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Tuesday, October 16
5:00-6:00pm Early Registration
Wednesday, October 17
7:30-8:30 am Registration, Morning Coffee
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Tech-nol-o-gy (tìk-nõl'o-jé) n., pl.-gies
the application of science, especially to industrial or commercial
objectives
Ex-po-si-tion (êk'spo-zîsh'on) n. a
discourse that conveys information about or explains a subject or
introduces the themes |
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TECHnology Platform EXPO
Explore available next generation screening
platforms as presented by sequencing leaders. An unparalleled
opportunity to compare and contrast these next generation
sequencing platforms to best suit your research needs.
8:25 Chairperson’s Opening Remarks
Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
8:35 Why Length Matters in Next Generation Sequencing
Michael Egholm, Ph.D., Vice President, R&D, 454 Life
Sciences, A Roche Company
The Genome Sequencer FLX developed by 454 Life Sciences, a Roche
business, continues to improve with increasing sequencing read lengths
soon to approach 500 base pairs, higher densities of sequencing reads,
and the ability to use unique identifications for sample pooling. These
improvements have allowed the GS FLX to be used in a wide variety of
applications from small RNA studies to full length de novo cDNA projects
to sequencing complex genomes to HIV mutation detection. An overview of
the technology and data from the above applications will be presented.
9:20 The SOLiD™ System : A Technology Enabling New
Applications
Michael D. Rhodes, Ph.D., Senior Applications Manager, High Throughput Discovery, Applied
Biosystems
The decreasing cost of sequencing is driving the development of genome-wide applications based on sequence data. Instead of needing different platforms for applications such as gene expression, genotyping and sequencing, it is becoming possible to use sequencing as the universal currency for most, if not all, genetic analysis. The SOLiD™ System is a ligation-based, massively parallel sequencing system that can currently generate in excess of 1 Gb of DNA sequence per run. Investigators can elect to use either fragment or mate-paired libraries and can run one or multiple samples at a time. We are taking advantage of the high throughput and system flexibility of the SOLiD™ system to collaborate with a number of scientific groups to develop a range of applications. An update on application development and examples of the data generated will be presented.
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9:50 Technology Spotlight
SGI Solutions for Life Sciences: Accelerating the Pace of Research
Deepak Thakkar, Ph.D., Bioscience Solutions Manager, SGI
SGI’s Life Sciences solutions have been developed to address major challenges faced by pharmaceutical, higher education and biotech organizations in areas such as data management, maximizing scientific productivity, matching computing needs to critical applications, data storage etc. Our targeted workflow driven solutions address these challenges by using industry leading computing and storage platforms including clusters, shared memory systems, scalable storage and FPGA solutions optimized for life sciences applications.
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Sponsored by
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10:05 Coffee Break, Poster and Exhibit Viewing
10:30 What Will It Take to Sequence The Human Genome
Error-Free, In Minutes, For Pennies?
Sadeg M. Faris, Ph.D., Founder, Chairman, and CEO, Reveo, Inc.
Astonishing advances have been made to reduce the time and cost of
sequencing an entire genome sequence by 10 orders of magnitude. What
will it take to reduce these parameters an additional 10+ orders of
magnitude to enable DNA sequencing for personal use? We will present a
disruptive instrument concept that uses physical (not chemical) methods
to interrogate entire chromosomes directly and non-destructively. The
success of this instrument relies on concepts borrowed from the
semiconductor, optics and micro- fabrication industries. In doing so
gives this instrument the potential to sequence an entire genome nearly
error-free, in minutes for pennies.
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10:50 Technology Spotlight
Droplet-Based Microfluidics: An Enabling Platform Technology for Next-Generation
Sequencing
John Leamon, Ph.D., Project Leader, Nucleic Acid Applications, RainDance Technologies,
Inc.
RainDance Technologies’ next-generation fluid handling platform is based on the use of micron-sized NanoReactor droplets to encapsulate samples for a wide range of molecular assays. Processing samples at the rate of up to 10,000 droplets per second, the Professional Laboratory System
(PLS) utilizes application-specific microfluidic chips to manipulate samples through a series of precisely controlled operations prior to analysis and sorting of each individual droplet. Droplets containing single DNA template molecules are amplified by 30 cycles of PCR in under fifteen minutes. The precise control provided by the PLS allows the design of microfluidic chips in which single DNA-capture beads are encapsulated in droplets providing a extremely robust and efficient automated amplification process for next-generation sequencing platforms. In this talk we will describe additional applications of the PLS including examples of NanoReactor chips designed to enable de-facto multiplex amplification of thousands of exons as well as examples of high-yield isothermal template amplification.
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Sponsored by
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11:05 Technology Spotlight
Next Generation Sequence Analysis with SLIM Search
Leonard N. Bloksberg, Ph.D., Cartesian Gridspeed Ltd
The genomics era is maturing with a vengeance and biologists are feeling the pain of the massive data overload required to even participate in modern biology. Sequence searching is a simple but fundamental process that consumes all the hardware you can afford and more. How have computational methods evolved and why can’t computers keep up any more? By evaluating the root functionality at the machine level we show that there are some useful approaches to sequence analysis which can address the need for massive speed and increased sensitivity. SLIM Search has been designed to work with high volumes of short read length sequences. Examples of how this new algorithm can enable modern biology will be discussed.
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Sponsored by
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11:20 Roundtable Discussion: Challenges and
Opportunities - Where are We Now?
Host: Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
Panelists:
Michael Egholm, Ph.D., Vice President, R&D, 454 Life Sciences, A Roche
Company
Samuel Levy, Ph.D., Senior Scientist, Human Genomic Medicine, J. Craig Venter
Institute
Michael D. Rhodes, Ph.D., Senior Applications Manager, High Throughput Discovery, Applied
Biosystems
Meredith Yeager, Ph.D., Scientific Director, Core Genotyping Facility, Advanced Technology Center, National Cancer Institute
12:00 pm Lunch on Your Own or
Luncheon Technology
Workshop (Sponsorship Available)
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Genome Resequencing for Mutation Screening
1:30 Chairperson’s Remarks
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1:35 Sequencing is Dead. Long Live Sequencing!
Kevin Ulmer, Ph.D., President & C.S.O., Genome Corp.
Despite the fact that the Sanger dideoxy terminator method has generated
>99% of all the world’s DNA sequence information over the past 30
years, there are now several would-be heirs to the throne jousting to
topple the reigning monarch. What characteristics of the ideal
sequencing method will determine The Once and Future King? Will the
kingdom now be divided among warring princes, or will a single
commercial platform ascend to dominate the next chapter in sequencing?
What lessons are to be learned from the history of sequencing
technology, and what does the crystal ball of one of the earliest
proponents of single-molecule sequencing predict for the future? |
2:20 Genetic Testing for Cancer Predisposition:
Opportunities Offered by Next Generation Sequencing
Alexander Gutin, Ph.D., Senior Vice President, Bioinformatics,
Myriad Genetics, Inc.
Three genes, MLH1, MSH2, and MSH6, implicated in predisposition to colon cancer have been resequenced in several patients using 454 and Sanger sequencing technologies. All detected sequence variants in all patients were consistent between the two technologies. We have analyzed sequence coverage needed to provide clinical quality mutation detection using 454 technology. In particular, we have demonstrated the capability of 454 technology to reliably detect mutations altering lengths of long homopolymer stretches.
2:50 Toward a Non-Coding RNA Revolution in the Cancer
Society
George A. Calin, M.D., Ph.D., Associate Professor,
Experimental Therapeutics & Cancer Genetics, University of Texas, MD
Anderson Cancer Center
Alterations in miRNA genes and other non-coding RNAs play a critical
role in the pathophysiology of many, perhaps all, human cancer: cancer
initiation and progression can involve microRNAs (miRNAs) - small
non-coding RNAs that can regulate gene expression. At the present time,
the main mechanism of microRNoma (defined as the full complement of
microRNAs present in a genome) alteration in cancer cells seems to be
represented by aberrant gene expression, characterized by abnormal
levels of expression for mature and/or precursor miRNA sequences in
comparison with the corresponding normal tissues. Loss or amplification
of miRNA genes has been reported in a variety of cancers and altered
patterns of miRNA expression may affect cell cycle and survival
programs. Germline and somatic mutations in miRNAs or polymorphisms in
the mRNAs targeted by miRNAs may also contribute to cancer
predisposition and progression. The causes of the widespread
differential expression of miRNA and other non-coding RNA genes between
malignant and normal cells can be explained by the genomic location of
these genes in cancer-associated genomic regions, by epigenetic
mechanisms as well as by alterations of members of the processing
machinery. MicroRNAs expression profiling has been exploited to identify
miRNAs that are potentially involved in the pathogenesis of human
cancers. MicroRNAs and other non-coding RNAs profiling achieved by
various methods has allowed the identification of signatures associated
with diagnosis, staging, progression, prognosis and response to
treatment of human tumors.
3:20 Refreshment Break, Poster and Exhibit Viewing
4:00 The Consensus Coding Sequences of Human Breast
and Colorectal Cancers
Will Parsons, M.D., Ph.D., Instructor, Division of Pediatric
Oncology, Ludwig Center for Cancer Genetics and Therapeutics, Sidney
Kimmel Comprehensive Cancer Center, Johns Hopkins
The elucidation of the human genome sequence has made it possible to
identify genetic alterations in cancers in unprecedented detail. To
begin a systematic analysis of such alterations, we determined the
sequence of more than 13,000 well-annotated human protein-coding genes
in a set of breast and colorectal cancers. The vast majority of the
mutated genes identified were not known to be genetically altered in
tumors and are predicted to affect a wide range of cellular functions,
including transcription, adhesion, and invasion. These data have helped
to define the genetic landscape of two human cancer types, provide new
targets for diagnostic and therapeutic intervention, and open fertile
avenues for basic research in tumor biology.
4:30 Deep Genomic Analysis of Tumors for the
Discovery of Sequence Variation: From the Surgical Suite to the Genome
Sequencer
Raphael Bueno, M.D., Division of Thoracic Surgery, Brigham
and Women's Hospital
5:00 Common Variation at 8q24 and Prostate Cancer
Risk
Meredith Yeager, Ph.D., Scientific Director, Core Genotyping
Facility, Advanced Technology Center, National Cancer Institute
Recently, several groups have reported strong associations between
common DNA polymorphisms that span a segment of chromosome 8q24 and the
risk of prostate cancer. There is
evidence that at least three regions of this segment (chromosome 8:
126501167-128998553) are independently associated with risk and are also
dependent on the ethnic origin of prostate cancer cases. As an extension
of the Cancer Genetic Markers of Susceptibility project (http://cgems.cancer.gov),
preliminary association studies of more than 4000 cases and 4000
controls of European origin have identified haplotypes on which
disease-contributory mutations most likely exist. We have extensively
characterized common genetic polymorphisms present for two of these
regions, totaling > 148kb, using Roche/454 next-generation resequence
analysis (chromosome 8: 128470954-128619305) of 40 prostate cancer cases
and 40 controls of European origin and seven individuals from a CEPH
family in which a common predicted susceptibility haplotype is
segregating. The characterization of this region is important to rapidly
identify common genetic polymorphisms so that they can be investigated
for functional significance. There is growing evidence that these
regions are also implicated in other cancer types; these observations
underscore the importance of characterizing common genetic variation at
8q24.
5:30 Networking Reception
6:30 Close of Day
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