Archived Content
Cambridge Healthtech Institute’s Sixth Annual
Successful Sequencing
Projects…Pipelines…Platforms…Progress
March 7-8, 2012| Hilton San Diego Resort | San Diego, California
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THURSDAY, MARCH 8
Sponsored by
7:30 am Breakfast Presentation
A Scalable Unified Architecture for NGS Data Storage and ManagementJose L. Alvarez, World Wide Director Life Sciences, Data Direct Networks, Inc.DDN will highlight a scalable, high performance unified data storage and management solution that will simplify and accelerate Genomic research. Instruments data ingestion, sequencing pipeline performance and intelligent archive and sharing of research data in a geo-distributed model will be discussed. DDN is partnering with NGS industry leaders to deliver an array of flexible, highly scalable and easy to manage storage solutions that are helping research groups around the world accelerate their time to discovery.
8:00 Successful Sequencing Discussion Groups
These focused groups are designed for conference attendees to discuss important and interesting topics related to sequencing and genomic tools. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse areas to exchange ideas, experiences, and develop future collaborations around a focused topic.
View Successful Sequencing Discussion Groups
8:45 Chairperson's Remarks
Marc Salit, Ph.D., Leader, Multiplexed Biomolecular Science Group, NIST Chemical Science and Technology Laboratory
»8:50 Featured Speaker:
ERCC External RNA Controls for RNA-Seq Experiments
Marc Salit, Ph.D., Leader, Multiplexed Biomolecular Science Group, NIST Chemical Science and Technology Laboratory
The External RNA Control Consortium developed a set of RNA control sequences useful to establish the technical performance of gene expression measurements. These controls are now commercially available, and a DNA library of the reference sequence set will be available as a Standard Reference Material (SRM) from NIST. Various applications of these controls will be described, with a focus on recent experience with RNA-Seq.
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9:25 Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
Jennifer Beane, Ph.D., Assistant Professor, Section of Computational Biomedicine, Department of Medicine, Boston University Medical Center
The goals of our study were to use RNA-Seq of pooled bronchial airway epithelial cell brushings to understand the field of molecular injury in response to tobacco smoke exposure and lung cancer and to compare gene expression estimates by microarrays and different RNA-Seq library preparation protocols. RNA-Seq libraries were prepared using 2 distinct approaches, one capable of capturing non-polyadenylated RNA and the other designed to measure only polyadenylated RNA followed by sequencing. The results demonstrate that transcriptome sequencing has the potential to provide new insights into the biology of the airway field of injury associated with smoking and lung cancer.
Sponsored by
10:00 A Selective Priming Method for Strand-Specific RNA-Seq
Steve Kain, Ph.D., Director, Product Management, NuGEN Technologies, Inc.
The Encore Complete RNA-Seq Library Systems from NuGEN enable low input preparation of strand-specific RNA-Seq libraries from total RNA without the need for rRNA reduction or poly(A) selection. Greater than 95% strand retention is achieved with <25% rRNA reads using Human RNA samples.
10:15 Networking Coffee Break in the Exhibit Hall with Poster Viewing
10:45 RNA Analysis Using RNA-Seq and Microarrays
Steven Head, Director, Microarray and NGS Core, The Scripps Research Institute
Options for analysis of RNA using NGS technology are reviewed and compared to microarray-based methods. Methods, data, sensitivity, sample requirements for RNA-Seq and relative costs to microarray-based methods will be discussed.
11:20 Targeted Next-Generation Sequencing Based Clinical Diagnostics Using Formalin Fixed Tissue
Eric Duncavage, M.D., Assistant Professor, Pathology, Anatomic and Molecular Pathology; Laboratory and Genomic Medicine, Washington University
To date, most NGS tools and techniques have focused on the identification of constitutional single nucleotide variation and are unsuitable for clinical diagnostic testing. Using hybrid-capture enrichment of DNA derived from fresh and formalin-fixed tissue we obtain high coverage (>1000x) of a panel of genes involved in cancer prognosis. We demonstrate that this approach allows for the highly sensitive detection of mutations with allele frequencies of 10% while maintaining a high positive predictive value. Further, we show that a full spectrum of clinically-relevant DNA structural variation including insertions, deletions, gene amplifications, and translocations can be detected from targeted NGS data.
11:55 Biospecimen Quality Control for Sequencing Applications
Belynda D. Hicks, Director, Quality Management, Genetics and Genomics, Advanced Technology Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick
Current genomic technologies demand biospecimens that are well characterized and well qualified for downstream analysis. Sample requirements will shift as the technology progresses, so it is important to understand the best QC technique that will be predictive of downstream performance. Formal post-project assessments of metrics versus performance will assist in determining the best QC measurement techniques and sample acceptance criteria. Particular attention should be paid to quality control measures in support of transcriptome sequencing, as there are known preanalytical variables that have a significant impact on assay performance.
Sponsored by
12:30 pm Luncheon Presentation
Revolutionize Your Desktop Sequencing Workflow with HaloPlex Next-Gen PCRMaria Celeste M. Ramirez, Ph.D., Application Scientist, Sequencing Specialist, Agilent TechnologiesDuring this presentation I will introduce the HaloPlex technology, covering some of its key benefits and applications. HaloPlex enables target enrichment of thousands of targets in a single tube, in less than a day. Gene panels can easily be customized using HaloPlex Design Wizard. HaloPlex provides premium performance with superior coverage enabling comprehensive mutation detection.
1:45 Chairperson's Remarks
Nalini Raghavachari, Ph.D., Core Director, Genetics and Development Biology Center, NHLBI, The National Institutes of Health
»1:50 Featured Speaker:
Transcriptome Profiling and Sequencing of Differentiated Human Hematopoietic Stem Cells Reveal Lineage Specific Expression and Alternative Splicing of Genes
Nalini Raghavachari, Ph.D., Core Director, Genetics and Development Biology Center, NHLBI, The National Institutes of Health
Hematopoietic differentiation is strictly regulated by complex network of transcription factors that are controlled by ligands binding to cell surface receptors. From a clinical standpoint, deciphering the transcriptome of differentiated cells during hematopoiesis may help unravel disease-specific mechanisms in hematopoietic malignancies. This presentation would delineate the gene expression and alternative splicing events during erythropoiesis using a human in vitro hematopoietic model system. Herein we provide a molecular portrait of events that regulate differentiation of hematopoietic cells exploiting the microarray and next-gen sequencing technologies.
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Sponsored by
2:25 Sequencing of mRNA and DNA from Individual Circulating Tumor Cells for Molecular Phenotyping at Single Cell Resolution
Abizar Lakdawalla, Marketing, New Technologies, Illumina
Circulating tumor cell counts are often used for early diagnoses and monitoring response to cancer therapy. Molecular phenotyping (RNA, meDNA) of the isolated cells would provide substantial additional diagnostic value. We have optimized an RNA-seq method on Illumina’s MiSeq and HiSeq platforms, to determine the tissue origin of individual CTCs by sequencing RNA extracted from single circulating tumor cells (CTCs). The RNA-seq data provides a comprehensive gene expression profile, with additional information on gene fusions, cSNPs, and transcript isoforms from an individual cell. The single cell RNA-seq method also has high value in developmental biology to track the spatial and temporal patterns of gene expression in dividing cells at single cell resolution. We will also present data on whole genome analysis of individual cells to determine genome variation in single somatic cells.
Sponsored by
3:00 Insight into Prostate Cancer Mechanisms via Integrated in Silico RNA-Seq Analysis of NGS Patient Data
Sandeep Sanga, Ph.D., Bioinformatics Product Development Scientist, Next Generation Sequencing Lead, Computational Biology, Ingenuity Systems
This presentation will explore some insights into the mechanisms of prostate adenocarcinoma, putative biomarkers and therapeutic targets by leveraging next generation sequencing (NGS) data through in silico RNA-seq analysis and interpretation using CLC bio and Ingenuity IPA.
3:15 Networking Refreshment Break, Last Chance for Poster and Exhibit Viewing
Sponsored by
4:00 Poster Awards
4:15 Transcriptome Instability in Prostate Cancer
Liguo Wang, Ph.D., Research Scientist, Division of Biostatistics, Department of Molecular and Cellular Biology, Baylor College of Medicine
Deregulation of alternative splicing is a common feature of many human diseases including cancer. Through deep sequencing the transcriptome of 20 prostate cancer patient samples, we found the incidence of deregulated alternative splicing was significantly increased in prostate tumors compared with matched benign tissue. We have developed a bioinformatic tool that is able to quantify and identify genes marked with elevated aberrant splicings. We provide a unique angle to pinpoint disease (cancer) related genes.
4:50 A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes
Christopher Maher, Ph.D., Research Investigator, Pathology, University of Michigan Medical School
5:30 Close of Conference
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