Immediately following "Second Annual Microarrays 2 Macroresults" April 23-25, 2001
Special discount registration rates for combined registration with Microarrays 2 Macroresults.

WEDNESDAY, APRIL 25

THURSDAY, APRIL 26

SAMPLE COLLECTION, ISOLATION, AND STORAGE

8:30 Chairperson's Opening Comments
Dr. Kent Bottles, Chief Knowledge Officer, Genomics Collaborative, Inc.

8:40 A Summary of Techniques to Isolate Rare Cells of Interest from a Complex Cell Mixture
Dr. Jeffrey J. Chalmers, Professor, Department of Chemical Engineering, The Ohio State University
This presentation will attempt to summarize various cell separation strategies and techniques. Topics will include negative and positive separations, issues surrounding performance evaluations, and actual specific approaches/technologies.

9:10 Procurement, Retrieval, Storage, Processing, and Shipping of Human Samples for Genetic Studies: Initial Efforts toward a Data-Driven Industry Standard
Dr. Kent Bottles
As the genomics field attempts to capitalize on the potential for improved diagnostic tests and therapies for chronic diseases, it becomes more and more important that industrywide standards are developed for the optimal way to procure, ship, and store specimens for genetic studies. With the rapidly expanding large number of high-throughput platforms for genotyping and expression studies, it becomes essential that pathologists procure and store specimens in a way that allows them to be used by a variety of researchers utilizing a variety of techniques. We will survey the traditional dogma of tissue storage and also present some emerging data that point toward a new standard of tissue storage for genetic investigations.

9:40 New, Standardized Methods for Stabilization and Purification of RNA and DNA from Blood, Biopsies, and Other Clinical Samples
Dr. Lynne Rainen, Scientific Director, Research and Development, PreAnalytiX GmbH
As cancer research, pharmacogenomics, and genetic studies evolve into clinical applications, methods used to collect and process RNA and DNA samples will need to be standardized. Gene expression patterns in patient blood and tissue samples need to be stabilized immediately at collection, and integrity of RNA needs to be guaranteed during transport and sample processing. By combining BD's expertise in sample collection systems with QIAGEN's innovative nucleic acid stabilization and purification technologies, PreAnalytiX's integrated reagent-container systems will provide immediate stabilization of RNA and DNA in cells and tissues and days, even weeks, of stability at room temperature. The development of safe, easy-to-use products that are compatible with clinical laboratory practices and offer significantly improved specimen quality and enhanced accuracy of RNA and DNA test results will help to open up the benefits of modern nucleic acid-based testing methods to all patients.

10:10 Poster and Exhibit Viewing, Refreshment Break

10:50 Optimized Real-Time PCR for Detection of Single Alleles of Single-Copy Genes in Single Cells
Dr. Lawrence J. Wangh, Associate Professor of Biology, Department of Biology, Brandeis University
We are developing techniques for single-cell, single-gene, single-allele detection via real-time PCR with molecular beacons. In this talk, I will discuss the need for reliable lysis of single cells, including enzymatic and nonenzymatic conditions used for cell lysis, and the effects of various salts, pH, temperature, and reducing agents. Each of these variables has been optimized by quantitating the rate, extent, and reproducibility of the real-time reaction.

11:20 Utility of FTA Technology for Archiving and Analysis of DNA and RNA
Dr. Martin Smith, Manager, Research and Development, Whatman Bioscience
FTA technology enables the room-temperature archiving of DNA in biological samples (blood, buccal samples, tissue, etc.). DNA analysis on the archived sample can be performed days, months, or years later utilizing a very simple protocol. More recently, my laboratory has focused on the utilization of FTA paper for the archiving and analysis of RNA. In addition, we have also focused on automation of the processes involving FTA.

11:50 Panel Discussion

12:20 Lunch (on your own)

 

EXTRACTION OF SAMPLE FOR GENOMIC ANALYSIS

 

1:35 Chairperson's Comments
Dr. M. Allen Northrup, Chief Technology Officer, Cepheid

1:40 Development of Functional Biochips for Sample processing
Dr. Xiaobo Wang, Senior Director for Sample Preparation, AVIVA Biosciences Corporation
Bioanalytical procedures essentially involve processing, manipulation and detection of cells and molecules in a fluidic suspension. While substantial advances have been made in miniaturizing and integrating these processes through the development of biochips, on-chip sample processing remains significant challenges. In AVIVA, we are currently developing advanced biochips for processing and handling biological samples through on-chip generated physical forces including acoustic, dielectrophoretic, magnetic and mechanical forces. In this talk, the operational principles and practical uses of these chips for separation, concentration, transportation and manipulation of cells and molecules are described. Significant advantages of AVIVA’s approach of utilizing multiple-forces for sample processing are discussed.

2:10 Novel Methods for the Preservation and Extraction of Nucleic Acids from Bacterial, Plant, and Animal Cells
Dr. Brian H. Taylor, Marketing Manager, Genomics, QIAGEN, Inc.
The preservation and efficient extraction of nucleic acids are essential but often overlooked elements of molecular research and diagnostics. To accommodate the broad range of sample types, throughput needs, and yield requirements demanded by new genetic research applications, QIAGEN is continuously expanding its portfolio of both manual and automated purification technologies. This discussion will focus on new approaches for purifying genomic DNA, RNA, plasmid DNA, and PCR fragments for DNA sequencing, microarray analysis, and cloning applications.

2:40 Pressure Cycling Technology (PCT)-Based Nucleic Acid Sample Preparation for Diagnostics and Genomics
Dr. Feng Tao, Project Scientist, Research and Development, BBI BioSeq, Inc.
An extraction system is being developed at BBI BioSeq using a proprietary Pressure Cycling Technology, or PCT, that employs cyclic hydrostatic pressures to lyse, separate, and purify nucleic acids. Results from the feasibility studies demonstrate that the use of PCT affords significant advantages in several phases of the nucleic acid extraction procedure. For example, the release of nucleic acids is equivalent to that obtained using commercially available kits, and this system is particularly useful for difficult-to-lyse cells and tissue. Purification of high-quality nucleic acid is achieved by preferential elution from a binding matrix using pressure. The simplified extraction format features few manipulations and the use of minimal or no harsh chemicals and is readily adaptable to automation.

3:10 Automated Nucleic Acid Sample Preparation for Genomics Research
Dr. David W. Ruff, Staff Scientist and Chemistry Team Leader, Sample Preparation Systems, Applied Biosystems
The genomics revolution has demanded significant improvements in automation for management of nucleic acid materials. Applied Biosystems has introduced an automated, nucleic acid purification workstation that supports molecular analysis applications. This system, the ABI PRISM 6700 workstation, is based on 96-well format purification of nucleic acid templates for various applications, including quantitative gene expression analysis and genotyping. Current protocols support biological input sources such as tissue culture cells, leukocytes, and macerated animal and plant tissues. Protocols under development include sequence-specific affinity capture and nucleic acid purification from blood and serum. The ABI PRISM 6700 system is a very efficient, flexible, and cost-effective solution for supporting molecular analysis procedures.

3:40 Poster and Exhibit Viewing, Refreshment Break

4:20 Xtra Bind™ Nucleic Acid Extraction Matrices: Rapid Sample Preparation Combined with High Sensitivity
Dr. Shannon E. Beard, Vice President, Technology Development, Xtrana, Inc.
Xtrana has discovered several proprietary, solid-phase, nucleic acid-binding matrices (Xtra Bind™), providing novel systems of DNA and RNA extraction. Certain of the Xtra Bind™ matrices capture not only nucleic acid but also cells, providing a unique means of sample preparation from complex samples. The various versions of the Xtra Bind™ matrix are compatible with direct amplification of the nucleic acid bound to the solid phase. This allows for a sample preparation protocol with no vacuum filtration or centrifugation and is therefore ideal for high throughput. Amplification conditions for use with these matrices have been developed to provide for multiplex gene analysis and greatly enhanced sensitivity.

4:50 High-Throughput Genomic Technologies: Using Knowledge from High-Throughput Screening Automation
Dr. Jason Armstrong, Chief of Drug Discovery, Zymark Corporation
High-throughput technologies enabling activities in PCR and plasmid preparations will be discussed. Zymark has been involved in laboratory automation for over 18 years and in recent years has radically changed its technologies following acquisitions and collaborations. Platform technologies will be presented that enable low cost, high capacity, and high throughput and with a small footprint. These approaches have utilized Zymark's experience in integrated robotics for HTS drug discovery and expanded them to include genomics. We have developed two platform technologies that enable plasmid isolation at a rate of approximately 10,000 per day in 96-well format and 38,000 in 384-well format. Approaches for high-speed robotics with novel storage technologies enabling a small footprint will also be discussed as supporting tools for sample prep in such activities as PCR and microarraying. Additionally, a novel benchtop robotic device for handling glass slides and biochips will be presented.

5:20 Panel Discussion

5:50-7:00 Reception (sponsored by Cambridge Healthtech Institute)

 

FRIDAY, APRIL 27

8:00am Poster and Exhibit Viewing and Light Continental Breakfast

 

MICROSCALE SAMPLE PREPARATION

 

8:30 Chairperson's Comments
Prof. Bruno Frazier, School of Computer and Engineering, Georgia Institute of Technology

8:35 Microscale Systems for Cell Signaturing, Sorting, and Lysing
Prof. Bruno Frazier
Over recent years, advancements in micro systems processing technologies have enabled the development of micro fluidic systems for a broad array of applications. One area of particularly strong interest has been micro instrumentation systems for performing biological and chemical analysis. Within this area of micro analysis, there has been significant interest in developing micro systems for interfacing with viable cells. Interfacing micro engineered systems with biological cells are interesting for many reasons including: 1) enabling fundamental scientific studies of cells, 2) the development of pharmacological screening techniques, 3) the development of long term interfaces for bio-computing, and 4) the development of bio-sensing systems. Once drawn into the problem of interfacing biological cells with micro engineered systems, one of the fundamental problems to resolve is manipulation of cells within the micro systems. The goal of this presentation will be to offer several techniques for manipulating cells within micro fluidic systems. In particular, biochemical and electromechanical techniques will be discussed for cell manipulation, cell sorting and concentrating, as well as downstream analytical processing of sorted, concentrated cells within micro systems.

9:05 Automated Microfluidic-Based Sample Processing Technology for Nucleic Acids
Dr. M. Allen Northrup
We are developing a family of technologies and products for miniaturized, integrated sample processing and detection of nucleic acids in complex samples. One technology uses disposable plastic cartridges for point-of-care applications, and the other is based on continuous-flow, automated, reusable systems for unattended operation. Examples from each type of system showing the complete processing and quantitative analysis of pathogens, such as spore-forming bacteria, will be presented.

9:35 An Integrated, Electronically Driven Sample Preparation Chip
Dr. Michael Krihak, Senior Staff Engineer, Systems Development, Nanogen, Inc.
The electronically driven sample preparation chip is a component intended to integrate with Nanogen's microarray technology. By tailoring the electrode design for sample preparation, the chip will perform electronically enhanced functions that include cell concentration, cell sorting, and cell lysis. Although currently being developed for biowarfare, the chip will maintain a versatile platform that will also be utilized in human genome applications and clinical diagnostics.

10:05 Poster and Exhibit Viewing, Refreshment Break

10:45 Towards the Integration of DNA Purification and Amplification into Microfabricated Electrophoretic Devices
Dr. James P. Landers, Department of Chemistry and Pathology, University of Virginia
As microfabrication technologies are refined for the creation of rapid analytical devices for biochemical interrogation, the need for a spectrum of functionalities that extends beyond separation processes becomes apparent. This is certainly the case with genetic analyses carried out on electrophoretic microfabricated chips, where analyses carried out in a few hundred seconds are coupled to sample preparation that may take hours or days. With respect to the PCR amplification portion of the sample preparation, we describe the utilization of an inexpensive infrared heat source (tungsten lamp) for heating small volumes of PCR buffer in plastic and glass microfabricated chips. The rapid and accurate temperature control of microliter and even nanoliter volumes allows for the successful amplification of DNA in 240 seconds. DNA extraction is an aspect of sample prep that is also time-consuming. We describe preliminary results showing that solid phase extraction in a microminiaturized format can be effective for purifying PCR-ready DNA from whole blood in a few hundred seconds.

11:15 High-Throughput Nanoscale Preparation of DNA Samples for Sequencing and Genotyping
Dr. Stevan B. Jovanovich, Science Director and Manager, Advanced Research, Molecular Dynamics/APBiotech-Sunnyvale
New genomics technologies are required to reduce sample volumes and increase analysis throughput for DNA sequencing and genotyping. We have developed the NanoPrep System™ to prepare 500 nL volumes of PCR, genotyping, cycle sequencing, and other reactions. The reactions are performed in arrays of capillaries and then analyzed in an unmodified MegaBACE™ 1000 or in microchips. The NanoPrep approach has been validated using 16- and 96-channel capillary cassettes and is robust for PCR reactions as well as for dye-primer and dye-terminator cycle sequencing reactions. Typical PCR yields are over 10 ng from the 500 nL volumes with the 96-channel cassettes. Over 400,000 bases have been sequenced with readlengths and success rates equivalent or better than that obtained with full-scale reactions. In addition, the NanoPrep System can sequence verify cDNAs directly from ready-to-spot solutions for microarrays, simplifying the bioinformatics and eliminating potential re-arraying problems.

11:45 Panel Discussion

12:15 Luncheon (sponsored by Cambridge Healthtech Institute)

 

Preparation for Microarray and Other Technologies

 

1:30 Chairperson's Comments
Dr. Rudy Spangler, Senior Research Associate, Laboratory of Molecular Endocrinology, The Rockefeller University

1:35 Laser Capture Microdissection-Generated Target Sample for High-Density Oligonucleotide Array Hybridization
Dr. David T. Wong, Associate Professor, Oral Medicine and Diagnostic Sciences, Harvard School of Dental Medicine
This study presents data to demonstrate the feasibility of generating target sample from laser capture microdissection (LCM) tissues suitable to hybridize high-density oligonucleotide arrays for gene expression profiling. RNA was successfully isolated by LCM from five paired cases of oral cancer and linearly amplified using T7 RNA polymerase. Subsequent hybridization of the samples to the HuGenFL GeneChipR probe arrays revealed that 26.5-33.0% of the ~7,000 represented genes are expressed in each of the ten samples. These results demonstrate that LCM-generated tissues can generate sufficient quality cRNA for high-density oligonucleotide microarray analysis, an important step to determine comprehensive gene expression profiling using this high-throughput technology.

2:05 Small Size Sample Preparation for GeneChip Analysis
Dr. Yanxiang Y. Cao, Senior Staff Scientist, Applied Research, Affymetrix Inc.
Most microarray technologies require a fair amount of starting materials. However, in many biological processes and clinical practice only limited samples are available. We have developed robust assays that allow us to monitor genomewide gene expression from as little as a few hundred cells, even single cells. We have applied these methods to study specific properties of the cells in nervous systems using microarrays.

2:35 Rapid Preparation of RNA and Confirmation of mRNA Alterations Detected on Microarrays
Dr. Rudy Spangler
The increased interest in studying alterations in gene expression brought about by the advent of microarrays has led to an increased need for high-throughput methods for preparing RNA extracts as well as for confirming at least a subset of the alterations seen on the microarrays. As many of the researchers newly attracted to the field of gene expression do not have experience working with RNA, there is a need to develop RNA extraction and analysis techniques that can be carried out with a minimum of training. Our laboratory has been applying 96-well format technology to standard RNA extraction procedures as well as to RNase protection analysis procedures. Methods of preparing RNA that can be reverse-transcribed, and for quantitating mRNA to confirm microarray signals, will be described.

3:05 Poster and Exhibit Viewing, Refreshment Break

3:35 Microscale Analysis on Microchip Platforms
Prof. Joseph Wang, Professor, Department of Chemistry, New Mexico State University
The development of miniaturized analytical systems, referred to as "lab-on-chip" devices, has witnessed an explosive growth in recent years. Such microfluidic devices represent the ability to shrink conventional "bench-top" analytical systems with major advantages of speed, integration, cost, portability, and solvent/sample consumption. This presentation will cover fundamental and practical aspects of "lab-on-chip" microsystems and will illustrate their promise for genomic analysis.

4:05 Sample Pooling Approaches to High-Throughput Genetic Analysis
Dr. Russell Higuchi, Research Leader, Human Genetics, Roche Molecular Systems
The measurement of differences in gene allele frequency between case and control populations is used to find associations between genes and disease. This task can be made much more efficient by employing pooled DNA samples. Equal amounts of DNA from all the members of a population are pooled. That one pool, rather than each of perhaps thousands of samples, is subjected to assays that can measure accurately and precisely the relative amounts of different alleles. An approach for this using allele-specific, kinetic PCR will be described in detail.

4:35 Using Lab On A Chip Technology to Access Sample Quality for Microarrays
Dr. Deborah Vitale, Applications Chemist, Agilent Technologies
Microarray technology enables parallel measurement of thousands of expressed genes while minimizing sample consumption. One important step in the microarray process is sample preparation. Lab-on-a-Chip technology provides a complete solution to improving sample preparation for DNA microarrays by identifying potential problems that may result in poor array performance. For example, RNA preparations that are degraded or contain ribosomal RNA or genomic DNA may result in poor probe labeling and can easily be identified using the RNA6000 kit. Fluorescently labeled probe preparations that may result in poor array performance can also be determined. The Agilent 2100 Bioanalyzer rapidly analyzes RNA preparations for integrity, yield, and genomic DNA contamination. Information with regard to amount, size, and the degree of purification of fluorescently labeled cDNA and cRNA probes can also be obtained and strongly correlates to array performance.

5:05 Close of Conference

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CORPORATE SPONSOR BIOGRAPHIES
Ardais Corporation, based in Lexington, Massachusetts, is a leading provider to academe and industry of clinical materials and information needed to accelerate drug discovery research and development. The Company is channeling financial and intellectual resources into a dedicated collaborative effort with medical institutions across the country to systematize and standardize the process of collecting and integrating such materials and information into research-appropriate clinical genomics tools. The Company's family of products and services will enable scientists to validate the clinical relevance of potential biological targets and new therapeutic approaches. The Company believes that its efforts will improve the success rate of drug discovery and overall health care, while reducing costs.

QIAGEN - Innovation Working for You
QIAGEN is the world's leading provider of innovative technologies and products for separating, purifying, and handling nucleic acids. The company's portfolio includes state-of-the-art automation systems for nucleic acid purification and other molecular biology and molecular diagnostics applications. QIAGEN also offers contract services for DNA sequencing, genome analysis, and manufacture of cGMP-grade plasmid DNA.

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TRAVEL INFORMATION
Special Airline Discounts Available
Special zone and discount fares have been established on United Airlines for this conference. Please call Great International and National Travel at 617-527-0800 and ask for Joyce Dunn or e-mail her at jdunn@greatintltravel.com. Or you may call United Airlines Reservations Center directly at 1-800-521-4041. You must reference ID # 579YS.

HOTEL INFORMATION
Seaport Hotel
One Seaport Lane
Boston, MA 02210
T: 617-385-4000
F: 617-385-4001
Room Rates: $159/S • $184/D
Cut-off Date: March 30, 2001

Please call the hotel directly to make your room reservation. Identify yourself as a Cambridge Healthtech Institute conference attendee to receive the reduced room rate. Reservations made after the cut-off date or after the group room block has been filled (whichever comes first) will be accepted on a space-and-rate-availability basis. Rooms are limited, so please book early.

CALL FOR POSTERS
Cambridge Healthtech Institute encourages attendees to gain further exposure by presenting their work in the poster sessions. Please fill out the registration form, with the poster title and primary author. To ensure inclusion in the conference binder, a one-page summary must be submitted and registration must be paid in full by March 23, 2001.
POSTER INSTRUCTIONS

CALL FOR EXHIBITORS
Delegates at Genomic Sample Preparation will be comprised of the top managers and lab directors involved with clinical research held at both a commercial and academic institutes. Companies with services or products relating to lab automation and the collection, handling, storage, and final microarray analysis of nucleic acid samples should seriously consider exhibiting at this event.

Please contact John Rodolewicz at 617-630-1352 to obtain an exhibitor package. Exhibit space is limited so call now and secure this opportunity for your company.

Phone: 617-630-1300
Fax:  617-630-1325
Email: chi@healthtech.com