Exploring Next Generation Sequencing - Day 2

TUESDAY, SEPTEMBER 22, 2009

Sponsored by
7:30am Breakfast Presentation   

Validation of Genome-Wide Expression Screens with the NanoString nCounter Platform
Sean Ferree, Ph.D., Research & Development Manager, NanoString Technologies, Inc.
Digital expression profiling on Next Generation Sequencers generates vast amounts of data across the entire transcriptome, but at the cost of a laborious and expensive workflow.   The nCounter Analysis System is the ideal companion technology for the focused validation of whole-genome expression screens.  In this seminar we will discuss the benefits of the nCounter System including digital readout, sensitivity, multiplexing power, relative low cost and ease of use.  Finally, data will be presented to show the system’s flexibility and robustness in measuring a variety of input materials including formalin fixed, paraffin embedded tissues (FFPE) and cell or blood lysates.

8:15-9:15 Successful Sequencing Discussion Groups

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

Table 1: Sequencing Applications for the Illumina Genome Analyzer II
Host: Iwanka Kozarewa, Ph.D., Sequencing Technology Development, Wellcome Trust Sanger Institute
This discussion will be focused on recently developed applications of the Illumina NGS sequencing and on troubleshooting protocols for these applications. Discussion topics include:

• Amplification-free sequencing
• Multiplexing
• Targeted sequencing
• Metagenomics
• High-throughput insertion sites sequencing

Table 2: SNP Discovery, Analysis and Confirmation Using Next-Gen Sequence Data
Hosts: Tom Schwei, General Manager, DNASTAR
Schuyler Baldwin, Senior Software Engineer, DNASTAR

• Tools for sorting through large volumes of data
• Determining significance – what information is needed?
• False positives vs. false negatives – what is my preference?

Table 3:  Considerations for Experimental Design of Targeted Resequencing Studies
Host:  Jeremy Lambert, Product Manager, Raindance Technologies
Discussion to include:

• Understanding coverage models and sequencing requirements
• Resequencing of Pooled Genomic DNA Samples for Population Genetics Studies
• Data standards
• Clinical resequencing
• Impact of third generation sequencing platforms

Table 4:  mRNA-seq - Can We Really Still Call It "Gene Expression"?
Host:  Mike Levivelt, Ph.D., VP, Genomics, Partek, Inc.

• Does alignment impact mRNA-seq?
• Are we measuring genes or transcripts?
• What do you do with the stuff that doesn't align?

Table 5:  High-throughput Sequencing for Microbiome Studies
Host: Rob Knight, Ph.D., Assistant Professor, Chemistry/Biochemistry, University of Colorado at Boulder

• Read length vs. depth of coverage:  What's enough for what types of study?
• Which techniques are appropriatefor clustering community data?

Table 6: Understanding and Working in Color Space
Host: Michael Zody, M.SC., Chief Technologist, Broad Institute; Uppsala University
Discussion will be focused on:

• How 2-base encoding works
• Advantages and disadvantages
• Aligning, data correction and converting to base space

Table 7: Sequencing Library Preparation: Garbage In, Garbage Out?
Host: Nicholas Caruccio, Ph.D., Director of Marketing Development, EPICENTRE Biotechnologies
Discussion will be focused on:

• Quality and quantity of starting material
• Library recovery and quantitation
• Assessment of library quantities

Table 8: Sequence Data Management and The Cloud: The Road to Discovery
Host:  Ron Ranauro, CEO, GenomeQuest, Inc.
Bioinformatics managers need to move sequence data between a number of third party and open source tools. Discussion points include:

• What is the best strategy for accomplishing these goals?
• How does this strategy change if the IT resources are buried in the cloud?
• What are the IT challenges of sharing sequence data across an organization?
• What is the strategic value of a sequence data management platform approach?

Table 9:  Why Not Use NGS More Frequently?

Host: Heather Koshinsky, Ph.D., CSO, Eureka Genomics

Discussion points include:

• Acquisition costs (hardware, reagents, training)
• Quality of data & available bioinformatics software
• Characteristics of the ideal NGS sevice provider
• Availability of sequence generation and/or bioinformatics service providers

Table 10:   NGS Five Years Down The Road
Host:  Gulu Kamalakar, GenomeQuest, Inc.
In five years time NGS will have gone from "sexy new technology" to "established and mainstream". The price of sequencing and analysis will come down, the complexity and volume will go up. What will remain from our efforts today, and what will NGS analysis look like?

NGS INSIGHTS, STRATEGIES AND SOLUTIONS

9:30 Chairperson’s Remarks

9:40 Three Keys to a Successful Launch of a Next-Generation Sequencing Platform

Joseph Boland, M.S., Manager, Dedicated Science Operations, Core Genotyping Facility, NIH/NCI

Within the Core Genotyping Facility, my team has successfully integrated a next generation sequencing platform into our laboratory’s service offerings. Looking back on the planning and installation of the system, three simple keys led to the successful launch of our next generation sequencing offering. The keys range from proper upfront planning (ask the right questions: lab space, sample flow, quality review, etc.) and established data storage and transfer (having an established data pipeline will ease the strain on the lab to deliver data), to having have a comprehensive sample quantitation protocol in place (allowing for maximum recovery of samples per study). While our success centers on a single next-generation platform, I feel these three simple keys are applicable across platform and laboratory.

Sponsored by
10:10 Technology Presentation:

The Power to Detect: HybSelect™
for Targeted Sequence Capture

Michelle Lyles, Ph.D., Vice President of Marketing and Sales, febit inc.

The proliferation of NGS platforms has increased DNA sequencing throughput by orders of magnitude, however, it still takes months and several hundreds of thousands of dollars to finish a typical mammalian-sized genome at a reasonable depth of coverage. Certain “high value” regions of the genome have been associated with certain disease states, phenotypic traits, or responses to drug treatment or other environmental stimuli. Targeted re-sequencing of genomes can identify variants faster and at a much lower cost than whole genomes sequencing. Genomic hot-spots ranging between tens and thousands of kilobases are excellent targets for HybSelect, a new automated microfluidic solution for sequence-specific capture from febit. Integrated HybSelect automation allows walk-away convenience and only requires 30 minutes of hands on time, offering the simplest targeted sequence capture method available.

10:25 Networking Coffee Break, Exhibit and Poster Viewing

11:15 Alternative, Amplification-Free, Method for Illumina Library Preparation and its Applications to Pathogen Sequencing

Iwanka Kozarewa, Ph.D., Research Fellow, Sequencing Technology Development, Wellcome Sanger Trust

The high yield achievable with the Illumina GAII system, (>30X coverage of P.falciparum genome from one flowcell lane), is very well suited for pathogen de novo sequencing or resequencing. However, this application is hindered by amplification artifacts, introduced during library preparation that cause a high number of duplicates and uneven coverage distribution across targeted sequencing reads. We developed an alternative, amplification-free method of library preparation that reduced the incidence of duplicate sequences, improved read mapping and single nucleotide polymorphism calling and allowed de novo P.falciparum assembly from short reads.

11:45 Building a Next-Generation Sequencing Core at NYULMC

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

NYU Langone Medical Center has had one year of experience implementing a Next-Generation Sequencing Core facility.

We have learned something about the planning, costs, time, and staff necessary to be successful with this technology. We have found it useful to merge Next-Gen sequencing with our existing Genomics (microarray) laboratory into a single Genome Technology Core to allow for cross-training of technicians and coordinated management. We have completed 20 runs of our Illumina GA II, and we are about to go live with Roche/454 sequencing. We have also learned something about data management, and data analysis. Some details of our ChIP-seq data analysis methods will be presented.

12:15pm Close of Session

Sponsored by
12:30 Luncheon Presentation
The Agilent Technologies SureSelect Target Enrichment System
Maithreyan Srinivasan, Ph.D., Senior Director, Genomics Research & Development, Agilent Technologies
Agilent launched the new SureSelect Target Enrichment Platform to enable researchers to focus on genomic regions of interest upfront of next-gen sequencing. SureSelect leverages Agilent’s ability to design and synthesize probes greater than 100bp through eArray, our online custom design application. In-solution and on-array methods are available to uniquely suit studies of any size, small to large. The custom in-solution method can efficiently capture up to 3.3 Mb genomic regions while Agilent’s Human Exome kit will capture ~38Mb.  Representative data for SureSelect products supporting the Illumina GA with Paired-End sequencing, Life Technologies SOLiD System and Human Exome capture will be presented. 

NEXT-NEXT GENERATION SEQUENCING

2:00 Chairperson’s Remarks

Abizar Lakdawalla, Ph.D. Sequencing Systems, Illumina

2:05 Developing High-Throughput and Low Cost DNA Sequencing Technologies

Peiming Zhang, Ph.D., Associate Research Professor, The Biodesign Institute at Arizona State University

We are developing a DNA sequencing technologies with high-throughput and low cost.  For DNA re-sequencing, we are developing a universal DNA nanoarray based platform, which is designed to contain all possible probes with a length of ≥ 16 nucleoside (416 10 ≈ 4.3 billion) in a 1 x 1 inch area.  For de novo DNA sequencing, we are developing a technology called sequencing by recognition.  This technology is based on electronically recognizing individual DNA bases by forming triplex complexes on the end of nanopores.  Reported will be the progress in fabrication of the universal DNA nanoarray using nanocontact printing, and on progress on the sequencing by recognition. 

2:30 Genome Sequencing by Natural DNA Synthesis

Xiaohua Huang, Ph.D., Professor, Bioengineering, University of California at San Diego

The new sequencing technology called natural DNA sequencing by synthesis will be presented. We will present the principle, theoretical basis and the results from Monte Carlo in silico simulations of the technology. We will also present the experimental results on the performance of the technology.

2:55 Solid-State Nanopores as Single-Molecule Hybridization Detectors for Genomic Sequencing

John Oliver, Ph.D., Vice President Reasearch, NABsys, Inc.

 
3:20 Networking Refreshment Break, Exhibit and Poster Viewing

4:00 Marrying Mass Spectometry with Nanopores for Single-Molecule DNA Sequencing
Derek Stein, Ph.D., Assistant Professor, Physics, Brown University
Nanopores are promising tools for DNA sequencing because they can compel the bases of individual molecules to translocate rapidly in single-file order.  However, a reliable method for directly discriminating each passing base has so far proved elusive.  In this talk, I will describe our strategy for single-molecule DNA sequencing strategy that aims to combine the benefits of nanopores with the speed, sensitivity, and robustness of molecular sensing by mass spectrometry.

4:25 Single Molecule DNA Sequencing using Nanopores and Optical Probes

Amit Meller, Ph.D., Department of Biomedical Engineering, Boston University

Presented will be the development of a third-generation single-molecule DNA sequencing method aimed at the “$1,000 genome” target set by the National Human Genome Research Institute at NIH. Our method involves two steps: 1) a highly parallel circular genome conversion to a binary format that facilitate high speed readout using nanopores, and 2) high throughput optical readout of the converted DNA by threading the biopolymers through an array of solid-state nanopore. Our method eliminates the need for enzymes during the readout stage, thus permitting a high speed readout. In this talk I will discuss our progress, and feasibility demonstration of our method.

4:50 Close of Day

Co-located Event:   Next-Generation Sequencing Data Analysis

For more information, please contact:
Mary Ann Brown
Executive Director, Conferences
Cambridge Healthtech Institute
Email: mabrown@healthtech.com
Phone: 781-972-5497

For exhibit and sponsorship information, please contact:
Angela Parsons
VP, Business Development
Cambridge Healthtech Institute
Email: aparsons@healthtech.com 
Phone: 781-972-5467