk discusses the integrated approach we used in combining public resources, abstracts, and research articles to construct this map.

4:45 Quality Assurance: An Essential Step for Gene Expression Analysis Using Deep Sequencing

Dan Kearns, Director, Software Development, Maverix Biomics, Inc.
Dave Mandelkern, CEO & Co-Founder, Maverix Biomics, Inc.

With the advancement of deep sequencing technologies, researchers expect to obtain high quality results from their studies. However, this cannot be obtained solely by successful sequencing runs. Multiple data checks and pre-processing must be performed before downstream analysis. In this case study, we will present an automated quality assurance pipeline that helps improve gene expression analysis results.

5:00 DDN LS Appliance - Simple Platform for NGS Analysis, Data Distribution and Collaboration

Jose L. Alvarez, WW Director Life Sciences, DataDirect Networks

With this unique approach the DDN LS appliance can deliver flexible data ingest options, optimized data analysis resources, a policy based data tiering/archive solution and a geo-distributed secure collaboration platform. The appliance delivers 1.46X better performance on popular LS applications like Bowtie when compared to NFS based solutions. 

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes

THURSDAY, APRIL 11

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

Gene Mapping & Expression 

8:45 Chairperson’s Opening Remarks

Mathukumalli Vidyasagar, Ph.D., Cecil & Ida Green Chair in Systems Biology Science; Head, Bioengineering Department, University of Texas at Dallas

8:50 Network Biology and Personalized Medicine in Multiple Sclerosis

Mark Chance, Ph.D., Vice Dean for Research, Proteomics, Case Western Reserve University

Almost nothing is known about biological factors underlying the remarkable disease heterogeneity observed across multiple sclerosis (MS) patients, and there are no accurate biological predictors of disease severity that can be used for guiding clinical treatment options. Learn about the network biology methods we are using to analyze blood cell gene expression and understand good and poor responders to therapy.

9:20 GeneSeer: A Flexible, Easy-to-Use Tool to Aid Drug Discovery by Exploring Evolutionary Relationships between Genes across Genomes

Philip Cheung, Bioinformatics Group Leader, Scientific Computing, Dart Neuroscience

GeneSeer is a publicly available tool that leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as human. This talk describes GeneSeer’s underlying methods and the user-friendly interface.

9:50 Cloud Computing For Smart People

Dave Maples, Senior Vice President, Bright Computing

Smart people are turning to the cloud as a powerful option for pharmaceutical and life sciences computing. This presentation is about how to make the most of cloud computing without becoming IT experts or reallocating research time to manage cloud resources. Two scenarios will be offered: creating cloud-based servers on the fly, and extending on-premise servers into Amazon EC2.

10:05 Sponsored Presentation (Opportunity Available)

10:20 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

10:45 Plenary Keynote Panel Chairperson’s Remarks

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

10:50 Plenary Keynote Panel Introduction

Yury Rozenman, Head of BT for Life Sciences, BT Global Services

Niven R. Narain, President & CTO, Berg Pharma

12:15 Luncheon in the Exhibit Hall with Poster Viewing

 Panel Session: Building the IT Archetecture of the New York Genome Center 

2:00 Closing Featured Panel Session Introduction

Wanmei Ou, Senior Product Strategist, Oracle Health Sciences

2:10 Panel Session: Building the IT Architecture of the New York Genome Center

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

Chris Dwan, Acting Senior Vice President, Information Technology and Research Computing, New York Genome Center

Jim Harding, CTO, Sabey Corporation

Sanjay Joshi, CTO, Life Sciences, EMC Isilon Storage Division

Robert B. Darnell, M.D., Ph.D., President & Scientific Director, New York Genome Center

George Gosselin, CTO, Computer Design & Integration LLC

In 2011, a consortium of 11 major academic and medical organizations in and around New York announced the creation of the New York Genome Center (NYGC). Under the direction of Robert B. Darnell, the NYGC aspires to be a world-class genomics and medical research center, and is currently undergoing construction in the heart of Manhattan. NYGC management has the opportunity to design and create a state-of-the-art IT and data management infrastructure to handle, store and share the output from what will rapidly become one of the world’s foremost genome sequencing facilities. This series of talks will describe the thinking that went into the design, creation and construction of the NYGC’s IT infrastructure and entire data management strategy.

4:00 Conference Adjourns

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