Beyond Sequencing - Day 2



7:30 am  Morning Coffee

8:15-9:15 Successful Sequencing Table Discussion Groups

Grab a cup of coffee and join a facilitated discussion group focused around specific sequencing themes. This unique session allows conference participants to exchange ideas, experiences, and develop future collaborations around a focused topic.

Concurrent Breakout Sessions


Downstream Data Analysis

9:30 Chairperson’s Remarks
Stuart Brown, Ph.D., Associate Professor, Center for Health Informatics & Bioinformatics, New York University School of Medicine

9:35 Relating Microbial Communities to Function: Insights from High-Throughput Sequencing

Rob Knight, Ph.D., Associate Professor, Chemistry & Biochemistry, University of Colorado, Boulder

High-throughput sequencing is providing high-resolution views of differences in microbial communities, yet relating these differences to different functional outcomes has been challenging. Here we report on methods for relating 16S rRNA and metagenomic data to differences in physiological state within and between individuals, and environmental samples, with particular emphasis on methods of identifying taxa and pathways responsible for those differences.

10:05 Assembly in the Metagenomics Era

Jason Miller, Ph.D., Software Engineering Manager, J. Craig Venter Institute

10:35 Networking Coffee Break, Poster Viewing in the Exhibit Hall

11:15 Analysis and Comparison of Very Large Metagenomes with Fast Clustering and Functional Annotation

Weizhong Li, Ph.D., Staff Scientist, Center for Research in Biological Systems, University of California, San Diego

The very large amount of available metagenomic data requires tremendous computational analyses. Fast sequence clustering algorithms combined with rapid metagenomics-specific annotation tools provide an effective way to analyze, annotate and compare metagenomes. Clustering can also improve the performance of metagenomic sequence assembly and gene prediction.

Sponsored by
Eureka Genomics
11:45 High Throughput Sequencing: Application Specific Data Analysis Pipelines for Metagenomics
Heather Koshinsky, Ph.D., CSO and Co-Founder, Eureka Genomics
High Throughput Sequencing (HTS) technologies, such as Illumina’s Genome Analyzer, produce gigabases of sequence data in a single run at a relatively low per-base cost. Significant limiting factors of HTS data generation include understanding the quality of this data, the steps where errors occur and the best applications specific data analysis pipelines to utilize. 

12:00 pm Close of Morning Session

12:15  Lunch on Your Own

Upstream Sequence Run

1:30 Chairperson’s Remarks
Joseph Boland, M.S., Dedicated Scientific Operations Leader, SAIC-Frederick, NCI

1:35 Covering All the Bases: Managing a Multi-Platform Sequencing Center

Paul Blainey, Ph.D., Postdoctoral Scholar, Bioengineering, Stanford University

Sequencing facilities operating multiple high throughput sequencing platforms can utilize the strengths of each technology to produce more efficient solutions and orthogonal validation for diverse applications. Managing sequencing projects from microbe to man requires extensive documentation of sequence data and metadata using a dedicated LIMS. A flexible and multi-faceted system combining sample documentation, run status, run statistics, data tracking and basic analysis tools allows integration of project efforts and facilitates communication between collaborators.

2:05 NGS of the Human Microbiome: A Spotlight on Bacterial and Viral Metagenomics

Joseph F. Petrosino, Ph.D., Assistant Professor, Department of Molecular Virology and Microbiology, Human Genome Sequencing Center, Baylor College of Medicine

2:35 Technology Presentation
(Sponsorship Opportunity Available)

2:50 Networking Refreshment Break and Last Chance for Poster and Exhibit Viewing

3:30 Virus First, Disease Next: Viral Discovery Using Metagenomics

Eric Delwart, Ph.D., Director, Molecular Virology, Blood Systems Research Institute; Professor, Laboratory Medicine, University of California, San Francisco

Using pyrosequencing we identified known and novel DNA and RNA viruses from human samples and commercial biologics. Sample preparation and random PCR amplifications method will be discussed. Viral metagenomics is resulting in the identification of many new human and animal viruses whose pathogenicity is not yet determined.

4:00 Sequencing of Single Microbial Cells

Tanja Woyke, Ph.D., Research Scientist, Department of Genome Sciences, Lawrence Berkeley National Laboratory/ DOE Joint Genome Institute

The majority of microorganisms on this planet elude culturing attempts, severely limiting access to their genomes. While various enrichment methods as well as metagenomic approaches have been applied successfully to aid the genome analysis of such non-cultivable environmental microbes, these methodologies are not suitable for countless community members of interest. Single cell genomics is a new approach, which aims to access the genome from an individual microbial cell.

4:30 Panel Discussion with Metagenomics Speakers

5:00 Close of Meeting


Upstream Sequence Run

9:30 Chairperson’s Remarks
Kevin Knudtson, Ph.D., Director, DNA Facility, University of Iowa

9:35 Sample Quality Control for Deep Sequencing: Pre-Sequencing Confirmation of Sample Quality and Identity

Andrew Brooks, Ph.D., Director, Bionomics Research & Technology, Rutgers University Cell and DNA Repository, RUCDR

The issues of sample quality have been raised to a new level given the cost and time associated with next generation sequencing applications. Qualitative analysis with respect to sample identity ensures that targeted sequencing results are commensurate with both clinical and meta data that are essential for comprehensive data analysis. We will discuss the adoption of a standardized platform for the quality control of DNA and RNA samples for next-generation sequencing applications.

10:05 Developing and Assessing Cost Effective Targeting Strategies in Cancer Genome Resequencing for Population Scale Clinical Studies and Diagnostic Applications

Hanlee Ji, M.D., Assistant Professor, Oncology, Stanford University

The advent of next-generation DNA sequencing technology allows us to identify diagnostic personalized DNA signatures for any individual’s tumor; however, clinical resequencing of cancer genomes requires additional development of cost effective and high quality strategies which yield high quality data. To reach this goal requires integrating novel molecular assays, next-generation DNA sequencing technology and infrastructure to readily capture clinical populations and their tumor samples.

10:35 Networking Coffee Break, Poster Viewing in the Exhibit Hall

11:15 Mutation Profiling in Human Cancer by Next-Generation Sequencing

David A. Wheeler, Ph.D., Co-Director of Bioinformatics of the Human Genome Sequencing Center, Baylor College of Medicine

Sponsored by
Complete Genomics
11:45 Generating Thousands of Complete Human Genome Sequences for Basic and Clinical Research

Steve Lincoln, Vice President, Scientific Applications, Complete Genomics, Inc.
Complete human genome sequencing is fast approaching a scale and a cost which will allow it be broadly applied to many biomedical research programs. In these data sets lie the keys to understanding the genetic basis of disease susceptibility and therapeutic response. While interpretive tools and IT infrastructures must keep evolving rapidly to deliver on this promise, tremendous progress has already been made in developing methods to provide high-quality actionable results from these enormous data sets. We will review this progress using current data from both normal and cancer genomes and discuss the new challenges these studies present. 

12:00 pm Close of Morning Session

12:15  Lunch on Your Own


Downstream Data Analysis

1:30 Chairperson’s Remarks
Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

1:35 Using Genomic and Transcriptomic Sequencing to Identify Recurrent Somatic Mutations in Non Hodgkin Lymphoma

Ryan Morin, Ph.D. Candidate, Computational Biologist, BC Genome Sciences Centre, BC Cancer Agency

Second-generation sequencing allows us to re-sequence the entire genome or transcriptome of a cancer enabling the rapid identification of somatic point mutations. Using a combination of these approaches, we have profiled numerous non Hodgkin lymphoma samples and have identified recurrent nonsynonymous mutations affecting multiple genes.

2:05 Mutation Discovery in Cancer using NGS and Probabilistic Models

Sohrab Shah, Ph.D., Post Doctoral Fellow, Molecular Oncology Breast Cancer Research Program, Centre for Translational and Applied Genomics, BC Cancer Agency

The capacity to discover mutations depends in large part on data processing and analytical techniques. Data from cancer genomes exhibit different statistical properties compared to normal genomes. This presentation will offer a statistical modeling framework for the discovery of single nucleotide variants from NGS data. Specific examples of applying this framework to the study of ovarian cancer and breast cancer subtypes will be presented.

Sponsored By:
2:35 Technology Presentation
Desktop Solutions for Next-Generation Sequence Assembly and Analysis:  from RNA-Seq to De novo Genome Assembly
Brian Anderson, Scientist, DNASTAR, Inc.
Next-gen sequencing technologies are utilized in a wide range of molecular biology applications: genome sequencing; gene expression analysis; epigenetic studies; and targeted gene analysis.  DNASTAR provides user-friendly desktop computer software with assembly and analysis tools for all important next-gen workflows.   We will discuss emerging uses of next-gen technologies and tools to support scientists in critical analytical areas. 

2:50 Networking Refreshment Break and
Last Chance for Poster and Exhibit Viewing

3:30 Investigating Prostate Tumor “Omes” With Next Generation Sequencing

Colin C. Collins, Ph.D., Senior Research Scientist, Vancouver Prostate Centre; Associate Adjunct Professor, Department of Urology, University of California, San Francisco

This presentation will discuss our experience analyzing the genomes, exomes, and transcriptomes of prostate tumors with next generation sequencing with the goal of identifying prognostic and predictive biomarkers as well as novel therapeutic targets. Special emphasis will be placed on obtaining and validating copy number data, fusion genes, and mutations, as well as on computational methods for extracting biologically and clinically relevant knowledge from tumor “omic” data.

4:00 Unraveling the Metastatic Process with Integrated Whole Genome Analysis

Timothy J. Triche, M.D., Ph.D., Pathologist-in-Chief, Childrens Hospital Los Angeles; Professor & Vice-Chair, USC Keck School of Medicine

Next-generation whole genome sequencing offers the opportunity to understand the evolution of cancer from a localized, treatment responsive primary tumor to a post-therapy, treatment-resistant, metastatic tumor. We have utilized Helicos single molecule sequencing to generate whole genome profiles of the constitutional genome, primary tumor, and metastasis of a Ewing sarcoma patient. The resultant integrated picture of the normal, primary, and metastatic genome provides numerous insights into the clonal evolution of the metastatic and chemotherapy resistant tumor phenotype.

4:30 Exome Capture Sequencing of Tumor/Normal Pairs
Steffen Durinck, Ph.D., Computational Biology Scientist, University of California, Berkeley, Lawrence Berkeley National Laboratory
Exome capture sequencing is an affordable and powerful method to study the transcribed regions of the genome.  This presentation will establish an analysis framework, computational challenges, and preliminary results of applying this methodology to study tumor/normal paired samples.

5:00 pm Close of Meeting

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