Cambridge Healthtech Institute’s Second Annual

Genomics & Sequencing Data Integration, Analysis and Visualization

Impact of Data Quality and Novel Bioinformatics Tools on Life Sciences Research and Clinical Decisions

February 19-20, 2015 | The InterContinental San Francisco | San Francisco, CA
Part of the 22nd International Molecular Medicine Tri-Conference


About this Symposium:

CHI's Second Annual Genomics & Sequencing Data Integration, Analysis and Visualization Symposium will present real-world cases on the impact of data quality, bioinformatics tools, and statistical analysis methods on life sciences research and clinical decisions using genomic data. The key is enabling researchers, scientists, and clinical data providers to derive insights and relationships in the big data sets from diverse groups and diverse origins to make better assessments, interpretations, and decisions. Thought leaders will discuss data quality, data type differences, who has the data, how is the data put together, what data is needed to address specific needs and unmet needs (e.g., research, drug discovery, diagnostics, clinical, patient health), and analytical strategies that demonstrate impact.

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Thursday, February 19

7:30 am Registration and Morning Coffee

Genome AND HEALTHCARE Big Data & Differing Perspectives: Trends, Challenges, OpportunitieS

9:00 Chairperson’s Opening Remarks

James Lyons-Weiler, Ph.D., Managing Director, Ebola Rapid Assay Development Consortium, Pittsburgh, PA

9:10 Trends in Genomic Data, Big Data Analytics, and Translational Informatics

Scott Kahn, Ph.D., Vice President, Commercial Enterprise Informatics, Illumina

As researchers switch their focus from single genome analysis to cohort-level genomic analysis, and with more comprehensive genomic characterization of each subject (eg, DNA, transcriptome, epigenome, microbiome, etc), the informatics challenges have moved into the realm of Big Data analytics. This presentation will put these trends into context and will provide a perspective on how these challenges are being met for addressing the needs of translational research.

9:40 Downstream Challenges in Whole Genome Sequencing for Clinical Studies

Nicholas J. Schork, Ph.D., Professor and Director, Human Biology, J. Craig Venter Institute

There are a number of challenges in the clinical use of WGS data, many of them occurring in the more ‘downstream’ interpretation and analysis aspects of sequence data. These challenges include accommodating global human genetic diversity, annotating variants, dealing with phase information, linking therapeutics to genomic alterations and creating reliable ‘filters’ that can pull out the most relevant variants in a particular patient’s genome. This talk describes these challenges, provides real-world examples of them and discusses approaches to overcoming them.

10:10 Accessing Human Genetic Variation in the Rising Era of Individual Genome Sequence

Ben Busby, Ph.D., Genomics Outreach Coordinator, NCBI, NIH

This presentation will describe how NCBI has enhanced several of its genomics resources in the last several months and how some of its public databases can be queried for computational biology and clinical questions. We are in the process of indexing the exons of over 1 million samples from over 800,000 individuals housed in the dbGaP database at every position in the human genome, as well as having expanded access to the raw data in several ways, and made variant data in these and our medical genomics databases widely accessible.

10:40 Coffee Break with Exhibit and Poster Viewing

11:15 Harnessing Clinical Data to Improve Care

Sorena Nadaf, Director, Translational and Biomedical Informatics; CIO, HDFCCC Translational Informatics, University of California San Francisco

11:45 Computational and -omic Stop Gaps in Policies that Thwart Advances in Translational and Individualized Medicine

James Lyons-Weiler, Ph.D., Managing Director, Ebola Rapid Assay Development Consortium, Pittsburgh, PA

The fundamental pieces are in place for an era of massive and rapid strides in biomarker-informed health care, and yet numerous –omic and computational-related policy stopgaps exist that must be, and can be, overcome by coordinated political, didactic actions. Specific examples that demonstrate flawed policies and practices will be shown. The role of government should be to protect people from undue harm from medical procedures, but it also should act to allow others to protect people from the harm of diseases and unnecessary treatments.

12:15 Session Break

MediSapiens12:25 Luncheon Presentation: Easy Large Scale Clinical and Genomics Dataset Integration, Management and Analysis with MediSapiens Explorer Platform

Ville Parviainen, Ph.D., Manager, Business Development, MediSapiens Ltd.

Next generation sequencing produces large amounts of genomics and descriptive data but causes data underuse and inefficiency due to problems in management and accessing of data. MediSapiens has developed a solution to answer these issues with MediSapiens Explorer Platform. Our flexible and scalable platform allows data management and integration in one system as well as development of customizable user interfaces and analysis tools to utilize that data in the same platform.

1:00 Session Break

Driving Data Integration and Analytics:
Dealing with Data Complexities

1:50 Chairperson’s Remarks

Michael Liebman, Ph.D., Managing Director, IPQ Analytics, LLC

2:00 From Drug Discovery to Patient Management: Dealing with the Data Complexities of the Real World

Michael Liebman, Ph.D., Managing Director, IPQ Analytics, LLC

Sabrina Molinaro, Ph.D., Head, Epidemiology, Institute of Clinical Physiology, National Research Council - CNR Italy

The real need to drive data integration and analytics resides not in the technologies of data generation and collection but rather in identifying the question that needs to be addressed and what data would be key to enable solving these questions. Two case studies will be presented, one impacting drug discovery through the analysis of co-morbidities and poly-pharmacy issues, the second dealing with patient management in a rare pediatric disease, pARDS.

2:30 Analytics of Functional Single Cell Data to Derive Insights into Drug MOA, Disease Profile, and Patient Stratification

Santosh Putta, Ph.D., Vice President, Computational Sciences, Nodality, Inc.

3:00 Refreshment Break with Exhibit and Poster Viewing

3:30 Finding a Needle in a Haystack: New Approaches to Identify the Single Disease-Causing Mutation in a Patient’s Genome Sequencing Data

Yuval Itan, Ph.D., M.Res., Postdoctoral Associate, Human Genetics of Infectious Diseases, The Rockefeller University

This presentation provides an insight into a new state-of-the-art gene-level metrics, tackling a crucial question in medicine genomics: how to identify the relevance of a mutated gene to a disease? We identified for the first time the accumulated mutational damage for each human gene and the biological distance between all human genes, and showed that both approaches are particularly powerful for the identification of disease genes in patients’ high-throughput data.

4:00 Pharmacogenomics Strategies in Precision Medicine

Dongliang Ge, Ph.D., Director, Bioinformatics, Gilead Sciences

4:30 Hardware and Software Infrastructure for Mining Big Metagenomic Datasets

Zhong Wang, Ph.D., Computational Biologist & Genome Analysis Group Lead, Lawrence Berkeley National Lab & DOE Joint Genome Institute; Adjunct Associate Professor, University of California at Merced

High throughput metagenome shotgun sequencing has evolved into a powerful tool for studying microbial communities consist of thousands of species that are difficult to culture. Analyzing metagenome data sets, however, poses great challenges computationally, both in hardware infrastructure and in software algorithms, as the datasets are large in volume (typically in terabase range) and complex in nature. This talk provides my personal experience in metagenome dataset analysis and our recent statistical framework to automatically predict single genomes from complex metagenomic datasets.

5:00 Close of Day

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Friday, February 20

8:00 am Morning Coffee

Large-Scale Data Analysis

8:25 Chairperson’s Remarks

Ben Busby, Ph.D., Genomics Outreach Coordinator, NCBI, NIH 

8:30 Large-Scale NGS data Analysis on Amazon Web Services Using Globus Genomic

Ravi Madduri, Fellow, Computation Institute, University of Chicago and Argonne National Lab

9:00 Genome Browser in a Box: Viewing Private Annotations and Custom Sequences Made Easy

Pauline Fujita, Ph.D., Training and Outreach Coordinator, UCSC Genome Browser

9:30 iReport: An Integrative “omics” Reporting and Visualisation Platform

Andrew Stubbs, Ph.D., Assistant Professor, Bioinformatics, Erasmus University Medical Center

Current tools in Galaxy lack the ability to summarise the results of an experiment on an individual sample basis, or across the whole experiment, from multi-platform “omics” results. We developed iReport, an integrative “omics” reporting and visualisation platform in Galaxy, used to deliver Genetic Test Reports, Fusion gene selection and immunodeficiency repertoire screening.

10:00 Talk to be Announced
Carlos D. Bustamante, Ph.D., Professor, Department of Genetics, Stanford University; Co-Founding Director, Stanford Center for Computational, Human, and Evolutionary Genomics; Director of Informatics, Stanford Center for Genomics and Personalized Medicine 

10:30 Coffee Break with Exhibit and Poster Viewing

11:00 Hadoop for Bioinformatics
Martin Gollery, CEO, Tahoe Informatics 



11:30 An Expert’s Guide through the Identity Landscape

Mollie Shields-Uehling, President and CEO, SAFE-BioPharma Association 

Identity trust is essential for secure Internet communications subject to regulatory requirements. The presentation overviews US and EU government and industry-driven identity management initiatives resulting in trusted industry/government and industry/industry communities of trust. Learn about types and levels of identity credentials (one serves as a single identity passport to the Internet), government and industry organizations involved in establishing industry trust infrastructures, applicable standards, governance models and approaches to cloud based identity management.

12:00 pm Using 1000 Human Genomes Project Data to Improve the Accuracy of Metagenomic Microbial Profiling

Jonathan Allen, Ph.D., Bioinformatics Scientist, Global Security Computing Applications, Lawrence Livermore National Laboratory

This presentation discusses the finding of microbial contaminants in the 1000 human genomes project and our assessment of the privacy implications for the human DNA inadvertently left in the human microbiome project data.

12:30 Close of Symposium

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 Precision for Medicine 


Silicon Biosystems 

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