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The G.O.T. Summit Pre-Conference
Short Course Tutorials*
Sunday, April 23
1:30 Registration
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Short
Course Tutorial One
2:00-5:00 Building a Basic and Clinical Science Gene Expression Infrastructure: A Practical Guide for the Laboratory
Andrew I. Brooks, Ph.D., Associate Professor of Environmental Medicine and Genetics & Director, Bionomics Research and Technology Center
(BRTC), Environmental and Occupational Health Science Institute, University of Medicine and Dentistry of New Jersey; and Associate Director, Technology Development, Rutgers University Cell and DNA
Repository (RUCDR), Department of Genetics, Rutgers University
Gene expression has become an integral technology in a variety of academic and industrial laboratories. Whether the focus of an experiment is centered on a cluster of well defined genes or more global profiling approach, a "model of consistency" should be established to ensure the minimization of technological variation. This tutorial will outline the development and implementation of standard practices for employing low, moderate and high-throughput gene expression technologies in your laboratory. Topics and protocols for sample accessioning, nucleic acid extraction and amplification, technology selection and data analysis will be among the topics covered in the tutorial.
Who Should Attend
Researchers, Clinicians, Core Directors, Graduate Students, Post-docs interested in learning about and implementing cutting edge gene expression technologies with a focus on sample preparation and microarray validation. Principles for laboratory organization, sample tracking and processing, assay and experimental design, and fundamentals of gene expression data analysis will be covered.
OR
Short Course Tutorial Two
2:00-5:00 Research & Compliance: IRB
Issues and Guidance
Greg Koski, MD, Ph.D., Former Director, Office for Human Research
Protections, U.S. Department of Health and Human Services; Associate Professor
of Anaesthesia, Massachusetts General Hospital, Harvard Medical School
and
Leslie E. Wolf, JD, MPH, Program in Medical Ethics, Center for AIDS
Prevention Studies, University of California San Francisco
The short course on regulatory compliance issues for researchers is will
provide an overview of the federal regulations governing human subjects
research, including the role of institutional review board (IRB) review of
research involving human subjects and the requirement for informed consent. In
particular, the course will focus on the ethical issues that arise in research
involving stored biological materials and how the regulations may apply to
this research.
*Separate registration required
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Tuesday, April 25
5:00-6:00 Early Registration
Wednesday, April 26
7:30-8:30 Registration and Morning Coffee
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Opening Plenary Session
8:30 Chair's Opening Remarks
Keynote Presentations
8:40 Probing Genomes, Pathways and Disease using Microarrays
Dr. Michael P. Snyder, Lewis B. Cullman Professor and Chair, Molecular and Cellular Developmental Biology Department, Yale University
We have been using DNA titling arrays to identify transcribed regions and regulatory elements throughout the human genome. Protein microarrays are used to probe biochemical activities and posttranslational modification networks and human disease.
9:20 'The 39 Steps' in Gene Expression Profiling: Deciphering Cellular States of Innate Tumor Drug Responses
Dr. Charles Auffray, Research Director, CNRS;
Genexpress, Functional Genomics and Systems Biology for Health, Pierre et Marie Curie University
Microarray technology is in a relatively immature stage compared to sequencing, with important limitations in the production of the accurate and extensive data required for integrative systems biology approaches to the complexity of living systems. To realize the full potential of microarray technology, and provide meaningful insights into the behavior of the biological systems investigated, it is essential to develop and implement standards at each and all steps of the process. These include careful study design, controlled annotation of resources and extensive quality control of experiments with associated quality metrics, the use of robust statistics including power analysis for hypothesis testing, and data description, registration and storage in public repositories using ontologies and controlled vocabularies. I will review the 39 key steps we found essential to establishing a generic quality assurance pipeline for gene expression profiling, using transcriptome analysis to decipher cellular states of innate tumor drug responses as a case study. I will highlight the potential of microarrays to uncover molecular signatures of diagnostic value, to provide a rich source of working hypotheses on underlying functional and regulatory networks, and to help identify targets for therapeutic intervention.
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10:00 Coffee Break
Concurrent Sessions
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Enhancing Microarray Quality
10:30 Chair's Remarks
10:35 Cancer Genomics using
Microarray-Based Resequencing
Dr. Torstein Tengs, Staff Scientist, Section of Food and Feed Microbiology, National Veterinary Institute
We designed GeneChip CustomSeq Resequencing arrays (Affymetrix) to test the performance of this platform when interrogating a large number of exons (164 total) from genes associated with cancer. To evaluate false positive and negative rates for the arrays, dideoxy sequencing was done for a large fraction of the bases interrogated by the arrays. The overall performance of the arrays was very good, with >99.99 of the bases covered being called correctly (~97.5% coverage). Several somatic and germline mutations were detected and some of these were investigated further using large scale MALDI-TOF genotyping.
11:05 Assaying Gene Expression Fingerprints: A High-Throughput Bead-Based System for Identifying Compounds with Estrogenic Potential
Dr. Jay Tiesman, Principal Scientist, Miami Valley Innovation Center, Procter & Gamble
Genome-wide expression profiling has been broadly used to identify subsets of gene transcripts that are associated with specific biological processes, such as therapeutic or toxic responses to a given chemical compound. Once these gene expression fingerprints have been identified, there is a need to develop a rapid and cost-effective assay that can be used to identify other chemicals with similar therapeutic or toxic profiles. We have developed a sensitive,
microsphere-based platform that allows the high-throughput screening of up to 100 transcripts per sample in a 96-well plate format. Using this platform, we have developed an assay for screening gene expression fingerprints associated with estrogenic response in mammals. This presentation will describe the development of this assay as well as outstanding technical issues currently being addressed.
11:35 Tiled Oligo Arrays for Detection of Transcription Factor Binding with ChIP on Chip
Dr. Thomas L. Volkert, Microarray Facility Manager, Center for Microarray Technology, Whitehead Institute
With recent advances in microarray technology, it is now possible to design arrays that tile large regions of a genome at high resolution. We have used arrays that tile the entire human genome at high resolution to monitor the binding of transcription factors using
ChIP-on-Chip techniques. This presentation will discuss the evolution of
ChIP-on-Chip
microarray technology, and its current state-of-the-art and application.
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Determining
the Molecular Basis of Disease
10:30 Chair's Remarks
10:35
The Application of LCM and Microarray Analyses for
Cell-Type Specific Gene Regulation in the Rhesus Monkey Endometrium:
Implications for Implantation
Dr. William C. Okulicz, Director, ILAT
Steroid RIA Lab and Associate Professor, Department of Physiology, UMass Medical
School
The upper region of the primate endometrium (functionalis) is a primary
target for blastocyst implantation. To further understand the molecular and
cellular pathways that may be involved in proper maturation of the endometrium
that will allow implantation, we combined the powerful techniques of LCM and
microarray analyses in an appropriate physiological model. cDNA populations
representing functionalis glandular epithelium (FG) and stroma (FS) isolated by
LCM were constructed from mid-secretory phase rhesus monkey endometria and the
two populations were used for oligonucleotide microarray chip analyses (Affymetrix).
The results from our experiments showed that >50 genes were up-regulated
>5-fold in FG, while >100 genes were up-regulated in FS. Likewise, these
up-regulated genes were down-regulated in the comparative cDNA population. These
data provide support for the use of combined LCM and microarray analyses in the
identification of differential cell-type specific pathways that play key roles
in essential physiological processes.
11:05 Cell
Type-Specific Gene Expression of Midbrain Dopaminergic Neurons Reveals
Molecules Involved in Their Vulnerability and Protection
Dr. Ole Isacson, Professor of Neurology, Harvard Medical School;
Director, Center for Neuroregeneration Research, McLean
Hospital/Harvard Medical School; and NINDS Morris K. Udall Parkinson's
Disease Research Center of Excellence
Transcriptome differences between specific brain dopamine (DA) neurons
may explain why the midbrain DA neurons in the A9 region selectively
degenerate in Parkinson's disease (PD) and all toxic PD models, when the
nearby A10 region DA neurons are relatively spared. To characterize
innate physiological differences between A9 and A10 DA neurons, we
determined gene expression profiles in these neurons by laser capture
microdissection, microarray analysis and real-time PCR. We found 42
genes relatively elevated in A9 DA neurons, whereas 61 genes were
elevated in A10 DA neurons [>2-fold; false discovery rate (FDR)
<1%]. Genes of interest for further functional analysis were selected
by criteria of (i) fold differences in gene expression, (ii) real-time
PCR validation and (iii) potential roles in neurotoxic or protective
biochemical pathways. Based on the patterns observed, blocking or
enhancing gene-effects indicated that certain differentially expressed
molecules in A9 and A10 DA neurons may play key roles in their relative
vulnerability to toxins and PD.
11:35 Proteomic
Analysis of LCM Samples using Ultramicroarrays
Mr. Michael Lynch, Product Manager, BioForce Nanosciences, Inc.
We describe the application of antibody ultramicroarrays, defined as
arrays with domain sizes in the two to twenty micrometer range, for
detection of human prostate specific antigen (PSA) from a
well-characterized human prostate carcinoma cell line, LNCaP. The cells
were grown on a slide and harvested by laser capture microdissection.
Data will be presented demonstrating that only about 100 cells are
required to unequivocally detect PSA from these cells.
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12:05 Lunch on Your Own
1:15 Technology Workshop
Build your own sundae and experience what new technologies have to offer |
Sponsored by |
Segmental AneusomyTM Software: Feasibility of a Data Analysis Method Featuring Novel Quality Metrics for Array CGH
Dr. Kathryn B Becker, WW Senior Product Manager, Instrumentation and Microarray Technologies, Abbott Molecular |
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Concurrent Sessions
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Biomarker Development
2:00 Chair's Remarks
2:05 Gene Expression Profiling in Peripheral Blood as a Biomarker Strategy
Dr. Jianyong Shou, Senior Research Scientist, Angiogenesis & Tumor Microenvironment Biology, Lilly Research Laboratories
Peripheral blood is a highly dynamic tissue that contacts virtually with every tissue in the body. It is recognized as a "sentinel tissue" that could potentially reflect systematic responses during disease progression. Profiling gene expression in peripheral blood cells using the microarray technology has emerged as a novel biomarker strategy for various disease indications. Blood is also readily accessible and allows for repeated biomarker measurements thus enabling pharmacodynamic studies with drug activity biomarkers. A few blood cell profiling platforms and their applications in biomarker discovery will be discussed.
2:35 Promoter Arrays for High-Throughput Direct Identification of Aberrantly Regulated Genes
Dr. Dan Mercola, Director, Translational Cancer Biology, Pathology, University of California - Irvine
We have developed arrays or promoter sequences (Promoter Arrays) for the direct identification of genes aberrantly regulated in cancer, stress, and other conditions in living cells and tissues (1-3). The method has been applied to identify gene regulated following genotoxic stress or identification of genes specifically methylated in prostate cancer. The method provides identity of directly regulated genes whereas in expression analysis it is a major challenge to related differential expression to a particular pathway. We conclude that this array-based method has promise for the identification of target genes for nove therapy development.
3:05 Classification of Toxicological and Pharmacological Endpoints through the Application of a Chemogenomics Reference Database
Dr. Brigitte Ganter, Principle Scientist, Chemogenomics and Toxicology, Iconix Pharmaceuticals
We have assembled a large toxicogenomics reference database, called DrugMatrix®, containing microarray expression profiles from short-term repeat dose rat studies for over 630 marketed drugs, withdrawn drugs, and reference toxicants. Expression profiles were collected from up to seven different tissues, in addition to standard clinical chemistry, hematology,
histopathology, and pharmacology data. Systematic mining of the expression domain using a two-class supervised classification methodology resulted in the creation of a library of more than 300 cross-validated toxicology and pharmacology biomarkers
(Drug Signatures®) that resolve distinct and uncorrelated end-points. This talk will describe successful toxicogenomics
applications when a reference database is used to contextually analyze gene
expression of compounds in drug development.
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Moving
into the Clinic
2:00 Chair's Remarks
2:05 Monitoring Performance Levels in Microarray Core Facilities
Dr. Wendell Jones, Senior Research Statistician, Bioinformatics, Expression Analysis
The quality of microarray results has improved over the last few years, but it is still difficult to measure laboratory performance or to even understand what constitutes excellent versus good results. We recently conducted a proficiency testing program for microarray facilities that generated 260 hybridizations of the same 6 RNA samples conducted at 18 different laboratories over nine months. During our analysis of the hybridization results, we observed characteristics of lab performance that translate into larger, higher-quality lists of differentially expressed genes. These relatively simple metrics are associated with sensitivity and specificity and can be used to compare lab performance. We have also used a mixed-model components of variance analysis to identify the impact of biological and relevant processing factors on variance in this study.
2:35 Technology Showcase
Novel Genomic Approaches for the Identification of Critical Regulatory
Nodes in the Cardiovascular System |
Sponsored by
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Mr. Eric T. Wang, Research Scientist, Center for Excellence in Vascular Biology, Harvard Medical School
Homeostasis in the cardiovascular system is maintained by a hierarchy of interacting genetic programs, the dysregulation of which contributes to the pathogenesis of complex disease processes, such as atherosclerosis and its complications—myocardial infarction and stroke. These genetic programs reflect the integration of multiple transcriptional networks whose upstream stimuli and downstream effectors play a pivotal role in cardiovascular health and disease. Thus, the identification of “critical regulatory nodes” in these transcriptional networks may provide penetrating insights into mechanisms, therapies, and prevention of cardiovascular disease. Towards this goal, we have used genome-wide analysis of gene expression in conjunction with newly developed computational biology tools to identify various transcription factors as prime targets for in-depth biological investigation. Gain-of-function and loss-of-function experiments demonstrated that one of these transcription factors,
kruppel-like factor 2 (KLF2), is a master regulator of endothelial-mediated
vasoprotection. Our observations validate this genomic and computational experimental paradigm, and suggest that similar approaches should be effective in the identification of regulatory nodes critical for the homeostasis of biological sys |
2:50 Protein Profiling the Coagulome to Improve Clinical Outcome of Thromboembolic Disorders
Dr. Robert S. Negm, Vice President, GenTel BioSciences, Inc.
The overall goal of anticoagulant therapy is to administer the lowest possible dose of drugs such as wharfin and heparin minimizing one’s thrombogenic potential while at the same time avoiding bleeding. We developed a quantitative antibody microarray to profile ten human plasma proteins related to clot formation and fibrinolysis called the COAG Chip™. We performed analytical measurements in parallel using planar antibody microarrays on PATH™ slides, an ultra-thin film nitrocellulose technology platform. Simultaneous analytical measurements of critical proteins related to hemostasis likely offers improved dose-response monitoring and provides a new method to evaluate safety and efficacy in clinical trials of anticoagulant drug candidates.
3:05 A Putative Signature of Chromosomal Instability Inferred from Gene-Expression Profiles Predicts Poor Prognosis in Six Cancer-Types
Dr. Zoltan Szallasi, Assistant Professor, Children's Hospital Informatics Program, HarvardMedical School
We have developed a computational method to identify chromosomal regions with signifi-cant localized aberrations in coordinate gene-expression activity and show that the result-ing profiles of "functional aneuploidy" could be used to classify tumors with respect to out-come. Furthermore, we show that a derivative univariate measure of total genomic imbal-ance was significantly associated with clinical outcome in several cohorts of lung andbreast cancer patients. Finally, we show that a gene-expression signature of genomicimbalance refined from these datasets was highly predictive of clinical outcome in six pub-licly available datasets representing four solid-tumor types, and was significantly associ-ated with the outcome in several additional cohorts representing two additional types ofhuman tumors. This signature represents the most accurate and most broadly applicablesignature of cancer prognosis so far. Due to its general nature, the signature may be ofparticular clinical relevance in diagnosis of cancers uncharacterized by large gene-expres-sion datasets.
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3:35 Refreshment Break, Poster and Exhibit Viewing
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Closing Plenary Session
Featured Presentations
4:15 Chair's Remarks
4:20 Functional Genomics and Proteomics Driving Individualized Medicine
Dr. Towia A. Libermann, Associate Professor of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School; Director, BIDMC Genomics Center, Dana Farber/Harvard Cancer Center Cancer Proteomics Core
Subtle genetic differences between individuals combined with environmental effects result in distinct
predisposition to and development of diseases as well as divergent responses to therapies. Patients with the same disease respond differently to drugs due to individual differences in the particular disease causing mechanisms. Similarly, human beings respond differently to drugs due to individual variations in drug metabolism. Functional genomics promises the design of therapies optimally tailored to each patient based on individualized molecular characterization of the patient's disease process and drug response, leading to more effective treatments and less adverse reactions. Examples of genomics and proteomics approaches to stratify patients based on their individual disease mechanism and to apply individualized, more targeted and more specific therapies will
be illustrated.
4:55 Molecular Network Analysis using Reverse Phase Protein
Microarrays: Towards Routine Clinical Use for Patient Tailored Medicine
Dr. Lance A. Liotta, Professor and Co-Director, Center for Applied Proteomics and Molecular Medicine, George Mason University
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5:30 Networking Reception
6:30 Close of Day
Thursday, April 27
7:30 Breakfast Technology Workshop
Application of Advanced Molecular Profiling Tools to Pre-Clinical and Clinical Studies
Dr. Patrick Hurban, Director of Investigational Genomics, Cogenics
Drug development is increasingly reliant upon molecular profiling technologies for the discovery of biomarkers. This workshop will feature a discussion on the application of genotyping, expression profiling, and metabolomics technologies. |
Sponsorsed
by
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Keynote
Presentations
8:30
Chair's Remarks
8:40
Improving the Efficiency and Reliability of Microarray Research to Study Prognosis and Response to Therapy
Dr. David F. Ransohoff, Professor of Medicine & Director, Clinical Research Curriculum, University of North Carolina-Chapel Hill
Hundreds of papers have been published reporting that transcriptional profiling, using
microarrays, may be used to predict cancer prognosis and response to therapy. Yet recent critiques suggest that many results may not be reproducible. What may be wrong with the process of evaluating molecular markers for cancer, and how can the efficiency and reliability of the process be improved?
9:20 Array CGH in Clinical Pathology: Progress and Challenges
Dr. Shelly R. Gunn, Instructor, Cellular & Structural Biology, University of Texas Health Science Center at San Antonio and
Dr. Mansoor S. Mohammed, CSO, CombiMatrix Molecular Diagnostics
Array CGH began as an effective laboratory tool for genome scanning. It is now poised to become one of the
most powerful diagnostic and prognostic tests in clinical pathology. Great progress has been made in the development of clinical diagnostic arrays for congenital abnormalities, and CGH arrays are also being developed to provide detailed outlines of hematopoietic and solid tumors. However, despite this progress there are still many challenges to be met before array CGH becomes a routinely ordered clinical test. |
10:00 Morning Coffee, Poster and Exhibit Viewing
Concurrent Sessions
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Determining RNA Quality Effects
10:45 Chair's Remarks
10:50 Expression Microarrays from Formalin Fixed Paraffin Embedded Tissue, Considerations in the Reduction to Practice
Dr. Stephen M. Hewitt, Chief, TARP Lab, NCI/NIH
There is great interest in the introduction of expression microarrays to routine clinical practice. The most common material available for extraction of RNA is formalin fixed paraffin embedded tissue. Obtaining RNA from archival blocks is possible, however the approach requires optimization at multiple steps in the Process. There are issues of specimen handling from the patient till RNA extraction that impact RNA quality. Defining the quality of RNA obtained from archival tissue is challenging. Array design can be anticipated to differ from current designs. Finally, interpretation must be considered. This talk will discuss the issues that have been identified and attempt to define what is known and what remains to be discovered as expression microarrays from formalin fixed paraffin embedded tissue become a tool for clinical medicine.
11:20 Molecular Profiling of Clinical Specimens with Degraded RNA/DNA
Dr. Richard Everson, Professor, Department, Karmanos Cancer Institute, Wayne State University
Will discuss high-throughput, highly-multiplexed assays for molecular profiling of clinical specimens with degraded RNA or DNA. Major focus will be on assays for gene expression using
formalin-fixed, paraffin-embedded clinical samples, and their use as diagnostic and prognostic factors in cancer research.
11:50 High-Quality Microarrays with RNA from FFPE Samples
Dr. Guido Krupp, CEO & President, AmpTec GmbH
Apart from RNA quantity, RNA from FFPE samples suffers from two major quality problems: cross-linking and degradation. Both issues result in very limited mRNA sequence availability for mRNA amplification and hence microarray hybridization. A new approach is presented, that permits specific mRNA amplification, even from mRNA fragments without any
poly(A) tail. Data will be presented, comparing microarray data (using fluorescent labelling as well as
biotin-labelling techniques) from fresh/frozen and parallel FFPE samples.Moving into the
into the.Clinic
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CGH Arrays Current Applications
10:45 Chair's Remarks
10:50 Application of Genomic Microarray in Reproductive Pathology and Preimplation Genetics Diagnosis after Whole Genome Amplification
Dr. Moncef BenKhalifa, Director, R&D, Advanced Technologies Laboratories; Scientific Director, Consultori Di Genetica & Genoma Laboratories; and Scientific Director, Women's Health Clinic
11:20 High-Density Array CGH and Its Integration with Other Molecular Profiling Technologies
Dr. John N. Weinstein, Senior Investigator, Laboratory of Molecular Pharmacology; Head, Genomics and Bioinformatics Group, Center for Cancer Research, NCI, NIH
High-density array CGH is illuminating in itself but more so when combined with other types of data on the same cells. Along with our collaborators, we have profiled the NCI-60 cell lines extensively at the DNA, RNA, protein,
epigenomic, functional, and pharmacological levels. Those data complement our profiling of the same cell types using three different array CGH platforms.
"Integromic" analysis of the diverse data sets poses formidable bioinformatic challenges that motivated us to develop the "Miner Suite" of computer resources for the purpose
(http://discover.nci.nih.gov). The combination of CGH and expression data can have significant translational implications, as will become apparent from an example to be discussed in the presentation.
11:50 Panel Discussion with Morning Speakers
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12:20 Lunch on Your Own
(Technology Workshop Sponsorship Available)
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Moving into the Clinic
Continued
2:00 Chair's Remarks
2:05 Clinical Applications of Microarray Diagnostic Tests
Dr. Alexander Kohlmann, Research Alliance Manager,
Pharmacogenetics, Roche Molecular Systems Inc.
Microarrays technology can be used for a variety of clinical applications; genotyping, re-sequencing and gene expression studies of disease tissue. Research studies have demonstrated effective uses of microarrays to obtain valuable clinical information. This information can serve as a basis for therapeutic target identification as well as molecular stratification of disease. This presentation will cover examples of such applications of microarray technology and how these methods can become useful tools for disease diagnosis.
2:35 Automated Clinical Diagnostic Platforms for
Multi-Analyte Protein and SNP Chip Analysis
Dr. Daniel Levine, Director, Clinical Research Laboratory, The Rogosin Institute
The Randox Evidence and Investigator perform simultaneous quantitative detection of a wide range of clinically relevant protein analytes and DNA mutation analyses in a biochip array format. The systems may be used for clinical analysis in laboratory medicine or in clinical trials where panels of tests include at the present time cytokines, thyroid and fertility hormones, drugs-of-abuse and SNPs associated with early stage colorectal cancer. The biochip is a 9mm² solid substrate containing an array of discrete test regions (proteins or
SNPs). The Evidence is an integrated fully automated floor-standing instrument, while the Investigator is a compact bench-top biochip reader. Both utilize a super cooled charge-coupled device
[CCD] camera to read a chemiluminescent image and dedicated software to quantify and report the results. This presentation covers data from beta testing, FDA submission and initial clinical use as well as a discussion of future capabilities presently under development.
2:50 The Role of an Automated High Throughput Biochip Array Analyzer in Biomarker Validation and Routine Clinical Testing
Dr. Stephen Hunsucker, Health Sciences Center, University of Colorado - Denver
Although there has been spirited activity in the biomarker discovery arena, primarily associated with uncovering new diagnostic and prognostic indices of human disease, there has been relatively little attention directed downstream at the validation, and clinical implementation phase. There is, however, increasing awareness that the discovery phase is of little value in and of itself, and that subsequently, large scale rigorous performed validation studies are crucial. The best analytical platform for undertaking these is yet to be determined, but most agree that the same tools that are employed to identify novel biomarkers can't deliver the requisite sensitivity, precision or throughput essential to the subsequent phases. An additional important consideration is that biomarker discovery studies frequently return a panel of putative biomarkers that need to be evaluated in the subsequent phases, and it is likely that optimal diagnostic sensitivity and specificity will be arise from evaluating multiple analytes simultaneously. In this talk I will describe the essential features of the automated biochip array analyzer system we have adopted for this specific purpose (Evidence, Randox Laboratories,
Crumlin, UK), present its performance characteristics, and show examples of its role in the process of biomarker validation and routine high volume testing of clinical samples.
3:05 Evaluation of a Microarray Platform for Clinical Application
Dr. Sunil Kadam, Principal Research Scientist, Eli Lilly and Company
Despite the application of microarray technology in pre-clinical research and exploratory clinical studies, for hypothesis generation, adoption of microarray testing in clinical laboratories is currently limited. In an attempt to determine how such assays would perform in a clinical setting, we evaluated the analytical variability of the Affymetrix microarray platform using two generations of human Affymetrix chips (U95Av2 and U133A). A study was designed to mimic potential clinical applications by using multiple operators, machines, and reagent lots, and by performing analyses throughout a period of several months. We conclude that our approach could be generally applied to clinical validation of other multi-step array platforms and that the analytical precision of the Affymetrix technique is sufficient to answer many biological
questions.
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Advancement of Array CGH Technology
2:00 Chair's Remarks
2:05 aCGH Technology Choices and Considerations
Dr. Todd Martinsky, Co-Founder & Executive Vice President, TeleChem International Inc.
aCGH users have many choices to make. To make their own
microarray, purchase from a vendor, or use a core facility. Microarray CGH designs can include
BACs, long oligos microarrays or very high density tiling arrays. If the user chooses to make their own microarrays considerations include: sample type, surface chemistry, buffer systems, detection and labeling systems. This talk will discuss some key aCGH technology choices and discuss the pros and con's of each path.
2:30 Sample Preparation Technologies for Genome Analysis and Array CGH
Dr. Todd Peterson, Vice President, Cloning and Protein Expression R&D, Invitrogen Corporation
The emergence of a variety of comparative genome methods, principally driven by comparative genome hybridization on high-density arrays, have recently enhanced our understanding of genetic disease and the mechanisms of genetic variation. Novel, simple, robust technologies and products for genomic DNA preparation that are compatible with and designed for methods employed for genome analysis have been developed. Manual and automated genomic DNA purification solutions in magnetic bead, column and plate formats ensure high yield and purity from a wide variety of sample types. The developed suite of PureLink™, ChargeSwitch® and GeneCatcher™ genomic DNA purification products and BioPrime®/AlexaFluor® CGH labeling and detection technologies will be discussed.
2:55 A Rapid and Reliable Method to Amplify and Screen Genomic DNA from Formalin-Fixed Paraffin Embedded (FFPE) Tissues: Implications for Array Analysis
Dr. Henry B. Sadowski, Senior Scientist and Director of Product Applications, Enzo Life Sciences
Despite the enormous potential for retrospective studies, researchers have been unable to fully utilize the wealth of clinically annotated repositories of FFPE tissues for functional genomic studies. This is due, in part, to the inability to rapidly and reliably screen for genomic DNA samples that will yield high quality data on BAC and oligo arrays. To address this need, we have developed a robust DNA amplification method that serves as quality check prior to labeling and/or hybridization on arrays. This method of whole genome amplification can generate greater than 10 micrograms of DNA from 10 nanograms of high quality genomic DNA in less than four hours. Differences in the amplification efficiencies can be used as a diagnostic tool to identify high, medium and low quality DNA. High and medium quality genomic DNAs can be directly labeled for array analysis. In cases where input DNA is limiting the amplified DNA can also be labeled for array analysis.
3:15 Approaches to Comparative Genome Hybridization using Electrochemically Synthesized Microarrays
Dr. Andy McShea, Vice President, Combimatrix Corporation
Array based comparative genomic hybridization allows the identification of gains and losses of genomic regions that lead to copy number changes and sequence rearrangements in chromosomes. This powerful technique allows investigators to pinpoint genomic regions that have undergone significant change. Genomic tiling arrays can be generated with capture probes designed for any interval of a sequenced region of a genome. Probes are selected for overall quality, as well as for uniqueness over the genomic sequence space, then synthesized in situ on an array of 12000 or 90000 microelectrodes.
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3:35 Refreshment Break, Last Chance for Poster and Exhibit Viewing
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Closing Plenary Session
Featured Presentation
4:15 Chair's Remarks
4:20 Structural Variation in the Human Genome: New Insights for Diagnostics and Disease Study
Dr. Stephen Scherer, Senior Scientist, Genetics and Genomic Biology; Director, The Centre for Applied
Genomics; Associate Chief, Research Institute, Hospital for Sick Children and University of Toronto
The first wave of information from the analysis of the human genome revealed SNPs to be the major source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of 'structural variation' in the human genome. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.
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4:55 Panel Discussion: Considerations for Moving into the Clinic
5:30 Close of
Conference
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