Track 5 is dedicated to advances in analysis and interpretation of next-gen sequencing data. Topics to be covered include analysis of sequence variants related to cancer research from NGS data, instruments facilitating a cloud approach for NGS, analysis tools and workflows, network biology/network medicine, and NGS standardization and performance testing.
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TUESDAY, APRIL 29
7:00 am Workshop Registration and Morning Coffee
8:00 - 11:30 Recommended Morning Pre-Conference Workshops*
Analyzing NGS Data in Galaxy
12:30 - 4:00 pm Recommended Afternoon Pre-Conference Workshops*
Running a Local Galaxy Instance
*Separate Registration Required. Click here for detailed information.
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 PLENARY KEYNOTE SESSION
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5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing
iPad® mini & Bose® QuietComfort 15 Noise Cancelling Headphones Raffle! Drawing held at 6:30pm!*
*Apple® & Bose® are not sponsors or participants in this program.
WEDNESDAY, APRIL 30
7:00 am Registration Open and Morning Coffee
8:00 Chairperson's Opening Remarks
Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute
8:05 PLENARY KEYNOTE SESSION
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9:00 Benjamin Franklin Award & Laureate Presentation
9:30 Best Practices Awards Program
9:45 Coffee Break in the Exhibit Hall with Poster Viewing
10:50 Chairperson's Remarks
Narges Baniasadi, Ph.D., Founder & CEO, Bina Technologies, Inc.
11:00 Global Next-Generation Sequencing Informatics Markets: Inflated Expectations in an Emerging Market
Greg Caressi, Senior Vice President, Healthcare and Life Sciences, Frost & Sullivan
This presentation evaluates the global next-generation sequencing (NGS) informatics markets from 2012 to 2018. Learn key market drivers and restraints, key highlights for many of the leading NGS informatics services providers and vendors, revenue forecasts, and the important trends and predictions that affect market growth.
11:30 High-Performance Databases to Manage and Analyze NGS Data
Joseph Szustakowski, Ph.D., Head, Bioinformatics, Biomarker Development, Novartis Institutes for Biomedical Research
The size, scale, and complexity of NGS data sets call for new data management and analysis strategies. High-performance database systems combine the advantages of both established and cutting edge technologies. We are using high performance database systems to manage and analyze NGS, clinical, pathway, and phenotypic data with great success. We will describe our approach and concrete success stories that demonstrate its efficiency and effectiveness.
12:00 pm Sponsored Presentation (Opportunity Available)
12:15 Next Generation Sequencing: Workflow
Overview from a High-Performance Computing Point of View
Carlos P. Sosa, Ph.D., Applications Engineer, Chemistry and Life Sciences Segment Manager, Cray, Inc.
Next Generation Sequencing (NGS) allows for the analysis of genetic material with unprecedented speed and efficiency. NGS increasingly shifts the burden from chemistry done in a laboratory to a string manipulation problem, well suited to High- Performance Computing. We explore the impact of the NGS workflow in the design of IT infrastructures. We also present Cray’s most recent solutions for NGS workflow.
12:30 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own
1:50 Chairperson's Remarks
1:55 High-Performance de novo Transcript Reconstruction Leveraging Distributed Memory and Massive Parallelization
Brian Haas, Senior Computational Biologist, Broad Institute
Exemplifying collaborative software development between industry and academia to tackle computational challenges in manipulating large volumes of next-gen sequence data, leveraging advances in algorithm development and compute hardware, we describe our efforts to optimize the performance of the Trinity RNA-Seq de novo assembly software. We explore a massively parallel computing architecture to tackle more efficient assembly of RNA-Seq data in the context of the Trinity assembly workflow.
2:25 'Titan' Supercomputer Helps Identify Pathogenic Bacteria in the Human Microbiome for Biosurveillance
Tae-Hyuk Ahn, Ph.D., Research Associate, Computer Science and Mathematics Division, Oak Ridge National Laboratory
This talk will present a new algorithm, SIGMA (http://sigma.omicsbio.org), for metagenomic biosurveillance. SIGMA has the unique capability of identifying the correct strain of a pathogen in a complex metagenomic background from many closely related candidates in the reference genome database. Using a top open-science supercomputer, Titan, pathogenic bacteria strains can be identified in an hour from the 100 million human microbiome sequences.
2:55 Sponsored Presentations (Opportunities Available)
3:25 Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 Multitier Infrastructure for NGS Data Computing and Management
Xiang Yao, Ph.D., Principal Scientist, Translational Informatics, the Janssen Pharmaceutical Companies of Johnson & Johnson
Pipelines having all NGS functions have provided us conveniences. But this bundling approach is inefficient in addressing different needs of the users ranging from IT professionals to biologists, and is difficult for frequent software and hardware upgrades. This talk describes a multitier infrastructure that is modular and interconnected, to accommodate different computing, storage and access needs of the users, and to maximize return on investments.
4:30 Integrated Tools for NGS Bioinformatics: Detection Pipeline, Assembly Pipeline, Metagenomic Discovery Tools, Sequence Toolbox and More
Raja Mazumder, Ph.D., Associate Professor, Biochemistry and Molecular Biology, The George Washington University
HIVE (High-Performance Integrated Virtual Environment: hive.biochemistry.gwu.edu) is an implementation of a multicomponent cloud infrastructure where distributed storage and computational powerhouse are linked seamlessly to provide a secure Big Data analysis platform. Development of HIVE-based pipelines for NGS analytics has been the focus of collaborative efforts by FDA and GWU research groups.
5:00 Sponsored Presentations (Opportunities Available)
5:30 - 6:30 Best of Show Awards Reception in the Exhibit Hall
THURSDAY, MAY 1
7:15 am Registration Open
7:15 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee
8:30 Chairperson’s Opening Remarks
Kevin Davies, Ph.D., Vice President Business Development & Publisher C&EN, American Chemical Society; Founding Editor, Bio-IT World
8:35 PLENARY KEYNOTE SESSION
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10:00 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced
10:30 Chairperson's Opening Remarks
10:35 Implementations of Cloud-Based Pipelines for Large-Scale DNA-Seq and RNA-Seq Data Analyses
Shanrong Zhao, Ph.D., Senior Scientist, Informatics, Johnson & Johnson
Due to reduced sequencing costs, more NGS data are produced by small research groups. Data storage and CPU resources required for large-scale whole-genome sequencing and RNA-Seq data analyses are too large for many individual laboratories to provide. To meet these challenges, we developed Rainbow and Stormbow: cloud-based software packages for large-scale DNA-Seq and RNA-Seq analyses.
10:55 Analyzing DNA-Seq Data Using DRAW: Lessons Learned from Using Amazon EC2 for Next-Generation Sequencing Studies
Li-San Wang, Ph.D., Assistant Professor, Pathology and Laboratory Medicine, University of Pennsylvania
DNA-Seq studies pose enormous challenges to many researchers who have limited access to dedicated IT support or high-performance computing. Cloud computing is a promising solution to address these needs. This talk covers our experience using the DNA Resequencing Analysis Workflow (DRAW) software to process >800 samples and our strategy to use Amazon EC2 effectively for DNA-Seq analysis.
11:15 Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs
Ravi K. Madduri, Fellow, Computation Institute, University of Chicago; Project Manager, Mathematics and Computer Science Division, Argonne National Laboratory
We describe the Globus Genomics platform. Globus Genomics provides an integrated platform for end-to-end data management using Globus Online and scalable analysis using the Galaxy framework and Amazon Web Services. We will walk through case studies of researchers and core labs at various universities that are leveraging the service to meet their rapidly growing genomics analysis needs.
11:35 Technology Advancements in High Density Compute and Storage that Power the Next Generation of Cloud Infrastructure
Brian Corn, Vice President, Marketing, Thinkmate
Thinkmate solutions accelerate discovery while reducing TCO, expanding scalability and enabling business continuity. Exciting new solutions from names like Intel, Supermicro, and Western Digital will be covered. This presentation is a “must see” for any attendees involved in hardware infrastructure design, testing, and procurement.
12:05 pm Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own
1:15 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing
1:55 Chairperson's Remarks
2:00 Characterization and Benchmarking of NGS Workflow Methods on Various Platform Architectures
Anthony Costa, Ph.D., Computational Scientist, Scientific Computing, Mount Sinai School of Medicine
We target numerically expensive pieces of the Next-Generation Sequencing (NGS) pipeline and investigate performance of many codes against a variety of CPU architectures and file systems. We further compare more recent methods implemented on non-traditional or heterogeneous architectures such as GPUs. The quality of the results from each method is also considered.
2:30 Avoiding Nonsense Results in your NGS Variant Studies
James Lyons-Weiler, Ph.D., Senior Research Scientist & Scientific Director, Bioinformatics Analysis Core, University of Pittsburgh
This talk presents an information-theory based paradigm that allows the objective performance comparison of pipeline components such as variant callers, study designs, read filters, and mapping algorithms. Our method solves the problem of concordance, increasing agreement among methods in one case from 32% to 86%. The evaluation methods I will present generalize to provide advanced quality control over sample prep protocols and will be useful for comparing sequencing platforms.
3:00 Bridger: A New Framework for de novo Transcriptome Assembly Using RNA-Seq Data
Guojun Li, Ph.D., Senior Research Scientist, Biochemistry and Molecular Biology, The University of Georgia
Full-length transcriptome assembly is highly challenging and not a well-solved problem. The most important broad impact of the study will be that our new capability for transcriptome assembly will lead to a new level of understanding about the detailed mechanism of alternative splicing in eukaryotic genomes, hence facilitating new studies of transcriptional mechanism. This talk presents a new de novo assembler Bridger that takes advantage of techniques employed in the reference based assembler Cufflinks to overcome limitations of the existing de novo assemblers.
3:30 Analysis of Transgene Sequence and Integration Site in the CHO Genome by Next-Generation Sequencing and Use to Improve Expression
Nic Mermod, Ph.D., Professor and Director, Institute of Biotechnology, University of Lausanne
This talk presents information on how to validate protein-expressing cell lines taking an NGS approach. We have sequenced the genomes of several CHO cell clones producing therapeutic proteins and compared them to the parental genome sequence. This yielded information on the transgene sequence integrity as well as on the genomic integration locus and sequence. In turn, this gave information on the molecular mechanisms allowing the genomic integration of the vector and provided approaches to further optimize transgene integration and expression from transiently or stably engineered CHO cells.
4:00 Conference Adjourns
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