Immediately following CHI's Seventh Annual Gene Quantification conference
Corporate Support:
The growing momentum of genomics and molecular analysis has enormous promise for numerous drug research applications as well as for diagnostics. Gene and protein-based assays can provide critical information, but they also raise important issues that need to be addressed if their full potential is to be realized. Analysis based on gene expression profiles may be of particular importance for improved understanding and diagnosis of disorders with the complexity of cancer. Molecular diagnostics, however, are generally viewed as expensive and labor intensive, which means that advances to improve automation, throughput, scalability, and reliability are critical. Leading researchers will be covering advances, experiences, and challenges relevant for each of these issues in detail, so plan to participate and gain useful new insights.
Sponsoring Publications
BBA-Gene Structure and Expression
Bioinform
Disease Markers/IOS Press
Genome Research
Journal of Molecular DiagnosticsSession Chairs
Dr. Philip Bernard, University of Utah Health Sciences Center
Dr. Russell Higuchi, Roche Molecular Systems
Dr. John N. Weinstein, National Cancer InstituteAdditional Speakers
Dr. Norman Arnheim, University of Southern California
Dr. Richard Barker, New Medicine Partners
Dr. Joseph P. Brown, LifeSpan BioSciences
Dr. Mark G. Erlander, Arcturus Engineering, Inc.
Dr. Dan Farkas, Motorola Life Sciences
Mr. Andrew Faucett, Centers for Disease Control and Prevention
Dr. Wayne W. Grody, UCLA School of Medicine
Dr. Myron Gross, University of Minnesota
Dr. Gordon Holt, Oxford GlycoSciences PLC
Dr. Ricardo V. Lloyd, Mayo Clinic
Dr. David D. Lo, Digital Gene Technologies, Inc.
Dr. Roberta A. Pagon, University of Washington School of Medicine
Dr. Cloud Paweletz, U.S. Food and Drug Administration
Dr. David Robbins, ViaLogy, Inc.
Dr. Bruce Seligmann, High Throughput Genomics, Inc.
Dr. Dennis Sgroi, Harvard Medical School and Massachusetts General Hospital
Dr. Steven A. Soper, Louisiana State University
Dr. Pothur Srinivas, National Cancer Institute
Overview
Biomarkers
Clinical Proteomics
High-Throughput Proteomics for Surrogate Markers
Cancer Detection and Diagnosis: Bench to Bedside
Open System Expression Profiling: Discovery and ValidationGenetic Diagnostics
Human Germline Cells
Modular Microfluidic Systems
FDA and Molecular Diagnostics: Challenges and Opportunities
Preconceptional and Prenatal Carrier Screening for Cystic Fibrosis
Genomic Competencies for Public Health Workforce
GeneTests and Genetic CounselingGene Expression
Real-Time PCR for Tumor Profiling
Gene Expression in Single Cells
Gene Expression Analysis of Human Breast Cancer
Automated Microarray Analysis across Biochip PlatformsIndustrializing Molecular Analysis
High-Throughput Genetic Analysis
Strategic and Financial Aspects of Molecular Diagnostics
New Technologies for Chemical and Biological Agent Detection
High-Throughput Protein Localization
A Cellular Genomic Approach to Profiling Cancer
Identification of Susceptibility Genes in Chronic Disease
Tuesday, February 12
5:00-7:00pm Early Registration and Exhibit Set-up
Wednesday, February 13
7:30am Registration, Poster Set-up, Exhibit Viewing, and Light Continental Breakfast
8:30 Chairperson's Opening Comments
Dr. John N. Weinstein, Laboratory of Molecular Pharmacology, National Cancer Institute8:40 Overview
Dr. John N. Weinstein
Biomarkers
9:10 Clinical Proteomics
Dr. Cloud Paweletz, U.S. Food and Drug Administration
Molecular medicine is moving beyond genomics to proteomics. Proteins do all the work of the cell-and ultimately dictate all biological processes and the cellular fate. The true scientific goal of proteomics is to characterize the information flow within the cell and the organism, mediated through and by protein pathways and networks. 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 targets of therapeutics. The next technologic leap will be the application of proteomic technologies to the bedside. It will soon be possible to analyze the state of protein signal pathways and complex proteomic patterns in the disease-altered cells before, during, and after therapy. This can herald the advent of true patient-tailored therapy, new biomarker pattern discoveries for early detection of disease, and monitoring of drug-related toxicity at the bedside.9:40 Using High-Throughput Proteomics to Discover Surrogate Markers of Drug Toxicity
Dr. Gordon Holt, Principal Scientist, Oxford GlycoSciences PLC
Selection of drug candidates based on the evaluation of their toxicity profiles as early as possible during development represents a major cost-saving opportunity. Proteomics can identify preclinical and clinical safety markers that will help this selection process. Examples of treatment-induced toxicity will be presented, including doxorubicin-induced cardiotoxicity studies done in collaboration with the U.S. Food and Drug Administration.10:10 Poster and Exhibit Viewing, Refreshment Break
10:50 Genomics and Proteomics in Cancer Detection and Diagnosis from the Bench to the Bedside
Dr. Pothur Srinivas, National Cancer Institute
Cancer proteomics encompasses the identification and quantitative analysis of differentially expressed proteins relative to normal tissue counterparts at different stages of the disease from preneoplasia to neoplasia. Protein expression and function are subject to modulation through transcription as well as through post-transcriptional and translational events. At the protein level, distinct changes occur during the transformation of a normal cell into a neoplastic cell that range from altered expression, differential protein modification, changes in specific activity, and aberrant localization, all of which affect cellular function. Identifying and understanding these changes is the underlying theme in cancer proteomics. The deliverables include identification of biomarkers that have utility both for early detection and for determining therapy. The NCI's Early Detection Research Network consortium will be discussed in relation to genomics and proteomics approaches being employed for rapid discovery and evaluation of cancer biomarkers for early detection and risk assessment.11:20 TOGA™ Open System Expression Profiling for the Discovery and Validation of Biomarkers
Dr. David D. Lo, Vice President of Integrative Biology, Digital Gene Technologies, Inc.
Despite the availability of genome sequence data, much still needs to be developed in identifying both the specific genes present in the genome and the differential regulation of these genes in tissue development, disease, and drug response. Open gene profiling systems such as DGT's TOGA™ technology provide an extremely sensitive way to systematically identify nearly all genes expressed within samples, allowing for ready comparisons and rational selections of candidates from among samples. Both known and novel genes are identified using this method, enabling comprehensive comparisons between multiple experimental or clinical samples and permitting identification of genes expressed at previously undetectable levels. We will present examples from our studies in cancer biology and type 2 diabetes.11:50 Panel Discussion
Questions from the audience will be answered by speakers from the above session.12:20 Lunch (on your own)
Genetic Diagnostics
1:40 Chairperson's Comments
Dr. John N. Weinstein1:45 Studies on Genomes of Individual and Pooled Human Germline Cells: Mutation and Abnormal Recombination
Dr. Norman Arnheim, Professor, Molecular Biology, University of Southern California
Using sensitive PCR techniques, analysis of single genomes from sperm makes it possible to study mutation and recombination in single human individuals. Very rare genetic events can also be studied in single individuals but this requires a PCR scheme that can specifically amplify only the target molecules. Examples of these two approaches applied to the study of human genetic disease will be discussed.2:15 Detection of Point Mutations in K-Ras Oncogenes Associated with Colorectal Cancer Using Modular Microfluidic Systems
Dr. Steven A. Soper, Professor, Department of Chemistry, Louisiana State University
We are developing integrated microfluidic systems for detecting point (single-base) mutations in particular gene fragments, which possess diagnostic value. Our current project is focused on analyzing K-ras oncogenes using Ligase Detection Reactions (LDR) to discriminate normal DNAs from mutant DNAs. Mutations in these gene fragments have been associated with the development of colorectal cancers. Microfluidic systems are being developed to process the sample in an automated format. The microfluidic platform consists of polymers (poly [methylmethacrylate], PMMA, polycarbonate, PC) that can be microfabricated rapidly and inexpensively to produce devices that are appropriate for clinical applications. The microfluidic devices are made using high-aspect-ratio micromachining techniques to fabricate molding dies (Ni-electroforms) that can be used for hot-embossing the final product. The microfabrication method used to construct our devices will be discussed as well as design and operation of several functional units required for the diagnostic assay.2:45 Bioelectronic Detection of Nucleic Acids: A Platform for Molecular Diagnostics.
Dr. Dan Farkas, Director, Clinical Diagnostics, Motorola Life Sciences
Motorola Life Sciences has developed the eSensor (TM) system that uses disposable biochips with clincally-appropriate densities for widespread DNA testing. DNA testing is poised to grow explosively, but current tests are limited by cost, convenience, and flexibility. The eSensor™ DNA Detection System will integrate accuracy and speed with the ability to perform an array of tests on a single sample, uniting convenience and cost saving in a single flexible system.3:15 Poster and Exhibit Viewing, Refreshment Break
4:00 Preconceptional and Prenatal Carrier Screening for Cystic Fibrosis: American College of Medical Genetics Recommendations
Dr. Wayne W. Grody, Professor, Divisions of Medical Genetics and Molecular Pathology, and Director, Diagnostic Molecular Pathology Laboratory, Departments of Pathology and Laboratory Medicine and Pediatrics, UCLA School of Medicine
Twelve years after the discovery of the causative gene, cystic fibrosis (CF) is set to become the first disease targeted for populationwide molecular genetic screening. As perhaps the most common lethal recessive disease in North America, it has long been an obvious target, but the identification of carrier couples who could then be offered prenatal diagnosis has been hampered by the large size and complexity of the gene, in which over 900 different mutations have been described. This presentation will discuss the rationale behind the 25-mutation screening panel recently recommended by a committee of the American College of Medical Genetics and the complex genetic issues that will need to be understood by physicians as they begin to offer this test and interpret the meaning of the results to their patients.4:30 Genomic Competencies for the Public Health Workforce: A Model
Mr. Andrew Faucett, Office of Genetic Testing, Centers for Disease Control and Prevention
In 2000 the Centers for Disease Control and Prevention (CDC) convened a team of leaders in public health who developed a set of skills, knowledge, and attitudes (competencies) to facilitate the integration of genetics into workforce training. The document consists of a list of three competencies for everyone in public health, a list for professionals, and a specialized list for each discipline including administrators, clinicians, environmentalists, epidemiologists, health educators, and laboratory directors. The document was designed to guide discussion as programs incorporate genomics and the development process in a successful model for other groups facing the same issues.5:00 GeneTests and Genetic Counseling
Dr. Roberta A. Pagon, Professor of Pediatrics, University of Washington School of Medicine
An immediate benefit of the Human Genome Project is the development of molecular genetic testing for use in patient diagnosis, management, and genetic counseling. Molecular genetic testing is increasingly being integrated into patient care through use of clinically available tests for more than 400 diseases. An essential aspect of genetic testing is genetic counseling, a process to educate family members at risk and to obtain informed consent for those situations in which testing serves personal decision making rather than medical management.5:30 Panel Discussion
Questions from the audience will be answered by speakers from the above session.6:00 Reception (sponsored by Cambridge Healthtech Institute)
Thursday, February 14
8:00am Poster and Exhibit Viewing and Light Continental Breakfast
Gene Expression
8:45 Chairperson's Comments
Dr. Philip Bernard, Department of Pathology, University of Utah Health Sciences Center8:50 Using Real-Time PCR Techniques for Tumor Profiling in the Clinical Laboratory
Dr. Philip Bernard
Microarrays are providing important information about the genetic changes that occur in cancer. Molecular classifications of tumors will clinically help in the prognosis and treatment of malignancy but will require a paradigm shift in anatomic pathology. The challenge for clinical diagnostics will be to provide valuable molecular information for tumors using reproducible, cost-effective, and time-efficient assays that can be integrated into the current framework of specimen processing. This talk focuses on the potential of real-time PCR methods to be used in clinical molecular diagnostics for the detection of sequence alterations and for gene expression profiling. The assays have advantages over microarrays for use in the clinical lab since they are fast, have more potential for automation, and can be done from a limited sample.9:20 Analysis of Gene Expression in Single Cells
Dr. Ricardo V. Lloyd, Professor of Pathology and Director of Molecular Anatomic Pathology and In Situ Hybridization Laboratory, Mayo Clinic
The use of immunophenotyping with specific antibodies, followed by laser capture microdissection and RT-PCR, has allowed for the analysis of gene expression in single cells. The practical applications and limitations of this approach will be discussed.9:50 Gene Expression Analysis of Human Breast Cancer
Dr. Dennis Sgroi, Assistant Professor of Pathology, Harvard Medical School; and Assistant Pathologist and Director of Breast Pathology, Department of Pathology, Molecular Pathology Unit, Massachusetts General Hospital
A major leap in functional genomic investigations would be the ability to perform global gene expression analysis with in vivo-derived genetic material originating from morphologically distinct cellular populations that constitute the various stages of breast cancer progression. The recent advent of high-density DNA microarray technology, with its capacity for simultaneous monitoring of thousands of genes, provides a unique opportunity for high-throughput genetic analysis of breast cancer. In the past, such an analysis has been hampered by limitations inherent in traditional in vivo analysis that often involved homogenization of clinical specimens with subsequent application of the macromolecular mixture to a particular assay. As a result, the accurate interpretation of such data, as it relates to a particular cell type within the sample, is severely limited. This limitation is further exacerbated when one tries to study the molecular alterations of preinvasive carcinoma, a stage that is often microscopic in size and constitutes a mere fraction of the total cellular population. The combined use of laser capture microdissection, cDNA microarray, and real-time quantitative PCR technologies now provides a unique opportunity to elucidate the in vivo genetic events that underlie the initiation and progression of human breast cancer.10:20 Poster and Exhibit Viewing, Refreshment Break
11:00 Automated Microarray Analysis: Active Interferometric Computing across Biochip Platforms
Dr. David Robbins, Director of Microarray Applications, ViaLogy, Inc.
ViaLogy is currently working on a series of validation studies to demonstrate biochip sensitivity and specificity gains of several orders of magnitude. Sensitivity improvements are demonstrated analytically by serial dilutions of samples across arrays. Currently available software requires relatively large amounts of input sample material; dilutions result in the loss of expression with decreased RNA input. In contrast, the same image data analyzed by interferometric computing show little or no loss of transcript detection after input dilution by several orders of magnitude. Interferometric analysis of array data at the highest sample input level approximately doubles the number of expressed genes observed. Data from completely independent platforms are also considered to demonstrate the wide applicability of Active Interferometric
Computing technology.11:30 ArrayPlate(TM) Expression and Protein Analysis Technology: A Platform for Research, Development, and Diagnostics
Dr. Bruce Seligmann, President & CEO, High Throughput Genomics, Inc.
The ArrayPlate(TM) provides a microplate array platform which can measure 16 or more DNA, RNA, or protein targets per well. A simple modified proprietary nuclease protection protocol is used to measure DNA and RNA expression which results in highly sensitive (1,000 or fewer cells/sample) and reproducible (3-13% CV) quantitative measurement of RNA. The simplicity, speed of custom assay implementation, automation friendliness, sample throughput, gene target multiplexing throughput, sensitivity and reproducibility combine to provide the ArrayPlate(TM) with superior performance. The need to identify and rely on "the right" gene or protein to monitor is eliminated by utilizing the ArrayPlate(TM) to measure a profile of expressed genes or proteins. The challenge of normalization to account for differences in sample size and cell content can be ameliorated by measuring multiple genes, including DNA, in the same well/sample using the ArrayPlate(TM). The problems of just measuring the gene, or just measuring the protein, are eliminated by the dual ArrayPlate(TM) measurement of RNA and protein from the same sample. The ArrayPlate(TM) introduces a technology which can make RNA expression analysis as reliable and useful a diagnostic technique as DNA-based nucleic acid diagnostics, and reduce the diagnostic complexity to quantitative analysis. Specific examples of application to target validation, dose response quantitative structure activity relationship analysis, detection of diseased cells and diagnostics will be discussed.12:00 Lunch (sponsored by Cambridge Healthtech Institute)
Industrializing Molecular Analysis
1:30 Chairperson's Comments
Dr. Russell Higuchi, Associate Director, Department of Human Genetics, Roche Molecular Systems1:35 High-Throughput Genetic Analysis
Dr. Russell Higuchi
As both a pharmaceutical and a diagnostics company, Roche has the opportunity to integrate research for both drug targets and disease markers. As part of this effort, we have developed high-throughput genetic analyses to both discover and confirm disease-associated genes. These include in-silico means of generating candidate disease genes based on mouse phenotypic and genotypic databases as well as means of genotyping either many samples or many polymorphisms simultaneously. These methods and their applications will be described.2:05 Strategic and Financial Aspects of Molecular Diagnostics
Dr. Richard Barker, New Medicine Partners
Molecular diagnostics have already established themselves as a major source of revenue and profit for selected participants. However, as new, higher-cost tests based on genomics, proteomics, and arrays hit the market, how successful will their innovators be in capturing the value that these can bring to the whole healthcare process? We will discuss both strategies and economic approaches to maximize value for diagnostics' new generation of technologies.2:35 Poster and Exhibit Viewing, Refreshment Break
3:00 High-Throughput Protein Localization
Dr. Joseph P. Brown, LifeSpan BioSciences
One of the greatest challenges facing pharmaceutical companies today is identifying and validating genes to target for drug discovery. As the leader in the field of molecular pathology, LifeSpan BioSciences believes that knowledge about cell-specific upregulation of genes and its direct correlation with disease is an essential part of this process. LifeSpan's rapidly growing Localization Databases combine proprietary immunohistochemical findings from a wide variety of normal and diseased human tissues, together with curated sequence and expression data mined from the public domain. These data, as well as custom services provided by LifeSpan, provide drug developers with unique, validated targets for the efficient discovery of more disease-specific drugs with fewer side effects.3:30 A Cellular Genomic Approach to Profiling Cancer
Dr. Mark G. Erlander, Vice President and Site Director, Arcturus Applied Genomics, Arcturus Engineering, Inc.
One of the greatest challenges and thus unprecedented opportunities in the post-genomic era is to integrate the human genome with that of clinical medicine. By integrating what is known about the human genome, "molecular signatures" (i.e., gene expression profiles) now can be discovered that will distinguish at a molecular level, the differences between ADH (atypical ductal hyperplasia) and DCIS (ductal carcinoma in situ). The key to this integration is the ability to isolate and extract genetic material (i.e. mRNA) from pure populations of cells (e.g., ADH and DCIS) that reside in the complex cellular milieu of a biopsy. Arcturus Applied Genomics or AAG has developed and is subsequently applying a proprietary cellular genomic platform for the study of cancers in order to discover biomarkers and molecular signatures that define pre-cancerous states for early detection and differential diagnosis, as well as those that define cancer subtypes to determine optimal choice of therapy and subsequent monitoring of response.4:00 The Identification of Susceptibility Genes in Chronic Disease: Tissue Sources, Automation, Quality Assurance and Analysis of Genetic Polymorphisms in Epidemiologic Studies: A Comparison of Currently Available Methods.
Dr. Myron Gross, Molecular Epidemiology and Biomarker Research Laboratory, Department of Laboratory Medicine and Pathology, University of Minnesota
The identification of susceptibility genes has great promise for the prevention of chronic diseases. It has potential for the identification of interindividual differences in susceptibility and patterns of genetic variation that are highly susceptible to the effects environmental agents. These genes generally have small effects in a large fraction of target populations and require large-scale analysis for identification. Sources of DNA can vary from target populations and present challenges for collection and analysis. Methods of sample collection and handling will be described and evaluated for epidemiologic studies. The advantages and disadvantages of currently available analysis methods will be described for their application in epidemiological studies. Considerations for the translation of these methods will be described for practical clinical testing.4:30 Panel Discussion
Questions from the audience will be answered by speakers from the above session.5:00 Close of Conference
Hotel Information
Hilton San Diego Resort
1775 East Mission Bay Drive
San Diego, CA 92109
T: 619-276-4010 o F: 619-275-8944
Room Rate: $195.00 S/D
Cut-off Date: January 21, 2002Please 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.
Travel Information
Special Airline Discounts Available
Special zone and discount fares have been established on United Airlines for this conference. Please call United Airlines Meeting Reservations Center directly at 800-521-4041. You must reference ID #579YS.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 January 11, 2002. Click here for poster instructionsCall for Exhibitors
Last year, there was a tremendous amount of interest in this conference. We found that the attendees interested in genetic diagnostics are also interested in the latest organic synthesis techniques as well as gene quantification and molecular diversity. Exhibiting at this event provides you with the unique opportunity to interact with a targeted delegate base from a number of different backgrounds. This year we expect to see even more growth and encourage any company offering services or products related to the use of biomarkers, multiplexing assays, gene functions, cellular processes, pathways and networks, as well as their clinical applications to exhibit at this event. For more information on exhibiting at this event please contact Mike Handy at 781-972-5492 or mhandy@healthtech.com.
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