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Overview

In it’s 3rd year, this internationally-recognized meeting will provide the latest technological developments in biochips technology for their practical applications in drug discovery, medical diagnostics and detection. Major challenges within this emerging technological field which will be addressed by this symposium include:

Conference presentations will discuss such topics as:
• Microarrays in drug discovery
• Array analysis from single cells
• Prioritizing drug candidates by gene expression profiling
• Clone engineering and selection in high throughput biochips
• Microfluidic devices for detection technologies
• Advances in droplet-based bio lab-on-a-chip
• Microarray probes for global gene expression
• Carbon nanotube nanoelectrode arrays for DNA detection
• Flexible high-density oligonucleotide microarrays
• Diagnostic microbial microarrays
• High throughput compound library analysis
• High throughput systems biology
• Microarray lab approach for data analysis and visualization

This half-day workshop will feature presentations based on the cutting-edge technology projects fulfilled at the microarray core laboratories in academic and industrial environments. The moderated discussion will address the many features of establishing and running these core research facilities with different profiles and in different organizational settings.

The scope of the workshop will include discussion of such microarray technology related issues as:

• Profile of a state-of-the-art microarray core facility in academia
• Innovative platform for array-based proteomics
• Microarray platforms: A comparison of oligonucleotide arrays vs. cDNA arrays
• Microarray production: Implementing automation inside the Tornado

Agenda

Wednesday, June 11, 2003

1:30 Registration, Poster Viewing and Refreshments

1:55 Chairperson’s Opening Remarks
Thomas L. Volkert, Director, Center for Microarray Technology, Whitehead Institute, MIT

2:00 Profile of a State-of-the-Art Microarray Core Facility in Academia
Thomas L. Volkert, Director, Center for Microarray Technology, Whitehead Institute, MIT
Core facilities in academia face many challenges as they try to serve the needs of a wide variety of scientific programs. This talk will present a case study in how one core facility has met these challenges. Topics include: Equipment decisions, workflow management, quality control, LIMS, data storage, budgets, integration of resources from other departments and matching technology to applications. Real programs, large and small, will be used to illustrate points.

2:45 PerkinElmer’s Innovative Platform for Array-Based Proteomics
Robert Cavallo, PhD, Product Manager- Protein Microarrays, PerkinElmer Life Sciences
Protein microarrays hold the promise of a faster and more complete understanding of proteomes. Advances in this field will enhance drug discovery by improving target validation and lead optimization. Although complete proteome-wide array-based research is not yet possible, practical applications of protein microarrays are possible today. PerkinElmer Life Sciences has developed platform that addresses the full range of needs for proteomics research in a microarray platform. Unlike nucleic acid microarray applications, protein microarray applications are often truly quantitative in nature. This requires both pecialized tools and a different experimental design. This is mplified by a 42-plex cytokine profiling microarray we are developing. To achieve the degree of precision required for this type of assay, microarrays are printed using PerkinElmer’s non-contact piezotipnology which yields spots with uniform morphology and highly reproducible quantities of probe. HydroGel™ Coated Slides, a three-dimensional matrix allow for probe immobilization in a protein-friendly, hydrophilic environment resulting in very sensitive assays. Assays are carried out on the ProteinArray Workstation, allowing for full automation of even complex, multi-step chemistries. Finally, processed arrays are imaged using a ScanArray laser confocal scanner. Sample data and details on technical approach will be discussed.

3:30 Discussion and Refreshments

3:45 Microarray Platforms: A Comparison of Oligonucleotide Arrays vs. cDNA Arrays
Ernest S. Kawasaki, PhD, Head, Microarray Facility, NCI Advanced Technology Center, National Cancer Institute
To date most gene expression microarrays have been constructed with PCR products derived from cDNA libraries or short oligonucleotides (25mers) synthesized in situ via photolithographic techniques. A third platform, long oligonucleotides (50mer-80mer), are an attractive choice to replace the cDNA arrays as oligo libraries corresponding to the entire coding sequence of many genomes are now available. Studies comparing and contrasting the three-microarray platforms will be presented.

4:30 Microarray Production: Implementing Automation Inside the Tornado
Patrick Yau, Production Manager, The Microarray Centre/University Health Network, Canada
Microarray technology has found numerous applications in gene expression studies, diagnostics and drug discovery. In less than 5 years, the Microarray Centre at the University Health Network has developed instruments and built capabilities in providing printed arrays and related services to research laboratories worldwide. During this period, we have constantly been facing challenges in meeting demands and improving infrastructure while being successful in applying the technology through different scientific collaborations. This presentation will discuss our effort in implementing automation and high-throughput processes so that we can spend our resources and energy on developing the next generation of microarray technology.

5:15 Discussion:
Microarray Core Facilities - Keys to Success in Research and Management

Facilitator - Thomas L. Volkert

5:45 End of Workshop

Main Conference

Thursday, June 12, 2003

8:00 Registration, Poster / Exhibit Viewing, Coffee and Pastries

8:45 Chairperson’s Opening Remarks
Ernest S. Kawasaki, PhD, Head, Microarray Facility, NCI Advanced Technology Center, National Cancer Institute

8:55 KEYNOTE ADDRESS - Multi-Functional Biochip for Pathogen Sensing and Medical Diagnostics
Tuan Vo-Dinh, PhD, Corporate Fellow, Group Leader, and Director, Center for Advanced Biomedical Photonics, Oak Ridge National Laboratory
This paper presents an overview of the development and application of advanced biochips for pathogen detection and biomedical diagnostics. Development of biosensors and biochips is aimed at providing selective identification of toxic chemical compounds at ultra-trace levels in biological systems. Unique antibody-based biochips have recently been developed for the detection of biological species or biotargets for disease diagnostics. Combining the exquisite specificity of biological recognition probes and the excellent sensitivity of laser-based optical detection, these biochips are capable of detecting and differentiating bio/chemical constituents of complex systems in order to provide unambiguous identification and accurate quantification. Development of biochips opens new horizons to biological sensing under field conditions, and biomolecular research in the laboratory. These, and many other biochip applications will be discussed using a novel, recently developed integrated Multi-Functional Biochip as an example of such detection device allowing the simultaneous detection of multiple biological pathogens as well as several disease end-points using different bioreceptors (DNA, antibodies, cellular probes) on a single biochip platform.

9:40 An Autonomous, Continuously-Operating Biodetection System
M. Allen Northrup, PhD, President and CEO, Microfluidic Systems Inc.
We will describe the development and results from a completely autonomous, continuously-operating pathogen detection and identification system. This system includes an air-sampler, complete fluidic sample processing and sample pre-concentration, and real-time, PCR-based detection. Samples that have been successfully detected and identified include pathogenic bacteria and spores. The system concentrates the nucleic acid from the sample by a factor of nearly 1000X and removes PCR inhibitors, making contaminated samples highly detectable.

10:15 An Integrated Plastic Microfluidic Device for Microorganism Detection
Z. Hugh Fan, PhD, Associate Professor, Dept of Mechanic & Aerospace Engineering, University of Florida
An integrated plastic microfluidic device was designed and fabricated for the detection and identification of microorganisms. The device integrates DNA amplification, microfluidic valving, amplicon injection, on-column labeling, and electrophoretic separation. A complete genetic analysis in the single monolithic device is demonstrated by detecting and identifying two food-borne pathogens, E. coli and Salmonella. The device may also be used for the diagnosis of bacterial infections and monitoring the presence of biological warfare agents.

10:50 Refreshment Break, Exhibit / Poster Viewing

11:20 Advances in Droplet-Based Bio Lab-on-a-Chip
Richard B. Fair, PhD, Professor, Dept of Electrical and Computer Engineering, Duke University*
Scalable biochip technology with on-chip sample handling as been demonstrated in a number of applications. The microfluidics control is based on electrowetting, which is a technology that is used for manipulating nano liter droplets of different biological solutions, including contamination-free transport of proteins and whole blood. On-chip functions such as automatic generation of controlled volume droplets, mixing, splitting, and optical detection have been demonstrated. Results will be discussed, including enzymatic assays, micro-PCR, DNA microarray stamping, and multiplexed assays for diagnostics.
*In collaboration with: M.G.Pollack, V.K.Pamula, V.Srinivasan, P.Paik, H.Ren, Duke University

11:55 Polymer-Based Microfluidic Devices
Gert Blankenstein, PhD, Project Manager, STEAG microParts GmbH, Germany
Microfluidic reaction platforms in microplate or microscopic slide format can be designed to integrate typical assay steps like flow propulsion, dosing, mixing or washing. By the use of these devices the instrumentation for sample handling, incubation and detection can be simplified considerably. However, the acceptance of such Lab-on-a-Chip devices strongly correlates with important features like low cost, easy handling, high reliability and a consistent and mature fabrication technology. STEAG microParts uses micro-replication techniques such as microinjection molding for the mass fabrication of polymer based microfluidic devices. Recent developments in molding and assembly allow the fabrication of polymer devices with superior flatness and extremely low fluorescent background. Providing well-suited surface properties STEAG microParts has developed novel polymer based devices for flow-based analysis with application in protein and DANN assays. Latest results on the performance of these lab-on-a-chips will be discussed. By example of such integrated assays the use of proven design elements and rapid prototyping methods will be presented. Different laser welding techniques as possible method to join plastic microstructures with micron precision will be presented and compared.

12:30 Luncheon Sponsored by The Knowledge Foundation

2:00 Chairperson’s Remarks
Emile F. Nuwaysir, PhD, Senior Manager, Technical and Client Services, NimbleGen Systems, Inc.

2:05 The Use of Microarrays in Drug Discovery
Gianfranco de Feo, PhD, Program Manager, Genomics Collaborations, Affymetrix, Inc.
The development and increased use of microarrays to study expression patterns of samples relevant for the study of disease and therapies has led to a wealth of knowledge previously unavailable to the drug development scientist. The use of microarrays to better understand the molecular mechanisms of disease, and in the identification of potential therapeutic targets is well established and has been shown to be extremely fruitful. However, more recently, many pharmaceutical companies are moving the use of microarrays, for expression monitoring or large-scale genotyping, to later stages in the drug development process. The use of arrays in target validation, toxicological investigations (or pre-clinical safety studies), and in clinical trials is growing and there are now examples demonstrating the advantages of using microarrays in downstream drug development processes. Published examples from the literature as well as examples from collaborations will be discussed in order to explore the uses of microarrays in target validation, toxicology and clinical trials.

2:40 Clone Engineering and Selection in High Throughput Biochips
Andrey J. Zarur, PhD, President & CEO, BioProcessors Corp.
BioProcessors Corp. has developed a novel high throughput biochip platform that allows for the fast generation and selection of clones for recombinant protein and monoclonal antibody production. This platform, named SimCell™, has the potential of significantly expediting the molecular biology aspects of biopharmaceutical development. Results of transfection and selection of mammalian cell lines for production of a drug candidate in this novel platform will be presented.

3:15 High Throughput Compound Library Analysis
Hugh McManus, PhD, Vice President, Applications Development, Nanostream, Inc.*
Pharmaceutical compound library integrity is a growing issue among pharmaceutical companies. In some cases, ten to twenty percent of compounds are less than 50% pure after a year. This high degree of uncertainty comprises the validity of high throughput screening data and increases costs to pharmaceutical companies. This talk will focus on a novel method for high throughput liquid chromatography that can economically screen large compound libraries. Recent results will be presented.
*In collaboration with: G.Dantsker, L.Zhang, P.Patel, J.Koehler, S.Hobbs, and K.Anderson, NanoStream, Inc.

3:50 Refreshment Break, Exhibit / Poster Viewing

4:20 Prioritizing Drug Candidates by Gene Expression Profiling
Leming Shi, PhD, Director, Informatics, ChipScreen Biosciences, Ltd., China*
DNA microarray technology is an important component of Chipscreen’s chemical genomics-based drug discovery platform (www.chipscreen.com). Changes in global gene expression profiles by Chipscreen’s compounds are compared to those resulted from the treatment by standard commercial products. Such comparisons, in combination with the characteristics of activity fingerprints from multi-target high throughput screening, provide critical information about prioritizing drug candidates for preclinical development.
*In collaboration with: W.Hu, Z.Ning, Z.Li, and X.Lu, ChipScreen Biosciences Ltd.

4:55 ArrayInformatics®: An Integrated Microarray Lab Approach for Effective Data Analysis and Visualization
Dile Holton, PhD, Product Manager - ArrayInformatics, PerkinElmer Life and Analytical Sciences
Data and information management in an active microarray laboratory is demanding new and flexible approaches be taken to address the quantity of data generated and provide comprehensive data analysis and visualization. Effective solutions will require networked instruments directly streaming workflow information and raw data into application focused relational databases. Microarray analysis and visualization tools must have the capability to easily access the stored and organized data, process the increasingly complex data sets and integrate the necessary information from multiple sources for validated data nterpretation. Emerging software packages, such as ArrayInformatics®, will impact data management by providing direct data flow paths from scanners, spotters, uantitation software and coordinating information retrieval from utside accessible databases.

5:30 Selected Oral Poster Presentations and Discussion

6:00 End of Day One

Friday, June 13, 2003

8:15 Poster / Exhibit Viewing, Coffee and Pastries

MICROARRAY APPLICATIONS AND NANOTECHNOLOGY

9:00 Chairperson’s Remarks
Richard B. Fair, PhD, Professor, Dept of Electrical and Computer Engineering, Duke University*

9:05 Flexible High-Density Oligonucleotide Microarrays
Emile F. Nuwaysir, PhD, Senior Manager, Technical and Client Services, NimbleGen Systems, Inc.
NimbleGen has developed a process that can manufacture custom oligonucleotide arrays with up to 786,432 unique oligonucleotide probes, in a 2.3 cm² area, in less than 3 hours. Collaborators are using these arrays for a wide variety of functional genomics applications, including eukaryotic and prokaryotic gene expression, genome mapping, comparative genomics, pathogen detection, resequencing, and molecular cytogenics. In addition, massively parallel genotyping assays are in development. Data from these experiments will be presented.

9:40 A Novel Method for Deriving Non-Redundant cDNA Probes for Microarray Production
Michael D. Kane, PhD, President, Trivera Bitoechnology
Conducting gene expression profiling is limited to the availability of cDNA clones and/or sequence information to produce cDNA-probe and oligonucleotide-probe microarrays, respectively. The lack of such resources has hindered genomic research in many research models and organisms. Presented is a method of deriving a set of non-redundant, 3’ cDNA fragments from the target tissue of interest for the purposes of producing DNA microarrays for genomic research in any organism.

10:15 Empirical Selection of 60-mer Microarray Probes for Global Gene Expression
Jim Collins, PhD, Senior Scientist, BioResearch Solutions, Agilent Technologies, Inc.
Agilent’s high-density Oligonucleotide Catalog microarrays consist of empirically selected 60-mer probes for precise monitoring of global gene expression. We have utilized the flexibility of the Agilent in situ platform to develop an experimental process that allows determination of the optimum probe sequence to represent each gene. The reproducibility and sensitivity of these microarrays allows for extremely accurate differential expression measurements, even when starting material is limited.

10:50 Refreshment Break, Exhibit / Poster Viewing

11:20 Optical Fiber Microarrays
David R. Walt, PhD, Professor, Chemistry Dept, Tufts University
We have used coherent imaging fibers to make fiber-optic chemical sensors. Sensors can be made with spatially-discrete sensing sites for multianalyte determinations. We are investigating the limits of our ability to create high-density sensing arrays containing thousands of microsensors and nanosensors. Micrometer- and nanometer-sized sensors have been fabricated by etching the cores of the optical imaging fiber to create wells and loading them with micro and nanospheres. Such arrays can be employed for making oligonucleotide and protein arrays, and cell-based biosensors.

11:55 Carbon Nanotube Nanoelectrode Array for Ultrasensitive DNA Detection
Jun Li, PhD, Senior Research Scientist, Eloret Corp. / NASA Ames Research Center*
A reliable nanoelectrode array based on vertically aligned multi-walled carbon nanotubes (MWNTs) embedded in SiO₂ is used for ultrasensitive DNA detection. Characteristic electrochemical behavior is observed using MWNT array electrodes for measuring both bulk and surface immobilized redox species. Oligonucleotide probes are selectively functionalized at the open ends of the nanotube array. The hybridization of a subattomoles of DNA targets is detected using electrochemical mechanism. This system provides a general platform for many applications requiring ultrahigh sensitivity as well as high-degree of miniaturization.
*In collaboration with: H.T.Ng, A.Cassell, W.Fan, H.Chen, Q.Ye, and J.Han, Eloret Corp./NASA Ames Research Center; J.Koehne and M. Meyyappan, NASA Ames Research Center

12:25 Lunch on Your Own

BIOANALYTICAL AND DIAGNOSTIC APPLICATIONS

2:00 Chairperson’s Remarks
Jim Collins, PhD, Senior Scientist, BioResearch Solutions, Agilent Technologies, Inc.

2:05 Array Analysis from Single Cells: A Review and Interim Results
Ernest S. Kawasaki, PhD, Head, Microarray Facility, NCI Advanced Technology Center, National Cancer Institute
Knowledge of the human genome sequence allows the esearcher to determine the identity of all genes expressed in normal vs. cancerous tissues. Most studies require a relatively large sample to obtain sufficient RNA for expression studies, making it difficult to obtain pure populations of cells. Array analysis from single cells can alleviate this problem but requires extensive amplification of mRNA sequences. Methods to accomplish this will be discussed, and preliminary data will be presented.

2:40 MassARRAY™: A Broad-Based DNA Analysis Platform Enabled by Mature Biochip Products and Highly Automated MALDI-TOF Detection
Paul J. Heaney, PhD, Executive Vice President, Research & Technology, SEQUENOM, Inc.
SEQUENOM’s MassARRAY™ system is based on MALDI-TOF analysis. A key technical enabler is the design and use of patented microchips, SpectroCHIP™, for the arraying and presentation of nucleic acid analytes. The array format also enables rapid fully automated analysis. SEQUENOM has expanded the applications to a wide variety of DNA analysis needs, including gene expression analysis, SNP discovery, resequencing, and allele frequency determinations. This presentation will focus on these performance enhancements.

3:15 Analysis of Cellular Pathways Using the eTag™ Assay System: An Approach to High Throughput Systems Biology
Dennis W. Harris, PhD, Senior Vice President, Systems Integration & Business Development, ACLARA BioSciences
The systematic analysis of genes and proteins associated with metabolic pathways demands a multiplexing platform that enables accurate, quantitative screening of tens to hundreds of analytes from thousands of samples. The eTag™ Assay System is a homogeneous method for the quantification of proteins and mRNA’s in cell lysates or whole cells. The ability to simultaneously study both proteins and mRNAs facilitates a systems biology approach. This presentation will explore the use of the System to analyze cell signaling and response pathways in normal and disease states.

3:50 Refreshment Break, Exhibit / Poster Viewing

4:20 Labeling DNA and RNA for Differential Gene Expression Using Microarrays
Patricia C. Mayer, Applications Lab Manager, PerkinElmer Life Sciences
Three labeling technologies are compared for use in differential gene expression experiments on nucleic acid glass microarrays. Conventional enzymatic fluorescence labeling using Cyanine 3 and Cyanine 5 labeled nucleotides, a signal amplification technology, TSA, and a new direct fluorescent labeling technology are compared in each technique’s sample RNA requirement, signal output, ease-of-use, and expression results. Emphasis is placed on a novel labeling technology, MICROMAX™ ASAP, which overcomes 3’ end labeling bias by directly labeling mRNA. An mRNA target exhibits far less bias between the 3’ and 5’ regions of the genes than corresponding cDNA assays. This novel mRNA labeling technology gives researchers the ability to study such phenomenon as, alternative splicing and mRNA isoforms where full-length gene representation is a necessity.

4:55 Diagnostic Microbial Microarrays
Levente Bodrossy, PhD, Research Scientist, Dept of Biotechnology, ARC Seibersdorf Research GmbH, Austria
A generally applicable set of techniques, based on readily available technologies and materials, was developed for the design, production and application of diagnostic microbial microarrays. A microarray targeting the particulate methane monooxygenase (pmoA) and ammonia monooxygenase (amoA) genes was developed for the detection and quantification of methanotrophs, aerobic ammonia oxidizing bacteria and functionally related bacteria. A microarray consisting of a set of 59 probes that covers the whole known diversity of these bacteria was validated with a representative set of extant strains and environmental pmoA/amoA clones. The potential of the pmoA/amoA microarray was tested with environmental samples. The results were in good agreement with those of clone library sequence analyses. The approach can currently detect less dominant bacteria down to 5% of the total community targeted. Initial tests assessing the quantification potential of this system showed very good correlation with the expected results with standard deviations in the range of 0.4-17.2 %. Reliable quantification of environmental samples with this method requires the design of a reference mixture consisting of very close relatives of the strains within the sample.

5:30 Discussion. Closing Remarks / End of Conference

Call for Posters

Industry and academic scientists are encouraged to submit poster titles for this event. One-page abstracts (8 1/2" x 11" with 1-inch margins) must be submitted no later than May 16, 2003 for inclusion in conference documentation. Additional poster submissions will be accepted until June 2, 2002 but may not be included in conference documentation.

Note: If you're submitting a poster, you MUST be registered and paid registration fee plus posterboard reservation fee in advance to ensure that a posterboard is reserved for you.

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