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Please click here to download the following podcasts: 

In the Wake of the Flood 

Taking NGS into the Clinic 

1000 Genomes Project: Cancer, Genetic Variation, and Drug Response 

Mapping Genomes in 3D 

The Human Microbiome Project: Next-Generation Sequencing and Analysis of the Indigenous Microbiota 

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


Conference Proceeding CD Now Available
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Wednesday, September 28

8:00 am Breakfast Presentations (Sponsorship Opportunities Available) or Morning Coffee


Sequencing Cancer from Development to Detection 

8:45 Chairperson's RemarksHong Sun, Ph.D., Assistant Professor, Environmental Medicine, NYU School of Medicine 

8:50 Transcriptomic, Genomic and Epigenomic Data: Pinpointing the Precise Alterations that Underlie Cancer Development

David Smith, Ph.D., Professor, Laboratory Medicine and Pathology, Mayo Clinic

We used the power of next-gen sequencing to analyze a group of oropharyngeal squamous cell carcinomas (along with matched normal tissue from each patient) that covered the full spectrum of distinct patients who develop this cancer. This included whole transcriptome sequencing, the 450K Methylation arrays from Illumina, and whole exome sequencing using the Illumina Sure-Select Target Enrichment System. The information provided just by whole transcriptome sequencing revealed many interesting molecular alterations in the distinct oropharyngeal cancers analyzed. We also demonstrate the power of whole transcriptome sequencing as a powerful clinical tool to better provide clinicians with insights to better inform clinical decisions. Finally, we describe our preliminary efforts to integrate the data generated from all three complementary technologies to provide a much better understanding of the important molecular alterations that are responsible for oropharyngeal squamous cell carcinomas with distinct underlying etiologies.

9:20 Detecting Structural Rearrangements in a Mouse Model of Lymphoma Using Mate-Pair Sequencing

Martina Mijuskovic, Ph.D., Postdoctoral Associate, Center for Health Informatics and Bioinformatics, New York University Langone Medical Center

In order to detect structural rearrangements in our recently developed mouse model of lymphoma, we chose the mate-pair whole genome sequencing strategy. We first performed simulations of mate-pair sequencing in order to specify the most suitable DNA library size (insert size), read length, necessary coverage and downstream analysis software to detect translocations and other rearrangements. We then applied these insights to our experiment planning and data analysis.

9:50 Selected Poster Presentation: Next-Generation Sequencing at Merck-BostonRichard Stevens, Ph.D., Team Member, Molecular Biomarkers, MRL Boston
10:05 Networking Coffee Break in the Exhibit Hall with Poster Viewing 

10:45 Highthroughput Scanning of Single Cell Cancer Genomes: Methodology and ApplicationsTimour Baslan, Ph.D., Postdoctoral Associate, Cancer Genomics, Cold Spring Harbor LaboratoryThe initiation and genetic progression of cancer and the dissemination of cancer cells throughout the body is basic to our understanding and efficient treatment of the disease. By adapting next-gen sequencing to obtain sparse rather than deep coverage, we have developed methods for efficient genomic profiling of hundreds of single cells from mulitple tumors. We applied Single Nucleus Sequencing (SNS) to the cellular analysis of primary tumors and metastatic sites and traced the genetic lineage of tumor cells during progression and dissemination. We will discuss the application of this technology to large clinical sample sets as well as informatic and experimental methods for multiplexing large numbers of cells per sequencing run.

11:15 Functional Validation of Somatic Mutations in Prostate Cancer

Mark Rubin, M.D., Weill Cornell Medical College

11:45 Close of Morning Session

12:00 pm Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own


Sequencing Cancer from Detection to Diagnosis 

1:30 Chairperson's RemarksKeith Robison, Ph.D., Lead Senior Scientist, Informatics, Infinity Pharmaceuticals, Inc. 

1:35 The Coding Genome of Chronic Lymphocytic Leukemia: Role of NOTCH1 Mutational ActivationGiulia Fabbri, M.D., Ph.D., Postdoctoral Associate, Cancer Genomics, Herbert Irving Comprehensive Cancer Center, Columbia UniversityRecent findings regarding the characterization of the genetic lesions associated with chronic lymphocytic leukemia, with a particular focus on NOTCH1 mutations in different clinical phases of the disease.

2:05 Combination of Cold-PCR with High-Throughput Sequencing Increases Confidence in Calling Low-Level DNA Variants in Clinical Samples

Mike G. Makrigiorgos, Ph.D., Associate Professor, Radiation Oncology, Dana Farber Cancer Institute

Using next-generation sequencing for identifying low-abundance mutations within wild-type DNA is important in several fields of medicine, including cancer, prenatal diagnosis, and infectious diseases. However, utilizing the clinical and diagnostic potential of rare mutations is limited by sequencing errors and depth of coverage. Here we describe the combination of COLD-PCR with sequencing. COLD-PCR technology enables amplification of genomic targets of interest while simultaneously enriches mutated alleles over wild type. Amplicon sequencing demonstrated a 20-50-fold improvement compared to using conventional PCR for the detection of low-level mutations and identified missense p53 mutations in lung and colorectal tumor samples that were not possible to call using the current approach. Furthermore, calling of COLD-PCR amplicons required 20-30-fold lower depth of coverage. The combination of technologies enables adaptation of next-generation sequencing to the clinical setting.

2:35 Pursuing Novel Oncology Biomarkers with High-Throughput Sequencing

Keith Robison, Ph.D., Lead Senior Scientist, Informatics, Infinity Pharmaceuticals, Inc.

We apply NGS to identifying biomarkers using material from clinical trials of novel mechanism-of-action anti-cancer compounds. This application includes evaluation & calibration of novel technologies & emergent sequencing platforms.

3:05 Networking Refreshment Break in the Exhibit Hall with Poster Viewing


Closing Plenary Session - Next-Next Generation Sequencing 

3:25 Chairperson's Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Sponsored by
3:30 Poster Award Winners Announced

3:35 High-Throughput Single Molecule Mechanical Sequencing of DNA

Vincent Croquette, Ph.D., Director of Research, Physical Statistics, École Normale Supérieure, Paris

Single molecule DNA sequencing can be done by detecting the positions of roadblocks (e.g. hybridized fragments) during rehybridization of a mechanically unzipped DNA. It can be implemented via sequencing by hybridization, ligation or polymerization. That technique is high-throughput and does not require the use of labeled nucleotides.

4:05 Sample in, Answer out: Clinical Sequencing Workflows on the GnuBIO Platform

John Healy, Vice President, Informatics, GnuBIO, Inc.

GnuBIO's sequencing technology is the first to enable clinical workflows on a single platform. An entire targeted sequencing run, from enrichment to sequencing to analysis, can be performed from a single touch point. The high-throughput, serial nature of the underlying emulsion-based microfluidics results in cost and turnaround times that scale linearly as a function of the number of samples and targets sequenced, rather than per run. The GnuBIO platform produces read lengths measured in the hundreds of bases, combined with per-base accuracies well above 99.9% bringing rare variants, linkage studies and structural events within reach. This unique set of capabilities is the first to satisfy the requirements of sequencing applications aimed to directly impact the clinical decision process.

4:35 Towards Optipore Single-Molecule DNA Sequencing

Amit Meller, Ph.D., Associate Professor, Biomedical Engineering and Physics, Boston University

We describe a novel method for high throughput DNA sequencing based on threading of individual DNA molecules in nanopore arrays and optical readout. The method takes advantage of the extremely high sensitivity of solid-state nanopores, and the parallel nature of the optical detection, which permits probing from hundreds of nanopores fabricated at high density. The combination of single-molecule sensitivity, high-speed and parallel detection will allow us to achieve an extremely high sequencing throughput, making our technology attractive for in vitro diagnostic applications.

5:05 Close of Meeting

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