Immediately prior to CHI’s Second Annual Genomic and Proteomic Sample Preparation

Microarrays have become the modern equivalent of the microscope, and one can imagine the day when they supplant the stethoscope too. While there is no question that they confer new insights into old problems, enthusiasm must be tempered with old-fashioned skepticism. So we must ask: What can microarrays reliably provide, and where is the greatest need for improvement? This conference will also examine critical questions to the application of these machines, to data analysis, and to the tacit assumptions researchers have made in the larger biological picture-sometimes without enough innovation or rigor. Lastly, we will take into account the large initial capital investment that can be a barrier to entry for microarrays, leading to what makes sense for your cents, alongside results that reward remuneratively.

Corporate Sponsors

Sponsoring Publications
Bioinform
Current Opinion in Molecular Therapeutics
Drug Discovery and Development
Disease Markers
Genome Letters
Genomics and Proteomics
Genome Technology
PharmaGenomics

Web Partners
Lab-on-a-Chip.com
Pharmacogenomicsonline.com

Technology
Dr. Stanley Abramowitz, Advanced Technology Group
Dr. Ronald K. Blackman, Millennium Pharmaceuticals, Inc.
Dr. Barry Bochner, Biolog Inc.
Dr. Gianfranco de Feo, Affymetrix Inc.
Dr. Dan Ehrlich, The Whitehead Institute
Prof. Roger Philip Ekins, University College London
Dr. Andy McShea, CombiMatrix Corporation
Dr. Lloyd M. Smith, University of Wisconsin-Madison
Dr. Peer F. Stähler, febit ag
Dr. Michael Van Dam, California Institute of Technology
Dr. David R. Walt, Tufts University

Informatics and Data Analysis
Dr. Warren Casey, GlaxoSmithKline
Dr. Gary A. Churchill, The Jackson Laboratory
Mr. Jason Goncalves, Iobion Informatics
Dr. Jonathan Greene, Schering-Plough Corporation
Dr. Ken Hess, M.D. Anderson Cancer Research Center
Dr. C. Bret Jessee, AnVil
Dr. Javed Khan, National Cancer Institute and National Human Genome Research Institute
Dr. Michael Leibman, Abramson Family Cancer Research Institute
Dr. Sayan Mukherjee, Massachusetts Institute of Technology
Dr. Toby Segaran, Incellico, Inc.
Dr. Richard Simon, National Cancer Institute
Dr. Jason Stewart, Open Informatics

Protein Arrays
Dr. Joanna S. Albala, Lawrence Livermore National Laboratory
Dr. Kevin Auton, NextGen Sciences Ltd.
Dr. Julian E. Beesley, LifeSpan BioSciences
Dr. Warren Casey, GlaxoSmithKline
Dr. Gengxi Hu, Shanghai Institute of Cell Biology
Dr. Karin A. Hughes, Prolinx, Inc.
Dr. Roland Kozlowski, Sense Proteomic Ltd.
Dr. Anil Sehgal, ChemGenex Therapeutics Inc.
Dr. David M. Sabatini, The Whitehead Institute
Dr. Stefan Schmidt, GPC-Biotech AG
Prof. Jens Schneider-Mergener, Jerini AG
Dr. Heng Zhu, Yale University

QC, Validation, and Comparisons
Dr. Rong Seng Chang, National Central University of Taiwan
Dr. David Gerhold, Merck & Co.
Dr. Trey Ideker, The Whitehead Institute

Applications
Dr. Bruce Aronow, University of Cincinnati and Children's Hospital Medical Center
Dr. George M. Church, Harvard Medical School
Dr. Elena V. Grigorenko, Millennium Pharmaceuticals, Inc.
Dr. Jutta Heim, Novartis Pharmaceuticals Research
Dr. Spyro Moussses, NIH
Dr. Thomas Meyer, LION bioscience AG
Dr. Matthew Meyerson, Dana-Farber Cancer Institute and Harvard Medical School
Dr. Emanuel F. Petricoin, U.S. Food and Drug Administration
Dr. John C. Rockett, U.S. Environmental Protection Agency
Dr. Ricardo Saban, Oklahoma University Health Sciences Center

Pre Conference Tutorial Conquering Microarray Analytics and Informatics Sunday, April 28, 2002 2:00 pm - 6:00 pm Conquering Microarray Analytics and Informatics Dr. Jack Pollard, Principal Investigator-Bioinformatics, 3rd Millennium Inc. This tutorial will present an overview of the major computational problems you have to solve to be successful with DNA microarrays in gene expression studies. The presentation is aimed at people who are just getting started with microarrays, as well as those who are stepping up from pilot projects to large-scale facilities. Dr. Pollard will cover data analysis in depth and will provide researchers with an introduction to relevant information systems issues. He will talk about the issues from a user's perspective and will help you understand the kinds of analyses and commercial and academic software packages that make sense for different kinds of experiments. Various algorithms and statistical methods will be discussed, though the survey nature of this tutorial does not permit us the time to delve deeply into the mathematical details.

 

Sunday, April 28

4:00-6:00pm Early Registration and Poster and Exhibit Set-up

 

Monday, April 29

7:30am Registration, Poster and Exhibit Viewing, and Light Continental Breakfast

 

Technology

8:30 Chair's Opening Remarks
Dr. Stanley Abramowitz, Co-founder, Advanced Technology Group

8:35 Where We've Been: Where We Should Go Integrating DNA Analysis in Microfabricated Formats
Dr. Stanley Abramowitz
The use of single chips or cartridges for the integration of all the steps of DNA analysis from sample preparations to answers will be discussed. Formats for a variety of analysis technologies including electrophoresis, hybridization, and mass spectrometry will be discussed with examples provided from the archival literature.

9:05 Keynote Presentation Ultrasensitive microarray technology. Prof. Roger Philip Ekins, Emeritus Professor and Head of Department, Division of Molecular Endocrinology, University College London Microarray-based assay methods, first developed by my colleagues and myself in the mid-80s, represent the latest form of ligand assay methodology, of which radioimmunoassay and DNA assay are well known examples. It is seldom recognised that microarray technology conflicts with previously accepted principles of ligand assay design, whose basic objectives were the maximisation of assay sensitivity and precision. It was our demonstration that microarray methods could be more sensitive and faster than contemporary ligand assay methods , whilst enabling the simultaneous assay of tens, hundreds or thousands of analytes, that led to our collaboration with Boehringer Mannheim in 1991 on the technology's industrial development, the outcome of which was the development of microarray methods some three orders of magnitude greater in sensitivity than achieved by others who have since entered the field.

9:45 Microfabricated "Chip" Device That Miniaturizes the Process of Electrophoresis
Dr. Dan Ehrlich, BioMEMS Laboratory, The Whitehead Institute
Microelectrophoresis chips for DNA genotyping and sequencing that are capable of resolving simple tandem repeats in a minute time frame and reading 400 bases in ten minutes and 800 bases in an hour will be discussed.

10:15 Poster and Exhibit Viewing, Refreshment Break

11:15 Desktop Synthesizers for Fabrication of Customized in-Situ Oligonucleotide Biochips
Dr. Andy McShea, Director, Applied Science Group, Combimatrix Corporation
CombiMatrix is developing a novel semiconductor-based desktop microarray platform that will fabricate custom oligonucleotide biochips overnight. Microarrays with unique content are designed and fabricated on the fly using a software-driven process to generate reagents electrochemically. DNA oligonucleotides are synthesized in situ according to the particular probe sequence design file whereby probe sequences are designed using a complex algorithm that has been developed and tested empirically on the CombiMatrix platform.

11:45 SNP Analysis Using Surface Invasive Cleavage Reactions on Addressed Arrays
Dr. Lloyd M. Smith, Kellett Professor of Chemistry, Department of Chemistry, University of Wisconsin-Madison
The structure-specific invasive cleavage of single-stranded DNA by 5’ nucleases is a useful means for sensitive detection of single-nucleotide polymorphisms or SNPs. Our approach to the parallelization of SNP analysis is to adapt the invasive cleavage reaction to an addressed array format. Results will be presented with both a fluorescence-based (FRET) surface detection method, and a label-free surface detection method utilizing imaging Surface Plasmon Resonance (SPR).

12:15 Luncheon (on your own)

1:30 Three Concurrent Technology Workshops
Sponsored by:

2:15 HTS Applications of Single Live Cell Arrays Fabricated on an Optical Imaging Fiber
Dr. David R. Walt, Robinson Professor of Chemistry, Tufts University
A high-density ordered array of microwells is fabricated on an optical imaging fiber's face with a packing density of 10E7 wells/cm 2. Each individually addressed microwell is used to accommodate a single living cell. A CCD detector is employed to monitor and spatially resolve the fluorescence signals obtained from each cell allowing simultaneous monitoring of physiological and genetic responses of all the cells in the array using reporter genes (lacZ, GFP, and its spectral mutants) or fluorescent indicators. Yeast, bacteria, and mouse fibroblast cell arrays were fabricated and used to demonstrate HTS cell assays at the single cell level. The rapid optical analysis allows simultaneous measurements of different strain responses by monitoring the unique multiple responses of individual cells from each strain. The single cell array technology provides a reliable and accurate tool for screening and validation of new disease-associated cellular targets and for early-stage evaluation of potential drug candidates.

2:45 Geniom® Technology: Exploring Nature's Plasticity with a Flexible Probing Tool
Dr. Peer F. Stähler, Vice President and Chief Scientific Officer, febit ag
Entering the post-genome era with an increasing amount of sequence data available in databases, a complex matrix of possibilities is opened for genome research. To address this vast arena of genomic questions, we designed a flexible probing tool based on DNA microarrays. The technology was designed to handle all kinds of genomic assays like expression profiling, genotyping, or resequencing for any given organism with the only prerequisite being that sequence data are available. The arrays are in-situ fabricated, hybridized, and analyzed within one single bench top instrument. The whole assay itself is defined by a software file (Digital Array) that holds the sequence data for all DNA-probes that will be put onto the array. New microarrays can be developed by altering the composition of these files, either creating completely new arrays or combining existing ones. Alternatively, the very same established array can be used repeatedly without any long-term ordering or manufacturing. The arrays can be shared by users easily via the Internet. Recently, the first prototype was placed for field tests at the German Cancer Research Centre (Deutsches Krebsforschungszentrum, DKFZ). Current projects on the new platform include assays for mutation detection in the BRCA 1 gene and development of chip-based HPV diagnostics, as well as expression profiling studies on microorganisms (S. cerevisiae, N. crassa) or human including efforts for analyzing splice variants associated with the progression of cancer. Concept of these applications and first results will be presented.

3:15 Poster and Exhibit Viewing, Refreshment Break

4:00 Microfluidics, Single Molecule Biophysics, and Microarrays
Dr. Michael Van Dam, California Institute of Technology
There are three current goals. (1) Decrease the amount of RNA needed. In many cases probe material is limiting the experiments. Smaller sample sizes will allow the study of histological samples and developmental studies. Presently, about 100 microgram of total RNA is required to do a microarray experiment. A substantial reduction in the sample size could be made by optimizing the hybridization process. (2) Increase the reliability of measurements. Typically, microarray experiments are compared to a control. The two are simultaneously hybridized to the microarray but labeled with different color fluorophores. Results are expressed as a ratio of the two measurements. When a gene is rarely expressed in the control, the ratio is often unreliable. By building a three-color scanner and using genomic DNA as an internal control, we may be able to make an independent measurement of the DNA content of each spot in the microarray. This will allow cross-comparison of measurements over time and between laboratories. (3) Provide new tools to interpret the data. A single experiment can easily generate data on 5,000 to 40,000 different genes. Software is needed to provide an interface to the wealth of data collected. New methods of analysis are being developed to make sense of the data.

4:30 Phenotypic Microarrays™ Provide Better Information Leading to Better Decisions in Drug Discovery Effort
Dr. Barry Bochner, Vice President of Research and Development, Biolog Inc.
The Biolog Phenotype Microarray™ technology is capable of measuring the effect of one gene in the cell under thousands of growth conditions simultaneously, providing researchers with the most comprehensive cell function information available from any existing cell-based assay format. PM technology provides snapshots of cell growth under a wide variety of conditions simultaneously, complementing both DNA microarray and proteomics studies. PM technology is actively being applied to the study of infectious diseases and to production and in a variety of steps in drug development. Phenotypic Microarrays™ have been successfully used to study changes in an organism's phenotype due to developmental changes, mutations, and environmental changes and in response to specific drug leads.

5:00 Using Complementary Whole-Genome Technologies to Reveal the Cellular Impact of Human Therapeutic Drugs
Dr. Ronald K. Blackman, Senior Scientist II, Functional Genomics Group, Millennium Pharmaceuticals, Inc.
While the biochemical targets of most drugs are known, the biological consequences of their actions are typically less well understood. We have been using two whole-genome technologies in Saccharomyces cerevisiae to determine the cellular impact of drug treatment. By combining population genomics, the screening of a comprehensive panel of bar-coded mutant strains, and transcript profiling, we can identify the proteins and pathways most affected by the compounds, including their cellular targets. Used together, these complementary technologies provide a general and powerful means to elucidate the cellular ramifications of drug therapies.

5:30 The Use of GeneChip Technology for Gene Expression and Genotyping Applications
Dr. Gianfranco de Feo, Program Manager, Genomic Collaborations, Affymetrix Inc.
GeneChip Technology has been recognized as a platform of choice for many academic and pharmaceutical researchers. I will briefly discuss some of the unique features of the technology and the advantages they bring to highly parallel gene expression and genotyping studies. I will then review several key studies that were performed by researchers using the technology.

6:00 DNA Microarrays: Characterization of Complex Biological Systems
Dr. Jutta Heim, Executive Director and Senior Scientific Expert, Molecular and Cell Biology, Novartis Pharmaceuticals Research
High-density cDNA or oligonucleotide arrays have been developed which allow for transcriptional profiling of a major fraction of genes in a given cell type or of any biological process. The temporal pattern of gene expression during induction of apoptosis has been chosen as experimental paradigm. Comparison of physiological with drug-triggered apoptosis points to intersections of genes commonly regulated, as well as to groups of genes representative for individual drugs. Different approaches of pattern recognition as well as high-throughput downstream functionalization of putative candidate genes are presented.

6:30 Reception (sponsored by CHI)

7:30 Close of Day One

 

Tuesday, April 30

7:30am Technology Workshop
Innovative Microarray Production and Analysis Technologies for Protein Applications
Robert Cavallo, PhD
Sponsored by

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

 

CONCURRENT TRACKS

Track #1: Informatics and Data Analysis 8:30 Chair's Remarks Dr. Michael Leibman, Director, Computational Biology, Abramson Family Cancer Research Institute 8:35 Microarrays: Handling the Deluge of Data and Extracting Reliable Information Dr. Kenneth R. Hess, Associate Professor, Department of Biostatistics, M. D. Anderson Cancer Center Application of powerful, high-throughput genomics technologies is becoming more common, and these technologies are evolving at a rapid pace. Genomics facilities are being established in major research institutions to produce inexpensive, customized cDNA microarrays that are accessible to researchers in a broad range of fields. These high-throughput platforms have generated a massive onslaught of data, which threatens to overwhelm researchers. Although microarrays show great promise, the technology has not matured to the point of consistently generating robust and reliable data when used in the average laboratory. This presentation addresses several aspects related to the handling of the deluge of microarray data and extracting reliable information from these data. We review the essential elements of data acquisition, data processing, and data analysis and briefly discuss issues related to the quality, validation, and storage of data. Our goal is to point out some of the problems that must be overcome before this promising technology can achieve its full potential. 9:05 The State of the Art in Microarray Data Format Dr. Jason Stewart, Co-founder, Open Informatics I am the primary instigator of Open Informatics, a contract bioinformatics consulting company. Besides educating scientists about the benefits of Open Source and inciting riots with petitions to get public funding agencies to endorse Open Source, I work on a number of Open Source projects including GeneX, MGED, MAGEstk), and GO. 9:35 Interpretation of Gene Expression Array Data Sets from the Perspective of the Toxicologic Pathologist Dr. Warren Casey, GlaxoSmithKline The perspective of a biologist on mathematical modeling during the "Omics" revolution will be presented. 10:05 Poster and Exhibit Viewing, Refreshment Break 10:35 Biomedical Informatics: Critical Issues for Analysis of Microarrays Dr. Michael Leibman The analysis and interpretation of microarray data are key challenges facing the functional genomics researcher today. The refinement of data acquisition and experimental design are the first steps in the essential but not complete pathway for analysis. A critical phase involves careful examination of the clinical aspects of the diagnosis and the ability to incorporate additional information in an investigative or confirmatory manner. The development of algorithms to support these efforts will be presented. 11:05 Application of Statistical Learning Theory to DNA Microarray Analysis Dr. Sayan Mukherjee, Massachusetts Institute of Technology The learning-from-examples paradigm is becoming important in problems in bioinformatics and functional genomics. The Center for Biological and Computational Learning, in collaboration with the Cancer Genomics Program, has been applying learning algorithms to problems in molecular classification of cancer. We have mainly focused on classifying microarray or gene expression data. The problems range from binary classifications of morphology or cell lines to predicting treatment outcome or drug sensitivity. A multiclass problem of classifying 14 different solid and liquid tumor types is also being addressed. In the framework of statistical learning theory, the main challenge in these problems is the high dimensionality and very small size of the training and testing sets. The basic problem of representation has a specific twist here because inputs are often sequences. Thus an active area of relevant research is designing kernels that take strings as inputs. 11:35 Classification and Diagnostic Prediction of Cancers Using Gene Expression Profiling and Artificial Neural Networks Dr. Javed Khan, Investigator, National Cancer Institute; and Adjunct Investigator, Advanced Technology Center, National Human Genome Research Institute Gene expression profiling, using DNA microarrays, permits a simultaneous analysis of multiple markers and has been used to categorize cancers into subgroups. However, despite the plethora of statistical techniques to analyze gene expression data, none so far has been rigorously tested for its ability to accurately distinguish cancers belonging to several diagnostic categories. Artificial neural networks (ANNs) are computer-based algorithms, modeled on the structure and behavior of neurons in the human brain, that can be trained to recognize and categorize complex patterns. We have developed a method of classifying cancers to specific diagnostic categories based on their gene expression signatures using ANN. 12:05 Lunch (sponsored by Cambridge Healthtech Institute) 1:30 Statistical Genetics Dr. Gary A. Churchill, Staff Scientist, The Jackson Laboratory Gene expression technology has seduced the genomics community with its power and promise to unravel the genetic program. However, the experimental paradigms for this technology are not yet fully developed. For example, the response function (signal as a function of RNA concentration) has not been carefully studied for most technologies. There are many levels at which experimental error and noise can enter into the system. 2:00 High-Dimensional Microarray Data Mining, Analysis, and Visualization Dr. C. Bret Jessee, Director, Program Management, AnVil High-throughout microarray technologies have greatly accelerated the rate at which multivariate experiments can be performed and have yielded truly massive quantities of data for analysis and interpretation. Due to the limitations of conventional means of analysis, viewing the "big picture" usually requires dimensional reduction of data sets before computing and visualizing data structures and meanings. At the high cost of generating mega- and gigabyte data sets, discarding data due to limitations imposed by choice of computational tools is neither economical nor technically justifiable. As a solution, we present visual analytical tools that preserve the value of information held in massive databases, using the leukemia data set of Golub and Slonim et al. (1999) as an illustration. While many groups have evaluated these data, our analysis makes unique and important contributions by providing analytical visualizations of cancer class clusters of the 72 patient samples in 6817-dimensional gene space as well as providing a diagnostic predictor for chemotherapy treatment outcome. We review our results in comparison to other published findings to emphasize the merits of initiating microarray analysis, using high-dimensional methods, on the complete data set. 2:30 Microarray Gene Expression Database Integration Dr. Jonathan Greene, Director, Bioinformatics, Schering-Plough Corporation Microarray hybridization experiments provide a quick pathway to potential data overload. Effective utilization of microarray expression data involves several facets including collection and storage of the data, a requirement for a robust query system to extract relevant data sets, and a requirement to interface with statistical analysis packages, as well as a means to gather pertinent information on the genes that are being analyzed. This presentation will discuss strategies to address these issues. 3:00 Poster and Exhibit Viewing, Refreshment Break 3:45 The State of the Art of Microarray Informatics Dr. Richard Simon, Chief, Biometric Research Branch, and Head, Molecular Statistics and Bioinformatics Section, National Cancer Institute Microarray expression profiling is a powerful tool for biomedical research, but currently both the technology and the methodology for data analysis are undergoing rapid evolution. There is considerable uncertainty among biologists about design and analysis issues to make effective use of microarray technology. This talk will provide an overview of the state of the art of microarray informatics. Effective design and analysis strategies must be tuned to the study or project objectives; data mining of arrays generated with no clear objective is not likely to be productive. I will review recently developed analytic strategies that are very effective for specific kinds of problems. I will also address design considerations, including recommendations on the levels and amounts of replication needed. Based on the experience of my group in the analysis of microarray data and the development of methods, we have developed software, BRB-ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html), to serve as a vehicle for training biologists in important aspects of microarray data analysis and for making available in one package analysis methods that are statistically valid and powerful for a variety of types of studies. 4:15 Assessment of Common Normalization Methods for cDNA Microarray Analysis Mr. Jason Goncalves, Chief Scientific Officer, Iobion Informatics We have developed a scheme to assess normalization methods using a metric for reproducibility between reciprocally labeled replicate experiments. Using a large set of reciprocally labeled replicate microarray hybridizations, we have assessed common normalization methods including approaches employing a single normalization value for the entire array vs. grid-by-grid normalization. We have also evaluated different spot-filtering criteria and their effect on normalization. We found significant differences between the assessed normalization methods. Our findings can be used to improve reproducibility of results from microarray experiments, thus allowing one to make the most of every hybridization. 4:45 An All-Inclusive Database Dr. Toby Segaran, VP, Research & Development, Incellico, Inc. Central to Incellicos' tools and applications is its patent-pending Coded Electronic Life Library™ (CELL™) database technology, derived from the consolidation and cross-referencing of biological entity information in an ontology-based system. CELL captures and identifies the relationships between biological entities contained within the data, allowing researchers to intuitively navigate webs of information, thereby enabling quicker access to the important data and streamlining activities in the discovery process. 5:45 Close of Day Two Track #2: Protein Arrays 8:30 Chair's Remarks Dr. Joanna S. Albala, Senior Biomedical Scientist, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratories 8:35 The impact of Functional Proteomics on Pharmaceutical R&D Dr. Roland Kozlowski, Chief Executive Officer, Sense Proteomic Ltd. I will talk about how functional protein arrays can be used for target identification, lead, and candidate optimization work. Examples from Sense will be provided. 9:05 Tissue Proteomics: Adding Value to Microarray Technology Dr. Julian E. Beesley, Vice President, Business Development, LifeSpan BioSciences Very high throughput screening of potential drug targets and molecules is accomplished with microarray technology. High-throughput tissue proteomics, utilizing immunohistochemistry to localize gene families directly in human tissues at the cellular level, contributes to more efficient prioritization of drug targets, to the identification of potential toxicity problems, and to the realization of new drug use indications. A database format with the addition of extensive bioinformatics further enhances the information thus obtained. LifeSpan BioSciences' gene family localization database approach, in conjunction with microarray technology, can contribute significantly to the drug discovery pathway. 9:35 Interpreting Gene Expression Data Sets : The challenge of Understanding the Biology Behind the Data Dr. Warren Casey, Toxicogenomics, GlaxoSmithKline The fields of Bioinformatics and Statistics have given rise to numerous techniques for analyzing data. Assessing the physiological significance of changes in gene expression much more difficult. Case studies will be presented which identify potential pitfalls and highlight the challenges associated with interpreting differential gene expression data. 10:05 Protein Expression Microarrays for Proteomics Dr. Joanna S. Albala, Senior Biomedical Scientist, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory The key advantage to array-based methods for protein study is the parallel analysis of thousands of samples in an automated, high-throughput fashion. In this "post-genomic" era, proteins and their study en masse, proteomics, are the next scientific frontier. We have developed a method to utilize I.M.A.G.E. (Integrated Molecular Analysis of Genomes and Their Expression) cDNAs to generate recombinant protein libraries using a baculovirus-based paradigm. Protein arrays are produced in a microtiter, automatable format that can be assayed using genomic technologies for structure or function. This work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48. 10:35 Poster and Exhibit Viewing, Refreshment Break 11:05 Global Analysis of Protein Activities Using Protein Chips Dr. Heng Zhu, MCD Biology, Yale University To facilitate studies of the yeast proteome, we have cloned 5,800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. We identified many new calmodulin- and phospholipid-interacting proteins; a common potential binding motif was identified for many of the calmodulin-binding proteins. The proteome chips can also be used to screen protein-drug interactions and to detect posttranslational modifications. 11:35 Towards Personalized Treatments for Breast Cancer: The Protein Biochip Consortium for Breast Cancer Prognosis Dr. Kevin Auton, Chief Executive Officer, NextGen Sciences Ltd. NextGen has formed a consortium of seven commercial and not-for-profit organizations to develop an integrated program leading towards individualized treatment for breast cancer. At the heart of this initiative is the consortium's ability to design, manufacture, and validate a series of protein biochips. Data from this program undertaken by NextGen, working closely with three European companies, three U.S.-based companies, and a leader in clinical diagnosis, will be presented. 12:05 Lunch (sponsored by Cambridge Healthtech Institute)1:25  1:25 Chair's Remarks Dr. Karin A. Hughes, Vice President, Research and Development, Prolinx, Inc. 1:30 Protein Array as a Platform for the Development of Novel Diagnostic Tools Dr. Gengxi Hu, Max-Planck Guest Laboratory of Genome Instability and Modifications, Shanghai Institute of Cell Biology Membrane-based protein array was developed for parallel analysis of multiple protein markers in blood serum for diagnostic applications. We have achieved antibody arrays that can quantitatively measure multiple tumor markers and antigen arrays detecting multiple antivirus antibodies. Clinical trials indicated that simultaneous measurement of disease markers is of significant value in faster and more precious diagnosis. The protein array technology is being further upgraded based on various sensor technologies. 2:00 The Benefit of Peptide Microarrays in Proteomics and Drug Discovery Prof. Jens Schneider-Mergener, Vorstand/Chief Executive Officer, Jerini AG Jerini's array technology platform enables the preparation of peptide/mimetic microarrays supporting Jerini's and its partners' proteomics and drug discovery programs. The array preparation comprises the parallel synthesis of several thousand soluble compounds by the SPOT™ technology and subsequent covalent printing onto glass chips. This novel approach to customized arrays is unmatched in its speed, versatility, and applications. Jerini applies its microarrays for (i) mapping protein-protein interactions, (ii) enzyme substrate profiling (kinases, proteases, phosphatases, and others), (iii) identification of peptide lead structures targeting enzymes and other protein targets, (iv) fingerprinting of the pharmacophore space of the identified leads, and (v) optimization of peptidomimetic leads towards druglike molecules. Thus, microarrays are now directly entering drug discovery programs and provide a novel and unprecedented parallel approach to target protein families. 2:30 Functional Protein Microarrays for Signal Transduction Profiling Dr. Stefan Schmidt, Group Leader, Protein Biochemistry/Proteomics, GPC-Biotech AG The DNA microarray revolution has largely contributed to the identification of novel differentially regulated targets. However, in most cases a functional analysis of those targets still remains unsolved. Ideally, the required analytical approach is also conducted in a highly parallel mode on protein microarrays. We have focused on profiling the activity of kinases. This is of particular interest because these are primary drug targets and frequently involved in malignant cellular developments. In the context of drug discovery, protein arrays are valuable tools to solve complex problems. By combining our HT protein expression and purification technology with our integrated protein-array-based characterization that also includes automated image analysis, we were able to analyze a broad set of different molecules involved in signaling processes. Substrate arrays can be utilized for analyzing the qualitative and quantitative specificities of kinases and the effect of activators or inhibitors. We will show a series of examples on array based-activity profiling including the process of how to generate and analyze those arrays. 3:00 Poster and Exhibit Viewing, Refreshment Break 3:45 Optimized Protein Microarrays Utilizing a Novel Chemical Affinity System Dr. Karin A. Hughes, Vice President, Research and Development, Prolinx, Inc. An emerging technology that holds significant promise for the high-throughput analysis of protein-ligand interactions is protein microarrays. Issues inherent in the fundamental nature of proteins-maintenance of functional three-dimensional structure and optimal presentation of active regions-must be addressed by the selected protein immobilization strategy. We will present our strategy for producing optimized microarray substrates based on a novel chemical affinity system, along with data assessing the quality of the protein microarrays produced utilizing these substrates. 4:15 Using Cell Microarrays as Protein Microarrays Dr. David M. Sabatini, Whitehead Fellow, The Whitehead Institute We have recently described a reverse transfection system for creating microarrays of cells expressing defined cDNAs. In this system, mammalian cells are cultured on a glass slide printed in known locations with nanoliter volumes of cDNAs in expression plasmids. The cells that land on the spots printed with the DNAs take up the plasmids and express the encoded proteins. These cell microarrays can be used as substitutes for protein microarrays to study properties intrinsic to proteins, such as drug binding, and have uses throughout the drug discovery process. 4:45 Applications of High Density Microarrays in Understanding the Mechanism of Drug Action Dr. Anil Sehgal, Director, Molecular Biology and Genomics, ChemGenex Therapeutics Inc. Microarrays have a variety of applications, including understanding the basic biology of cells as well as gene expression changes that can be responsible for disease phenotype. Lately, microarrays have been applied in the arena of drug discovery and development. At ChemGenex, we are applying microarrays tools integrated with cell based tools to understand the mechanism of drug action and in analog drug design. To understand the mechanism of action of two of our drugs in virto and in vivo, we have used high density microarrays. Using such approaches, we have identified a number of genes that were altered as a result of drug action. These genes expression changes were not reported to be altered previously by these drugs. By understanding the signal transduction pathways that were altered by these drugs, we can design analogs with improved therapeutic benefit. These rational approaches of genomics and drug design are currently being used for a number of compounds that may have critical clinical application in the treatment of cancer. 5:45 Close of Day Two

Wednesday, May 1

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

 

QC, Validation, and Comparisons

8:30 Chair's Remarks
Dr. David Gerhold, Senior Research Fellow, Genomic Pharmacology, Merck & Co.

8:35 Appropriate Statistical Methods for Coping with Error in DNA Microarray Measurements
Dr. Trey Ideker, Whitehead Pfizer Computational Biology Fellow, The Whitehead Institute
Often, a gene is said to be "differentially expressed" if its ratio of expression level in one population to the expression level in a second population exceeds a certain threshold. This thresholding scheme discards useful information on the error's structure. To address the need for a better statistical test for identifying differentially expressed genes, we developed VERA and SAM. VERA estimates the parameters of a statistical model that describes multiplicative and additive errors influencing an array experiment, using the method of maximum likelihood. SAM gives a value, lambda, for each gene on an array, which describes how likely it is that the gene is expressed differently between the two cell populations.

9:05 Microarray Validation: A Comprehensive Method
Dr. David Gerhold
Summary unavailable at time of printing.

9:35 Fast way to Quantitize and Locate the Biochip Dots by Circular Bar-Coding Rings
Dr. Rong Seng Chang, Professor, National Central University of Taiwan
Each microarray dot has been circled and bar-coded by multiple, concentrated, wide and thin rings to easily locate the actual position and size of the array chip in the robotic DNA dipping process as well as to quickly calculate the fluorescence intensity of each point. After the target points have been chosen, the detail image analysis of the targets by wavelet image fusion technology has been studied.

10:05 Poster and Exhibit Viewing, Refreshment Break

 

Applications

10:45 Chair's Remarks
Dr. Matthew Meyerson, Assistant Professor of Pathology, Dana-Farber Cancer Institute and Harvard Medical School

10:50 Keynote Presentation Array Quantitation for Modeling Mutations Affecting RNA, Protein Interactions, and Proliferation Dr. George M. Church, Professor of Genetics, Harvard Medical School; and Director of the Lipper Center for Computational Genetics Summary unavailable at time of printing.

11:30 DNAArrays for Biomonitoring Environmental and Reproductive Toxicology
Dr. John C. Rockett , Research Biologist, Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency
DNA arrays are receiving increasing interest as a tool for monitoring the developmental and reproductive impact of xenobiotics and other hazardous materials on human and wildlife populations. The primary tenet of toxicogenomics is that effects of environmental exposure on cellular functions are in most cases mediated by gene expression changes. Thus, profiling or "fingerprinting" the genes expressed in a given cell, population of cells, tissue or organ, promises to help define their "health" status by providing patterns of gene expression or biomarkers which are indicative of, for example, abnormal development or the presence of a toxicant. We are using commercially available and custom DNA arrays to carry out gene expression profiling in target and surrogate tissues of a number of important model and indicator species, including human, rat and sheepshead minnow. These arrays are being applied in various biomonitoring studies in anticipation that they will: (a) provide a tool for discriminating between different classes of toxicants; (b) help to elucidate mechanisms or modes of action of environmental toxicants in individual species; (c) identify common mechanisms of action across species; (d) assist in the early detection of toxicant exposure. This is an abstract of a proposed presentation and does not necessarily reflect EPA policy. arrays are receiving increasing interest as a possible tool for monitoring the developmental and reproductive impact of xenobiotics and other hazardous materials on human and wildlife populations. The U.S. Environmental Protection Agency is using commercially available and custom DNA arrays to carry out gene expression profiling of a number of important model and indicator species, including human, rat, mouse, Xenopus, and sheepshead minnow. These arrays are being applied in various biomonitoring studies in anticipation that they will (a) provide a tool for discriminating between different classes of toxicants, (b) help to elucidate mechanisms or modes of action of environmental toxicants in individual species, (c) identify common mechanisms of action across species, and (d) assist in the early detection of toxicant exposure.

12:00 Characterization of Factors Crucial for Bone Metabolism Using an Optimized Expression Profiling Setup
Dr. Thomas Meyer, Senior Scientist, LION bioscience AG
DNA array studies based on novel optimized cDNA probes have been designed to identify genes whose expression depends on a cell state or function of specific components of the transcription apparatus. With regard to bone biology this new approach allows the discovery of new factors involved in bone formation and provides highly potential targets for the treatment and prevention of osteoporetic conditions. The role of common regulators in bone metabolism was characterized using an integrated expression-profiling-analysis concept.

12:30 Lunch (on your own)

2:00 The Use of Protein Arrays for Clinical Applications
Dr. Emanuel F. Petricoin, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration
The cause of most human disease lies in the functional disregulation of protein-protein interactions. Understanding the role that protein networks play in disease will create enormous clinical opportunities, since these pathways represent the drug targets of the next decade. In the future, entire cellular networks, not just one disregulated protein, will be the target of therapeutics. The next technological leap will be the application of proteomic technologies at the bedside. We have developed reverse phase and antibody protein microarray technology (Paweletz et al., Oncogene 20, 1981-1989, 2001; Knezevic et al., Proteomics Oct. 2001) and are applying this technology to analyze the state of key signaling pathways in microdissected human tissue cells. In a series of ongoing clinical trials using subject biopsies, we are currently analyzing the state of protein signal pathways in the disease-altered cells before, during, and after therapy. This can herald the advent of true patient-tailored therapy.

2:30 Classification within Adenocarcinomas, the Most Common Lung Cancers
Dr. Matthew Meyerson
We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct subclasses of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

3:00 Role of Interleukin-10 on the Time Course of Gene Regulation: Cluster Analysis of cDNA Microarray
Dr. Ricardo Saban, Associate Professor, Oklahoma University Health Sciences Center
This work describes how to use cluster analysis to determine the effects of interleukin-10, an anti-inflammatory cytokine on LPS-induced gene expression during acute inflammation. In addition, I will discuss cluster analysis of gene array obtained with the following animal models: mast-cell-deficient mice and mast-cell-reconstituted mice.

3:30 Poster and Exhibit Viewing, Refreshment Break

4:00 Microarray Study of Microsamples: Application of T7-Based RNA Amplification
Dr. Elena V. Grigorenko, Scientist II, Millennium Pharmaceuticals, Inc.
With recent advances in molecular techniques such as microarray expression profiling and laser capture microdissection, the target identification process has an ability to examine transcriptional changes in histologically defined cell populations. We will compare results of high-density microarray screenings using T7-based amplified RNA samples from cell cultures and specific, laser-microdissected cell populations. Requirements for successful T7-based amplification procedures, possible modifications, and potential pitfalls will be discussed.

4:30 Translational Genomics
Dr. Spyro Moussses, Head, Genome Scanning Unit, National Human Genome Research Institute, NIH
Expression levels of thousands of genes or proteins can now be readily determined using microarray techniques. This has produced massive amounts of genomic data for hypothesis generation. However, this represents only the first step in understanding the biological and medical significance of these molecules. New high-throughput hypothesis testing platforms, such as tissue microarrays and cell based microarrays, can facilitate clinical and functional analysis of molecular targets at a scale to match genomic discovery

5:00 Creation and Mining of a General-Purpose Mouse Gene Expression Database
Dr. Bruce Aronow, University of Cincinnati and Children's Hospital Medical Center
We have analyzed mRNA expression profiles of 81 normal, developing, and disease mouse tissues using Incyte MouseGEM1 microarrays and a single common reference mRNA. Tissues within organ series included adult and developing lung, cardiac, CNS, GI, urogenital, immunologic, and endocrine tissues. Duplicate Cy3/Cy5 hybridizations with Agilent Bioanalyzer-graded mRNAs and day 1 whole mouse mRNA reference demonstrated excellent reproducibility (even with respect to genes expressed at very low level in the reference mRNA), equivalency to dye reversal, and agreement with direct sample comparisons. Use of multiple normalization strategies greatly improved quality assurance and expression pattern characterizations based on tissue and organ specificity and optimal replicate correlations. Excluding the most overexpressed genes reduced ability to classify tissue specificity, but less so organ origin. Tissues from CNS, immunologic, and GI systems exhibited impressive expression diversity and repertoire specificity. Probing for correlated genes with known biologic relationships within multiple gene ontologies and other known biologic relationships demonstrated the potential of the database to implicate functional associations and potential pathway relationships for unknown genes. These results support the hypothesis that systematic database mining by cross-comparative analysis of diverse biologic systems will greatly augment gene discovery, annotation, and pathway knowledge.In combination with phylogenetically conserved transcription factor binding site analyses the expression database offers a powerful means of discovering potential organ and cell type-specific gene regulatory regions.

5:30 Close of Conference

Corporate Sponsor
Apogent Discoveries, consisting of BioRobotics, Matrix Technologies, and Robbins Scientific, supplies high quality consumables and instrumentation to the pharmaceutical and biotech industries. Apogent Discoveries' product portfolio comprises a wide range of automated liquid handling systems, microarray fabrication robots, and other specialty equipment and disposables for high throughput, molecular biology, and genomic applications. BioRobotics, Hudson, NH, www.biorobotics.com Matrix Technologies, Hudson, NH, www.matrixtechcorp.com Robbins Scientific, Sunnyvale, CA, www.robsci.com
Corporate Sponsor
Iobion Informatics presents GeneTraffic software for two-color microarray data management and analysis. Installation of GeneTraffic is performed simply and quickly from the Iobion System CD, which installs all software required to create an Iobion Linux Appliance: Linux OS, PostgreSQL database, R statistical language and the Apache http server. Because the GeneTraffic Server is served through Internet Explorer on a desktop PC, you can access your data and projects from any location within your Network. You can manage unlimited data sizes, perform computational analyses and query your data because GeneTraffic software is built on the world's most advanced open source database, PostgreSQL. With GeneTraffic software you can qualify and validate your microarray data prior to biological analysis.Iobion Informatics is a Delaware LLC, headquartered in La Jolla, CA with offices in Toronto, Canada, and Austin, Texas.
Corporate Sponsor
Lion Bioscience facilitates and accelerates Life Science R&D by providing integrated information solutions for discovery. With our proven tools, solutions and advisory services our customers are reaching the cutting edge in the race for the scientific and business success. LION advances the quest for knowledge. We help life science companies address the challenges of modern product development by providing IT systems for turning data into information, as well as advanced solutions for refining information into knowledge. Our systems and solutions help Life Science companies to evaluate biological, chemical, pharmacological, toxicological and medical data and information more quickly, more effectively and more comprehensively. We apply our systems and solutions internally, together with state-of-the-art high-throughput technologies to fuel the integrated drug discovery and diagnostics research efforts carried out by our iD³-team.
CHI is pleased to present a new report on:
"DNA Microarray Informatics Key Trends and Commercial Opportunities" Cambridge Healthtech Institute's (CHI's) Genomic Reports are used by leading pharmaceutical, biotech, genomic, consulting, and financial companies to keep abreast of the genomics information explosion. These reports feature: Current and emerging technologies Drug and diagnostic applications Business activity/deals Key scientific and business issues Expert commentaries and insights "Maps" of key players and their technologies, with contact information Genomic Reports are based on in-depth interviews with experts in the field and supported by hundreds of hours of primary and secondary research. They provide comprehensive coverage of strategic issues in genomics-based drug discovery and development in a concise and well-organized format. For more information on this as well as other CHI reports please contact Vernette Roach at 781-972-5438 or visit our reports website at www.chireports.com