OverviewDay 1Day 2Short CoursesPDF DownloadPress Pass Request Brochure
OverviewDay 1Day 2Short CoursesPDF DownloadPress Pass Request Brochure
Published March 2009
The Future of Biobanks:
Regulation, ethics, investment and
the humanization of drug discovery
Order your copy today!
FFPE and RNA Extraction
Published Genome Technology July 2009
Advances in Gene
TUESDAY, NOVEMBER 17, 2009
7:30 am Breakfast Presentation (Sponsorship Opportunity) and Morning Coffee
8:15 Java and Jive Break-out 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 ideas, experiences, and develop future collaborations around a focused topic. Topics include:
TABLE 1: The Mouse Embryo as a "Model Organism" to Study Cancer and Other Human Diseases"
Host: Mylene Yao, M.D., Assistant Professor, Stanford University School of Medicine
Many genes that are implicated in cancer and other diseases, such as cardiac and neurological pathologies, are highly expressed in the preimplantation mouse embryo. We will discuss how the preimplantation mouse embryo model can help us gain unique perspectives on genes and human diseases.
TABLE 2: RNA from FFPE - Matching The Assay to The Purpose
Host: Stephen M. Hewitt, M.D., Ph.D., Chief, Tissue Array Research Program and Applied Molecular Pathology Laboratory, NCI/NIH
Discussion topics include:
• Few Targets, High Sensitivity
• Limited Targets, Assay Development
• Discovery, ScreeningTABLE 3: Maximizing the Precious Resources in your Biorepository: How do you Create a Renewable Resource?Host: Andrew Brooks, Ph.D., Associate Director, Rutgers University Cell and DNA RepositoryDiscussion Topics:
TABLE 4: Do we need Research into Preservation Science?Host: Allison Hubel, Ph.D., Professor of Mechanical Engineering, University of Minnesota
- Are all the techniques sufficient for current needs?
- Is existing technology sufficient?
- What advances would transform the field (room temperature storage for biospecimens, viable tissue specimens, etc.)? TABLE 5: Good Business Analysis can Improve Your Bio-BankHost: Nicholas, Ilasi, M.Sc., Business Analyst
• Business Analyst as Liaison
• Lab evaluation, Process Mapping and Lab Context
• Your Users: Customers
• Opportunities, Process Improvement, Requirements
• Achieving Quality Strategic GoalsTABLE 6: I Don’t Have The Cell Yield/Viability/Quality Following Transport or Cryopreservation That I Want,
and I Want to Vent!Host: Aby J. Mathew, Ph.D., BioLife SolutionsDiscussion Topics:
1. What unsatisfactory results are we seeing?
2. How do we ship/transport/hold cells/tissues before processing?
3. How do we cryopreserve cells/tissues?
4. Do we use a repeatable, GMP process for biopreservation?
5. Is this likely to affect the quality of cell components utilized for diagnostics?
6. Who is getting improved results and how?
7. Is there information/methods that could help that I do not know about?
8. Do we feel better after venting or no better off?TABLE 7: Challenges of Nucleic Acid Purification Faced by BiobanksHost: Eric B. Vincent, Ph.D., Product Manager, Genomics, Promega CorporationDiscussion Topics:
• What technologies are biobanks utilizing for nucleic acid purification?
• How are biobanks addressing painpoints/bottlenecks in their workflows?
• How can emerging technologies help biobanks perform better?TABLE 8: qPCR using TaqManHost: Jon Sherlock, Ph.D., TaqMan Array Product Manager, Consumables, Applied
Biosystems• miRNA strategies
• Gene Expression from precious samples (FFPE, single cells, LCM etc.)
• Copy Number Variation
• Validation: microarray/NextGen whole transcriptome/siRNA
TABLE 9: A Collaborative Network and Hinderances to BiobankingHost: Petar Stojadinovic, Professor, National University; Corporate Trainer, Automation Trainer• Lack of standarization, Overly Complex standardizations and Evolving Taxonomies
• Sample standardizations, storage costs, and controls
• Operating costs, Infrastructure, Equipment, and IT and the threat of Biobank closures with economic times
• Sample and data source brokerages
• Sample and Data Sharing in a collaborative network
DEFINING AND UTILIZING BIOSPECIMENS WITH AN EYE FOR
(Combined session with Gene Expression Profiling meeting)
9:00 Chairperson’s Remarks
Stephen M. Hewitt, M.D., Ph.D., Chief, Tissue Array Research Program and Applied Molecular Pathology Laboratory, National Cancer Institute, NIH
9:05 Looking to the Future – Regulations, Standards, Quality, and Clinical Trials
Elizabeth Mansfield, Ph.D., Director, Personalized Medicine Staff, Office of In Vitro Diagnostic Devices, CDRH/FDA
9:50 Defining Biospecimen Quality Within the Fit-For-Purpose Paradigm
10:20 Networking Coffee Break, Poster & Exhibit Viewing
11:00 Living Tissue Banks: The Road to Personalizing Treatments for Brain Tumors
Santosh Kesari, M.D., Ph.D., Assistant Professor, Neurosciences, University of California San Diego
With the availability of genome wide technologies for mutation analysis in cancer, we are on the advent of personalizing treatments for cancer. Growing individual cancer cell lines from patients may lead to novel insights into disease biology and opportunities to develop personalized treatments approaches.
11:30 Bridging the Gap between Biospecimen Procurer and User
Allison Hubel, Ph.D., Professor, Mechanical Engineering, University of Minnesota
Biospecimen procurers and users are separated by gaps, which are typically both physical (different location) and temporal (different time). The usefulness of a biospecimen is determined in large part by our ability to efficiently preserve the critical biological properties of the biospecimen. We will describe advances in preservation science, which will result in preservation of samples refractive to current preservation techniques and development of improve protocols.
12:00 Close of Session
12:15 pm Luncheon Presentation Sponsored by Gene Signature’ Focused Expression Analysis: Enabling the Assessment of Pathways, Disease States & Biomarker Sets, from Samples Including Single CellsJon Sherlock, Ph.D., TaqMan Array Product Manager, Consumables, Applied BiosystemsWith increasing biological knowledge and understanding scientists can now consider experimentally assessing and interrogating entire pathways, or evaluating whole gene classes, biomarker sets or disease states rather than studying single genes. To this end Applied Biosystems have developed >150 TaqMan® Gene Signature Arrays for human, mouse and rat in 384-well micro fluidic card and 96-well plate formats. Together with tools enabling single cell amplification and data analyses these provide scientists with a powerful system for biological investigations. Specific examples of the pluripotency gene signature from single embryonic stem cells and the lipidomics gene class will be discussed.
PROFILING GENE EXPRESSION
FROM TISSUE(Combined session with Gene Expression Profiling meeting)
2:00 Chairperson’s Remarks
Michael Barnes, Ph.D., Director, Cincinnati Biobank; Pathology, Cincinnati Children’s Hospital
2:05 Tackling Technical Barriers to Achieve High Fidelity Gene Expression Data from Formalin-Fixed Paraffin-Embedded Clinical Tissues
Jun Luo, Ph.D., Assistant Professor, Department of Urology, Johns Hopkins Hospital
Formalin-fixation and paraffin-embedding (FFPE) is a standard pathological procedure commonly applied to clinical specimens in preparation for pathological evaluation. This procedure however inevitably compromises genomic analysis, limiting the utility of clinical FFPE specimens. Dissecting the various technical variables during the FFPE procedure that contribute to inferior RNA quality will help to improve the quality of molecular data derived from FFPE specimens. In addition, a number of prospective measures that are relatively easy to implement should be taken to improve the processing, storage, and the utility of FFPE specimens for molecular analysis.
2:35 Comparison of Quantity, Quality, and Microarray Performance of RNA Extracted from Formalin-Fixed Paraffin-Embedded and Unfixed Frozen Tissue Samples
Marshall S. Scicchitano, M.S., Manager, Molecular Pathology, Department of Safety Assessment, GlaxoSmithKline
Archived pathology specimens used for retrospective analyses are typically preserved as formalin-fixed paraffin-embedded (FFPE) tissue. Formalin fixed tissues have been previously shown to yield compromised RNA compared with that obtained from frozen tissue. In order to assess and compare unfixed, frozen RNA and FFPE RNA quality and performance on an Affymetrix platform, RNA was isolated from LPS-stimulated human bone marrow stromal cells and either snap-frozen or FFPE RNA integrity was qualitatively assessed and compared between frozen and FFPE samples using the Agilent 2100 Bioanalyzer. Affymetrix quality control parameters were assessed and compared for each of these samples. Additionally, differentially regulated genes were analyzed with Ingenuity Pathway Analysis software for comparison of output data between frozen and FFPE samples.
Sponsored by3:05 Technology Presentation
Walk-Away Purification of Genomic DNA from Large Volume Blood Samples
Eric Vincent, Ph.D., Product Manager - Nucleic Acid Purification, Promega
Promega and Hamilton are setting a new standard for speed, reliability, consistency, and purity in high-throughput DNA isolation from large volume blood samples (up to 10ml). This new system, combining Hamilton's MICROLAB(r) STARplus liquid handling workstation with Promega's new all-in-one processing hardware and reagents, provides a walk-away solution that reduces processing time and increases successful runs. It delivers ready-to-use, high purity (A260/A280>1.7 and A260/A230=1.8-2.2) DNA from up to 96 fresh, frozen, or mistreated samples in under 8 hours using a single 50 ml processing tube per sample.
3:20 Networking Refreshment Break, Poster & Exhibit Viewing
4:00 Elucidating Lung Cancer Subtypes Using Genomics Technologies
George Vasmatzis, Ph.D., Molecular Medicine, Mayo Clinic Cancer Center
Our data derived from Laser Capture Microdissected (LCM) tumors and other public lung cancer expression profiles show a high degree of heterogeneity in these tumors. Because of variability in therapy response, more targeted therapies are being developed specific to lung cancer subtypes. Developing a panel of genes that could distinguish lung cancer subtypes in poorly differentiated tumors or in small biopsy specimens would be helpful in the management of patients with lung cancer.
4:30 Effects of Sample Processing Time on PBMC Gene Expression Patterns from JIA Patients
Many gene expression studies utilize Ficoll isolated peripheral blood mononuclear cells (PBMC) as a source of RNA. Prior to commencement of a multi-center longitudinal study of patients with juvenile idiopathic arthritis (JIA), the effect of processing time was evaluated using Affymetrix U133 plus2.0 GeneChips®. Gene expression differences were identified and the trends were confirmed in a group of over 300 experimental samples allowing selection of an acceptable window for sample processing. The talk will discuss lessons learned from this project and the effect of processing time on the quality and outcome of translational research that utilizes microarray technology to study gene expression.
5:00 Close of Day
5:30 – 8:30 pm Short Course 2*
Using Automation to Set-up a Successful Research Laboratory: From BioSample to Meaningful Biological Results
Nicholas Ilasi, M.Sc., Business Analyst
Petar Stojadinovic, Professor, National University; Lab Automation and LIMS Consultant and Trainer, AutomationTrainer.com
*Separate registration required
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