Microarray Symposium at PITTCON 2003
- Coalesce recruited top scientists to create the Microarray Symposium that was the highest attended Symposium at PITTCON 2003, next to those on Bioterrorism with 711 participants.
Presiding over the Microarray Symposium was Mark Schena, the 'Father of Microarray Technology.' While at Stanford, Mark co-authored the first published paper on microarrays (Science, 1995); it was considered a main catalyzing force in promoting academic and corporate interest in DNA chip technology. He was featured as one of the 'Stars of Genomics' on the NOVA television special 'Cracking the Code of Life,' broadcast in 2001 and again in August 2002. He edited the first two books on DNA Microarrays, and has recently completed the first microarray textbook for J. Wiley & Sons. He is currently a visiting scholar at TeleChem International Inc // arrayit.com. From his acknowledged historical position, as well as his current status as one of the 9 most important people in microarray technology today, his "foundational talk describing the underpinnings of microarray science," certainly "will bring the field into sharper focus." His talk included "a plethora of advanced technologies spanning surface chemistry, micro-machining, semi-conductors, optics, and computer science [that] have been brought to bear on this highly interdisciplinary and exciting field." (Quotes are from his abstract.)
Dr. Schena has given more than 70 lectures in a dozen countries since 1995. At his 4-hour advanced Microarray course at the October 2002 Chips to Hits conference, the standing-room-only audience enjoyed it so much that the conference organizers had to come in and ask people to leave at the end of allotted time. So not only is he a renowned pioneer and leader in the field, but he is also a very engaging speaker.
The Promise of Microarrays: Genomics, Proteomics and Beyond
CHAIRMAN: Mark Schena, Visiting Scholar, TeleChem International, Inc.
Mark Schena of TeleChem International began the symposium with an introductory talk designed to get everyone "up to speed" in terms of the foundational aspects of microarrays. Jay Tiesman of Procter and Gamble then presented approaches to minimizing variation in microarray data, by laying out a series of carefully designed experiments. Two additional talks in the symposium will describe some of the recent developments in protein microarray technology. George Grills of Harvard Partners Genome Center will discuss challenges and considerations involved in establishing a protein microarray core facility. Antibody arrays represent promising new tools for disease analysis, and Brian Haab of The Van Andel Research Institute will demonstrate how his group has utilized antibody arrays to analyze blood serum from cancer patients to identify clinically useful diagnostic markers. The symposium will conclude with a talk by Paul Kayne of Bristol-Myers Squibb, who will describe their efforts in utilizing microarrays for improving the specificity of medicinal compounds. Together, the talks will provide a nicely integrated Symposium for understanding the practical and theoretical aspects of this exciting new science.
Presentations
Introduction to Microarray Analysis
Mark Schena, Visiting Scholar, TeleChem International, Inc.
Microarrays are the biomedical equivalent of microprocessors, yielding biological information in a massively parallel, miniaturized and highly automated manner. DNA microarrays have been utilized extensively in functional genomics, to study gene expression patterns at the transcriptional (mRNA) level. Rapidly emerging protein microarrays extend what can be gleaned from DNA microarrays, allowing the study of gene expression patterns at the translation and post-translation (protein) levels. DNA and protein microarrays can be used, for example, to profile small molecule-induced changes in gene expression, thereby speeding drug discovery. Microarrays can also be used to study and potentially diagnose human disease. As the technology moves from genomics, to proteomics, and eventually into diagnostics, we face three critical challenges: (1) technological challenges with respect to assay sensitivity and accuracy, (2) logistical hurdles vis-à-vis implementing affordable and usable tests in clinical laboratories, (3) informational barriers pertaining to the mining, interpretation, integration and warehousing of microarray data. This symposium will address these and other questions by drawing on the opinions and expertise of key experts in the field.
Establishing a Protein Microarray Facility: Practical Considerations
George Grills, J. Decker, and R. Kucherlapati, Harvard Partners Genome Center, Harvard Medical School, 165 Landsdowne St, 3rd Floor, Cambridge, MA 02139; 617-768-8505; ggrills@rics.bwh.harvard.edu
George Grills is Director of DNA Sequencing at the Harvard-Partners Center for Genetics and Genomics and at the Albert Einstein College of Medicine. He was one of the six speakers that the BioAnalytical Decision makers interviewed in the BioAnalytical Research Report recommended as a speaker they wanted to see.
George organized a session on "Implementing Microarray Technologies in Facility Laboratories" for the ABRF'99 meeting in March of 1999. He set up a Microarray Facility at the Albert Einstein College of Medicine with both the Affymetrix GeneChip oligonucleotide array technology and a cDNA microarray robotic printer and scanner that they built themselves. The DNA Sequencing Facility performs automated fluorescent sequencing of DNA templates using Applied Biosystems 377 DNA Sequencers. Each sequencer can run 96 sample lanes per gel. Samples are analyzed using fluorescent cycle sequencing with dye-labeled terminators or primers. Single-stranded and double-stranded DNA, PCR products, plasmids, Cosmids, PACS, BACS, and genomic DNA purified templates are accepted for sequencing. The facility provides consulting for interpreting results, improving template preparation, editing, and methods for obtaining good sequence data. Submitted templates usually yield more than 500 nucleotides of reliable sequence.
Abstract
The Harvard Partners Genome Center has established a new Protein Microarray Facility using a novel technology from Zyomyx. This is a multianalyte assay biochip technology that utilizes antibody binding on a silica base. Our initial studies focused on qualitative and quantitative human cytokine profiling. We have developed quality control methods to monitor and troubleshoot high throughput protein microarray data production in a shared resource environment. We have evaluated and developed techniques to facilitate data production and analysis using this new microarray technology.
Antibody Microarray Analysis of Blood Serum from Cancer Patients
Brian B. Haab The Van Andel Research Institute, 333 Bostwick Avenue N.E., Grand Rapids, MI 49503; 616-234-5268; brian.haab@vai.org
Abstract
Antibody Microarray profiling of sera and other bodily fluids should offer new opportunities for biomarker discovery and insights into disease biology. We have used robotically spotted microarrays of antibodies and proteins to measure the relative abundances of multiple proteins in serum samples from prostate cancer and pancreatic cancer patients and controls. Serum proteins that had been coupled to either a fluorescent tag (e.g. Cy3) or a hapten (e.g. biotin) were incubated on the microarrays, and specific proteins bound to the immobilized molecules on the microarrays through specific interactions. After washing away unbound proteins, bound proteins were detected using the fluorescent tag or amplified signal (using rolling circle amplification) from the hapten-labeled proteins. An automated analysis process filters data by signal-to-noise ratio, averages replicate measurements, normalizes data, and filters data sets based on reproducibility. Comparisons of the Microarray data with independently measured protein concentrations (by ELISA) validated the accuracy of the Microarray measurements. Five serum proteins statistically distinguished a set of prostate cancer serum samples from the controls, and several serum proteins significantly varied between the pancreatic cancer patients and controls. Implications for the use of this technology in marker research and in the study of proteins in bodily fluids will be discussed.
Minimizing Microarray Data Variation Through Experimental Design
Jay P. Tiesman, Scott M. Hartman, Suzanne M. Torontali, Jennifer R. Paine, Robert L. Binder, Marilyn J. Aardema, Ting Hu, Gregory J. Carr, Kenton D. Juhlin , Procter & Gamble, Miami Valley Laboratories, PO Box 538707, Cincinnati, OH 45253-8707; 513-627-0396; tiesman.jp@pg.com
Jay Tiesman is Genomics Group Leader at Procter & Gamble’s Miami Valley Laboratories, and an acknowledged expert in the area of identifying sources of variability in microarray experiments. He has given many talks on this subject, at CHI and Marcus Evans Life Sciences conferences, including the Marcus Evans December 2002 seminar on "Data Analysis and Visualization: Approaches and Strategies in Determination of Gene Expression"; and the CHI September 2002 seminar "Microarray Data Analysis: Using Statistics and Standards to Navigate the Microarray Data Minefield." He was one of the first people to get into variability studies, and his work is on the forefront of this field today.
Abstract
Microarrays have revolutionized biology as the tool of choice for global gene expression analysis. Powerful statistical algorithms are now available to analyze this expression and to gain an understanding of how changes in gene expression patterns impact biological systems. However, with this increased power comes increased responsibility. We will show how microarrays are particularly sensitive to the myriad sources of biological and experimental variation associated with analyzing thousands of genes simultaneously. We will present the results of a series of carefully controlled experiments designed to isolate the most significant sources of experimental variation. We will also describe how variation can be minimized by optimizing experimental design parameters. These parameters have been instrumental in the execution of sensitive and highly informative microarray experiments. We will conclude with a discussion of our efforts to improve the reliability of experiments using very small quantities of input RNA.
Compound Profiling By Microarray Analysis
Paul S. Kayne, Petra Ross-MacDonald, Jian Cao, Johnny Park, Joseph Lu, Aiqing He, Michael Neubauer, Bristol-Myers Squibb Co., Pharmaceutical Research Institute, Applied Genomics, P.O. Box 5400, Princeton, NJ 08543; 609-818-5302; paul.kayne@bms.com
Paul Kayne currently heads the Expression Technologies Group of Bristol-Myers Squibb Co. in Princeton, NJ. In this position he oversees the Expression Profiling Group and is directly involved in the identification, evaluation and deployment of new gene expression technologies. Various technologies are currently employed for both monitoring and altering gene expression. He taught a short course on "Introduction to Pharmocogenomic Automation" at LabAutomation 2003.
Prior to joining Bristol-Myers Squibb, Dr. Kayne was a member of the Molecular Genetics Dept of SmithKline Beecham in King of Prussia, PA. He joined this department in 1995 to begin developing microarrays as a method for high throughput expression profiling. Dr. Kayne's academic research examined various aspects of transcriptional regulation. During his doctoral dissertation at the University of California, Los Angeles, he showed that histones were intimately involved in the transcriptional regulation of the silent mating type loci in S. cerevisiae. As a post-doctoral fellow, and staff scientist at the California Institute of Technology, Pasadena, CA, Dr. Kayne worked to develop techniques to explore gene expression of a set of seven cells responsible for vulval development in C. elegans.
Abstract
Creating a new pharmaceutical compound is a complex and long lived process. Essential to the process is structural identification and modifications that lead to increasing efficacy against the desired target. A number of assays are also employed to monitor off target activity, particularly in those pathways known to increase potential liabilities. The scope of these assays is limited, however, for a variety of reasons. Here we will explore the use of microarrays to monitor a substantially larger set of pathways and genes to feed back information relative to off target activity. This information, provided in a timely manner should allow chemists to incorporate this data as they design new compounds. The ultimate goal of this technology is to allow chemists to simultaneously maximize efficacy and selectivity.
This symposium was held at PITTCON® 2003 at the Orange County Convention Center in Orlando, Florida, March 12, 2003.