Beyond Sequencing - Day 1


Beyond Sequencing returns to San Francisco, CA on June 21-22, 2011

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Purchasing your next-generation sequencing (NGS) platform(s) was a major decision. Now that you have purchased a platform, how do you maximize the greatest potential for your investment? Realizing this potential requires efficient workflow strategies, careful experimental design, comprehensive targeted enrichment technologies, data analysis, management, and integration, in addition to maintaining your platform and people management all at maximum production. The central theme at Cambridge Healthtech Institute’s Inaugural Beyond Sequencing: Strategies for Success is efficient utilization of your NGS platform. Sessions will focus on common bottlenecks, case studies, real-world experiences and solutions from experienced users.

TUESDAY, JUNE 22, 2010

7:30 am Main Conference Registration and Morning Coffee


8:45 Chairperson’s Remarks
George Grills, Ph.D., Director, Advanced Technology Assessment, Life Sciences Core Lab Center, Cornell University

8:55 Challenges Inherent in Designing and Analyzing Experiments Using NGS

Ghia Euskirchen, Ph.D., Director of the DNA Sequencing Program, Center for Genomics and Personalized Medicine, Stanford University School of Medicine

Next-generation sequencing continues to enable an incredible number of promising applications. Each application has unique nuances which necessitate special consideration in designing and analyzing experiments. From a project management perspective, the constant implementation of new workflows and platforms requires perpetual assessment of commercial options as well as development of in-house solutions. A number of case studies illustrating these challenges will be presented.

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Sponsored by
9:25 Technology Presentation
A Novel Web 2.0 Solution to Address the NGS Data Analysis Bottleneck

Andreas Sundquist, Ph.D., CEO, DNAnexus
DNA sequencing output has completely outstripped the pace of Moore's law, making a data analysis bottleneck inevitable. At the same time, sequencing costs have plummeted, bringing large-scale sequencing projects within the grasp of more institutions. New, easily accessible informatics solutions are needed to enable researchers to fully harness the advancements in DNA sequencing technology for practical use. DNAnexus will present an integrated, web-based sequence analysis platform powered by cloud computing that removes the data analysis bottleneck from next-generation sequencing.

Sponsored by
9:40 Technology Presentation
Closing the Gap in Time from Raw Data to Real Science - Science as a Service (ScaaS)
Justin H. Johnson, Director of Bioinformatics, Edge Bio
Next generation sequencing has drastically changed the traditional infrastructure within the sequencing community.  There are several technologies that show promise, but it is not always intuitive where to start. This uncertainty is compounded by the fact that commonly used bioinformatics tools are difficult to build and maintain as well as require vast amounts of compute resources.  Many solutions and platforms, such as cloud computing, offer promises that address one or a small number of these challenges, but the inherent challenges with these are rarely discussed. Edge Bio will present information, research and case studies on how they facilitate Science as a Service (ScaaS) to the community through a technology agnostic approach, taking each individual project from conception and design through informatics and analysis.


9:55 Networking Coffee Break, Poster and Exhibit Viewing


10:45 Striking a Balance between Sequence Production and Sequence Management

William Farmerie, Ph.D., Associate Director, Interdisciplinary Center for Biotechnology Research, University of Florida

DNA sequencing technology is rapidly evolving toward increased productivity at lower cost. These two factors combined with recently developed applications drives higher demand for DNA sequence acquisition. Keeping our capacity for sequence data management in balance with sequence production is both a concern and a dynamic challenge for facility managers. We combine commercial products with locally-derived solutions by recognizing that each approach has strengths and benefits.

11:15 Next-Generation Sequencing at the FDA Center for Food Safety and Applied Nutrition: A First Year Assessment

Marc Allard, Ph.D., Research Microbiologist, Center for Food Safety and Applied Nutrition, FDA

This presentation will explore the process of setting up a next-generation sequencing laboratory, including both the laboratory instrumentation and meaningful data analysis. The milestones for this project include: the ability to provide all of the data generated from analysis of Salmonella enterica genomes of 116 foodborne pathogen cultures coming from isolates from the worst foodborne outbreaks over the last 20 years within the USA. We have also developed software that allows us to compare complete genomes of hundreds of taxa at a time, and the software outputs all the gene alignments and SNPs present in each Salmonella genome compared.

11:45 Close of Session


Applied Biosystems logo12:00 pm Luncheon Presentation
The $6,000 Genome and Beyond
Michael Rhodes, Ph.D.,  Product Applications Senior Manager, Applied Biosystems, Inc.
The amazing growth in the capabilities of Sequencing Platforms has outstripped Moores law over the past few years, both in terms of increases in throughput and decreases in cost of sequencing. Life Technologies is the world’s leading sequencing company and has a complete portfolio of sequencing solutions from a single capillary machine through to ultra high throughput sequencing, with single molecule solutions available soon.
This growth in throughput and range of solutions has made the decision on what solution to select challenging. With the ability to easily generate enormous volumes of data the challenges have moved to workflow and data analysis. The intellectual challenge becomes the process of designing and constructing libraries so that the desired information is sequenced and then extracting that data from the resultant sequences.
In this talk, various technologies will be presented, including the SOLiD™ system and Single Molecule Sequencing. The SOLiD 4 system generates up to 100 gigabases of mapped data in a single run, some of the applications successfully carried out on the SOLiD system include:
Complete cancer genome re-sequencing, single cell transcriptome analysis, Methylation and de Novo sequencing.  The latest applications will be presented including results and data analysis and automation solutions.
The SOLiD instrument is For Research Use Only, and is not intended for any animal or human therapeutic or diagnostic use.




2:00 Chairperson’s Remarks
Lisa White, Ph.D., Director, Microarray Core Facility, Baylor College of Medicine


Statistical Challenges in mRNA-Seq

Sandrine DudoitSandrine Dudoit, Ph.D., Associate Professor of Biostatistics and Statistics; Chair, Graduate Group in Biostatistics, University of California, Berkeley

This talk concerns statistical methods and software for the analysis of high-throughput transcriptome sequencing (mRNA-Seq) data. We will report on our investigation of several mRNA-Seq datasets in organisms from yeast to human. Additionally, we will address the process of deriving accurate measures of (differential) expression for genomic regions of interest (ROI) such as individual exons or multiple isoforms of a given gene. 


2:45 Defining Genome Sequences and Their Quality in an Ever-Changing Sequencing Technology Landscape

Patrick Chain, Ph.D., Scientist IV and Team Leader, NGS & Metagenomic Applications, Genome Science Group, Bioscience Division, Los Alamos National Laboratory

With an array of rapidly-adopted ultra-high throughput sequencing technologies, there also has been a wider array of genome sequencing “products.” For example, while prior efforts to obtain genome sequences required international efforts and collaborations among the world’s most productive genome institutes, now even small centers produce sufficient data of a novel genome to perform targeted analyses. To continue to make the most of available sequence information, we propose a graded approach to characterizing genome sequences.

3:15 An NGS Data Management and Analysis Pipeline for Studying Genetic Diversity in Maize

Qi Sun, Ph.D., Co-Director, Computational Biology Service Unit, Life Sciences Core Laboratories, Cornell University

In this study, we used the Illumina platform to sequence a large collection of maize inbred lines as well as a mapping population.  A pipeline of data management, analysis and visualization tools was created for the maize project. We are developing a distributable software package with a web user interface so that this pipeline can be applied to other population studies.

3:45 Networking Refreshment Break, Poster and Exhibit Viewing

4:15 Next-Generation Infrastructure

David Dooling, Ph.D., Assistant Director, Genome Center, Washington University

Analyzing vast amounts of human cancer sequence data from dozens of sequencing instruments requires researchers to devote thought and money to issues like software engineering and storage architecture, issues which researchers have traditionally handled “behind the scenes.” This talk will compare and contrast software frameworks and hardware infrastructures, including cloud computing, currently being evaluated for next-generation sequence data analysis applications like cancer and metagenomics.

4:45 Building a Genome Sequencing Center: Managing and Mining Two Years of NGS Data

Stuart Brown, Ph.D., Associate Professor, Center for Health Informatics & Bioinformatics, New York University School of Medicine

NYU has created a Genome Sequencing Center which has operated an illumina GAII for a bit less than two years and a 454 GS-FLX for about 6 months. We have created and modified our data management and data analysis workflows several times to cope with vendor upgrades while providing rapid access to processed data for our clients/investigators. We have participated in a number of projects including ChIP-seq, cancer transcriptome mutation screening, micro-RNA discovery, and de novo assembly of microbial genomes.

Click here to download podcast

5:15 Buyer Beware:  Limitations of Whole-Exome Sequencing Capture Methods and the Search for Rare, Mendelian Variants

Kevin Jacobs, Ph.D., Director, Scientific Operations and Bioinformatics, SAIC-Frederick, Inc. and Core Genotyping Facility, Division of Cancer Epidemiology and Genetics, National Cancer Institute

New technologies such as ‘whole’-exome sequencing capture methods have led to renewed excitement about discovering rare, Mendelian, high-risk susceptibility gene variants in humans. To assess the currently available sequence capture approaches with respect to coverage across the exome, we evaluated the content and the empirical performance of the currently-available ‘whole’-exome sequence capture methods [NimbleGen Sequence Capture 2.1M Human Exome Array; Agilent SureSelect Human All Exon Kit] on three sequencing platforms [454 FLX Ti (4 runs); ABI SOLiD (1 quadrant); Illumina GA II (2 lanes)]. The protein coding sequences (CDS) reported in the RefSeq database (build 36.3) served as the gold standard for our assessment. NimbleGen capture probes target 77% of CDS bases and Agilent capture probes target 83% of CDS bases. We observed 21.5 Mbps (65%), 25.0 Mbps (76%) and 23.4 Mbps (71%) of the 33.0 Mbps of CDS with ≥8x sequence depth for Nimblegen/454, Agilent/SOLiD, and Agilent/Illumina, respectively. Since identification of rare gene variants requires high per-gene coverage, we also computed the proportion of genes with >90% of CDS bases covered with ≥8X sequence depth. Only 42%, 55%, and 45% of genes were covered by Nimblegen/454, Agilent/SOLiD, and Agilent/Illumina, respectively. Since coverage across the gene CDS is incomplete, failure to identify a causal mutation should be interpreted cautiously.  It is notable that many characterized genes are not included in this first generation whole-exome capture products and that only 40-50% of genes are well covered across all known exons with the amount of sequencing performed. Our results underscore the limitations of current ‘whole’-exome capture products and have important implications for designing studies in families and unrelated populations.  In spite of the limitations, these products may still be useful to screen for disease variants within exons that are satisfactorily covered.  The design of future ‘whole’-exome capture products will likely be more expansive and performance will likely improve; however, careful attention must be paid to coverage in practice.

5:45 Networking Reception in the Exhibit Hall

7:00 pm Close of Day


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