Reporter: Aviva Lev-Ari, PhD, RN
Track 5
Next-Gen Sequencing Informatics
NGS, Genome-Scale Screening, and HTP Proteomics
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.
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
»»4:15 PLENARY KEYNOTE
Do Network Pharmacologists Need Robot Chemists?
Andrew L. Hopkins, DPhil, FRSC, FSB, Division of Biological Chemistry
and Drug Design, College of Life Sciences, University of Dundee
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 ® and Amazon are not sponsors or participants 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
»»8:15 PLENARY KEYNOTE
Atul Butte, M.D., Ph.D., Division Chief and Associate Professor,
Stanford University School of Medicine; Director, Center for Pediatric
Bioinformatics, Lucile Packard Children’s Hospital; Co-founder,
Personalis and Numedii
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 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., IST/High Performance & Research Computing,
University of Medicine & Dentistry of New Jersey (UMDNJ)
Sponsored by
Sponsored by
Sponsored by
Bio-ITWorldExpo.com 18
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
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 Sponsored Presentations (Opportunities 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
»»Plenary Keynote Panel
11:05 The Life Sciences CIO Panel
Panelists:
Remy Evard, CIO, Novartis Institutes for BioMedical Research
Martin Leach, Ph.D., Vice President, R&D IT, Biogen Idec
Andrea T. Norris, Director, Center for Information Technology (CIT)
and Chief Information Officer, NIH
Gunaretnam (Guna) Rajagopal, Ph.D., VP & CIO – R&D IT, Research,
Bioinformatics & External Innovation, Janssen Pharmaceuticals
Cris Ross, Chief Information Officer, Mayo Clinic
Matthew Trunnell, CIO, Broad Institute of MIT and Harvard
Sponsored by
Sponsored by
Sponsored by
19 Bio-ITWorldExpo.com
12:15 Luncheon in the Exhibit Hall with Poster Viewing
Panel Session: Building the IT Archetecture of the New York
Genome Center
2:00 Panel Session: Building the IT Architecture of the New York
Genome Center
Moderator: Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
Christopher Dwan, Acting Senior Vice President, IT, New York
Genome Center
Kevin Shianna, Senior Vice President, Sequencing Operations, New York
Genome Center
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 Nancy Kelley, 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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