Short Course | Wednesday | Thursday | Friday | Download Brochure
FRIDAY, MARCH 19, 2010
7:00 am Registration Open
7:30 Breakfast Presentation (Sponsorship Available)
8:30 Chairperson’s Remarks
Daniel McClernon, Ph.D., President, McClernon LLC
8:35 Real-time Quantitative HIV-1 Assay for Monitoring Low Viremia in Cerebrospinal Fluid: Correlation to Antiretroviral Therapy and Neurological Disease
Daniel McClernon, Ph.D., President, McClernon LLC
Development of quantitative assays for clinical evaluation can increase successful assay implementation into the realm of clinical practice. We present here a modified HIV-1 viral load test for monitoring low viremia in cerebrospinal fluid that demonstrates clinical utility and could assist physicians in patient management of HIV-associated neurological disease.
9:05 The Efficiency of Single Genome Amplification and Sequencing is Improved by Quantitation and use of a Bioinformatics Tool
Josué Perez Santiago, Ph.D. Student, Department of Bioinformatics, University of California, San Diego
9:35 Achieving Reproducible Viral Quantitation in qRT-PCR Assays
Linda Starr-Spires, Ph.D., Director, Global Clinical Immunology, Sanofi Pasteur
Validating qRT-PCR assays without the availability of commercial reference standards adds additional levels of complexity. The final method must produce standards which meet criteria for robustness and stability, with reproducible quantitation and minimal lot-to-lot variation. The reference standards can then be applied to the validation of the qRT-PCR assays intended for clinical trial applications.
10:05 Networking Coffee Break and Final Poster Viewing
Sponsored by
Poster Competition
10:45 A Fully Automated Assay for Quantitation of HIV-1 Viral Load
Cynthia Wagner, Senior Research Scientist, Siemens Healthcare Diagnostics
Siemens Healthcare Diagnostics has developed a fully automated viral load assay. The VERSANT HIV-1 RNA 1.0 Assay (kPCR) is an automated test for detection and quantitation of HIV-1 RNA in human plasma samples. This assay will detect and quantify HIV-1 RNA over the range of 37 copies/mL to 11,000,000 copies/mL with a 500 μL sample input volume.
11:15 A Novel, qPCR Based Approach to Measuring Endogenous Retroviral Clearance by Capture Protein A Chromatography
Min Zhang, Senior Research Associate, Process Virology, Genentech, Inc.
11:45 Panel Discussion with Morning Speakers
12:15 pm Close of Morning Session
Sponsored by
12:30 Luncheon Presentation
Deciphering Long Non-coding RNAs: From Antisense Transcription to Biomarker Discovery
Yulei Wang, Ph.D., Senior Staff Scientist, Genomic Assays R&D, Applied Biosystems
Widespread long non-coding RNAs (lncRNAs) and antisense transcription are postulated to represent a vast hidden layer of RNA regulatory networks and have been shown to associate with human diseases. To accelerate the discovery in the ncRNA field, we have developed a suite of gene expression tools, including >25,000 pre-designed TaqMan® non-coding RNA assays, > 2000 TaqMan® pri-miRNA assays as well as custom assay design tools. We have also developed strand-specific TaqMan® assays (SSTAY) for accurate quantification of sense/antisense RNAs. SSTAY utilizes a proprietary engineered thermal stable RT enzyme and resolves the prevalent artifacts associated with commonly used strand-specific RT-PCR methods. The SSTAY assays allows researchers to access the sense or antisense strand transcription without ambiguity and provides a useful tool for studying antisense RNA-mediated gene regulation. We will also present the utility of TaqMan® ncRNA assays in discovering novel lncRNA biomarkers for breast cancer prognosis and treatment.
(Combined Session with Now-Generation Sequencing)
2:00 Chairperson's Remarks
Lawrence J. Wangh, Ph.D., Professor, Biology, Laboratory of Molecular Medicine & Global Health, Brandeis University
2:05 Microfluidic Technologies for Single Cell Genetic and Expression Analysis
Yong Zeng, Ph.D., Postdoctoral Researcher, Chemistry, University of California, Berkeley
Single cell analysis is the new frontier for advancing our understanding of molecular mechanisms underlying cellular function and dysfunction. We will first discuss a fully integrated bioprocessor that enables sensitive single-cell gene expression profiling by integrating the capture of single cells, reverse transcriptase (RT)-PCR, product purification, and electrophoretic analysis. Second, a high-throughput single cell genetic analysis (SCGA) technique will be presented that combines a novel microfluidic droplet generator for encapsulation of single cells in nanoliter emulsion droplets with quantitative digital genetic detection via multiplex PCR. These techniques allowed us to resolve a distinct bimodal expression of the GAPDH gene in single Jurkat cells treated by siRNA knockdown, and to achieve extremely low-level detection of one E. coli O157 pathogen cell in a background of 105 E. coli K12 cells.
2:35 Strategies using LATE-PCR to Detect and Analyze Sequence Variations in Target Molecules
Lawrence J. Wangh, Ph.D., Professor, Biology, Laboratory of Molecular Medicine & Global Health, Brandeis University
LATE-PCR is an advanced form of asymmetric PCR that efficiently generates abundant single-stranded amplicons. LATE-PCR reactions can readily be multiplexed and quantitatively analyzed at end-point using low temperature probes. The accumulated amplicons can also analyzed by Dilute-’N’-Go sequencing. Application of these technologies to analysis of sequence variations will be discussed using examples of bacterial genes and mitochondrial genes.
3:05 Single Molecule Closed Complex DNA Sequencing
Ernest W. Kovacs, Ph.D., GE Global Research
GE Global Research is working to develop a new method of DNA interrogation that can be used for high throughput, single-molecule DNA sequencing. The proposed method utilizes novel nucleotide analogues that have a detectable tag attached to the terminal phosphate. We have found that in the absence of divalent cation, DNA polymerase can be frozen in a stable ternary complex (a “closed complex”) consisting of the DNA primer-template, the DNA polymerase, and the incoming nucleotide as encoded by the DNA template. This complex is “frozen” in the midst of a nucleotide incorporation event, and can be interrogated using single molecule fluorescent microscopy to determine the identity of the trapped base. After visualization, the complex is chased with divalent cation to allow incorporation of the trapped base, and the process repeated over and over to generate the DNA sequence.
3:25 A Strategy for High-Quality Clinical Resequencing of the Human Genome
Hanlee Ji, M.D., Assistant Professor, Oncology, Stanford University
3:45 Prospects for Nanopore-based Direct DNA Sequencing
Andrew D. Hibbs, Ph.D., CEO, Electronic Bio Sciences LLC
Passing a single unamplified strand of DNA through a small pore and reading the signal of individual bases by a direct electrical measurement, without intermediate reactants or consumables, approaches the limit of simplicity for sequencing. Controlling the random motion of the DNA as it passes through the pore is emerging as a critical factor to enable the ultimate success of the method. The basic issues and technology elements involved in such a measurement will be presented, and the remaining key scientific issues discussed.
4:05 Panel Discussion
4:30 Close of Conference
Back to X GEN Congress