Microarrays in Medicine

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					                                             Register by April 11th and Save up to $250!                     Final Agenda

                                                                  Ninth Annual

                                             Microarrays in
                      Optimizing Diagnostics and Therapeutics
        May 19-20, 2008 • Hilton Boston Logan Airport • Boston, MA

  Sessions Include:                                                Topics:
  •   Data Analysis                                                •   bench to bedside applications
  •   Models to Predict Responses                                  •   response markers
  •   Stability and Standardization                                •   pathogen surveillance and discovery
  •   Applied Microarrays                                          •   patenting microarray inventions

Keynote Presentations:

Molecular Targets & Diagnostics: Critical Role of Sample Preparation in Discovery
James L. Wittliff, Professor of Biochemistry & Molecular Biology, Graham Brown Cancer Center, University of Kentucky

Opportunities and Obstacles in Proteomic Analysis of Biofluids
Sunny Tam, Ph.D., Research Associate Professor, University of Massachusetts Medical School

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                                                                                  MONDAY, MAY 19
7:00 - 6:00 pm Registration Open
7:30 Morning Coffee
                               8:10    Opening Plenary Introduction
Keynote Presentations

                               8:20    Molecular Targets & Diagnostics: Critical Role of Sample Preparation in Discovery
                               James L. Wittliff, Professor of Biochemistry & Molecular Biology, Graham Brown Cancer Center, University of Kentucky
                               9:00    Opportunities and Obstacles in Proteomic Analysis of Biofluids
                               Sunny Tam, Ph.D., Research Associate Professor, University of Massachusetts Medical School
                               Proteomic analyses of biofluids, such as plasma or amniotic fluid, traditionally have the same obstacles due to the presence of abundant pro-
                               teins and large dynamic range of protein concentration. Recent fractionation reagents have helped in the isolation of abundant proteins to allow the
                               examination of lower abundant proteins. We have examined plasma from a diabetic rat model and important clinical diseases after adequate
                               fractionation schemes. The proteomic finding from gel based and iTRAQ based studies have yielded interesting observations after bioinformatics analysis.
                               Furthermore, the biological significances of the differential protein expression have been validated with traditional biochemical methods.

 9:40                   Grand Opening Coffee Break in the Exhibit Hall                              Most Gastrointestinal Stromal Tumors (GISTs) contain gain-of-function, i.e., oncogenic mu-
                                                                                                   tations in c-KIT or in Platelet Derived Growth Factor Receptor alpha (PDGFRa) and GIST
                                           DATA ANALYSIS                                           patients are treated with imatinib mesylate, originally referred to as STI571 or GleevecTM,
                                                                                                   an oral 2-phenylaminopyrimidine derivative that acts as a selective inhibitor against onco-
                                                                                                   genic forms of KIT, PDGFa, and BCR-ABL. What is becoming apparent is that clinical man-
 10:25 Chairperson’s Remarks                                                                       agement of GIST may benefit from molecular characterization, i.e., pre-selecting patients
 10:30 Microarrays: Bench-to-Bedside                                                               for treatment with imatinib or additional first and second line therapies based on c-KIT
 Towia Libermann , Ph.D., Associate Professor of Medicine, Beth Israel                             and PDGFRa mutational status or predictive gene signatures. As part of a recent Phase II
                                                                                                   Trial of neoadjuvant/adjuvant imatinib for advanced primary and recurrent operable GISTs
 Deaconess Medical Center
                                                                                                   (RTOG-0132), we used gene profiling of pre- and post-imatinib treated biopsies to better
 Functional genomics and proteomics approaches have rapidly evolved over the last years
                                                                                                   define prognostic markers. The analysis identified 38 genes as differentially expressed in
 and have provided the basis for groundbreaking discoveries in basic and clinical research.
                                                                                                   pretreatment samples between responders and nonresponders, with all genes present at
 As the technologies become more mature and validated, bench-to-bedside clinical applica-
                                                                                                   higher levels in nonresponders. Interestingly, seven of these genes mapped to a single
 tions rapidly emerge. Our focus has been to identify gene signatures in patients with vari-
                                                                                                   locus on chromosome 19p and a subset of these faithfully predicted likely response to
 ous types of cancer for early detection, cancer progression, metastasis, survival as well as
                                                                                                   imatinib-based therapy in naive panel of GISTs.
 resistance or sensitivity to therapy. We have developed novel bioinformatics approaches
 for biomarker discovery and individualized gene expression analysis that are enhancing the        2:00     COXEN: Genomic Prediction of Patients’ Responses to
 identification of aberrant signaling pathways in individual patients and clinical application
 of microarray data for patient stratification and management. Examples of microarray and
                                                                                                            Combination Chemotherapeutics
 bioinformatics approaches and their potential clinical applications in renal, prostate and        Jae Lee, M.D., Associate Professor, Public Health Sciences, University of
 breast cancer will be presented together with the implementation of the new fully automa-         Virginia School of Medicine
 tized Affymetrix platform for high throughput 96 well microarray analysis.                         The U.S. National Cancer Institute has used a panel of 60 diverse human cancer cell lines
                                                                                                   (the NCI-60) to screen >100,000 chemical compounds for anticancer activity. We asked
 11:00 Molecular Classification of Gliomas:                                                         whether it would be possible to identify common chemosensitivity biomarkers from that
       Let the Data Inform Treatment                                                               rich database to predict drug activity in cell types not included in the NCI-60 panel or,
 Jean Claude Zenklusen, Ph.D., Staff Scientist, Neuro-Oncology Branch,                             even further, clinical responses in patients with tumors. We address that challenge by de-
                                                                                                   veloping a novel pharmacogenomic prediction approach “Co-eXpression ExtrapolatioN”
 National Institutes of Health, National Cancer Institute
                                                                                                   (COXEN), which can effectively identify concordant genomic chemosensitivity biomarkers
 Primary brain tumors are the fourth leading cause of cancer mortality in adults under the
                                                                                                   between two independent expression profiling data sets, here extrapolating the genomic
 age of 54 and the leading cause of cancer mortality in children in the United States due
                                                                                                   expression patterns of NCI-60 biomarkers with those of clinical tumors. Applying our COX-
 to suboptimal therapeutic approaches, hindered by lack of understanding of the biology
                                                                                                   EN approach in a prospective fashion, we predicted anticancer drug activities on human
 of these tumors. In the framework of the Glioma Molecular Diagnostic Initiative at the
                                                                                                   patients in breast, ovarian, bladder cancer, and other types of cancer, who were treated
 NCI, we have collected and molecularly characterized (at both RNA and DNA) over 500
                                                                                                   with commonly used combination chemotherapeutics. We also used COXEN for in silico
 gliomas with corollary clinical data. Here we present a novel, comprehensive, classifica-
                                                                                                   screening of 45,545 compounds and identify a novel agent with superior growth inhibition
 tion of Gliomas (both high and low grade) based on their mRNA expression profiles, which
                                                                                                   activity against human bladder cancer.
 were analyzed using a variety of class discovery algorithms (HC, K-mean, NMF) without
 using any pre-conceived notion of their biological or clinical/histopathological grouping.        2:30     Use of Genomics as a Tool to Identify Stage-Appropriate
 The results were validated in a separate datasets (either produced by our own group or
 from previously published reports), and classify these tumors into six distinct subclasses
                                                                                                            Therapeutic Intervention Strategies
 having a nested hierarchy correlating with the tumor’s characteristics from both biological       Marti Jett, M.D., Chief, Department of Molecular Pathology, Walter Reed
 and clinical standpoints. This novel classification along with the wealth of genomic data          Army Institute Research
 produced by the GMDI may allow for the development of a more rational, objective, diag-           Genomic patterns have the potential to reveal the progression of host responses during
 nostic of gliomas and serve as an important starting point in the search for new molecular        illness and help to pinpoint early indicators of tissue involvement or organ failure. In com-
 therapeutic targets.                                                                              bination with limited proteomics, these findings can be used to identify markers that will
                                                                                                   permit therapeutic efforts to be focused to divert impending serious outcomes. Our stud-
 11:30 Microarray Data Analysis                                                                    ies using a systems approach to integrate clinical, physiological, -omics and mathematical
 Yudong He, Ph.D., Scientist, Rosetta Merck                                                        modeling have revealed stages of illness progression during which time certain standard
                                                                                                   therapies may no longer be effective, yet they also reveal other therapeutic strategies. The
 12:00 pm Lunch and Learn Workshops                                                                aim is to identify sets of biomarkers that could be rapidly determined for near-real-time
          (Sponsorship Available) or Lunch on Your Own                                             assessment of patient status.

                             MODELS TO PREDICT RESPONSES                                           3:00     Networking Refreshment Break, Poster and Exhibit Viewing

 1:25 pm Chairperson’s Remarks
 1:30                   Response Markers to Imatinib Mesylate in the Treatment of
                        Gastrointestinal Stromal Tumor
 Andrew Godwin, M.D., Member, Director, Clinical Molecular Genetics
 Laboratory; Director, Biosample Repository, Medical Oncology, Fox Chase
 Cancer Center

                                                                                                  Toxicology Research, FDA
                STABILITY AND STANDARDIZATION                                                     Evidence indicates that there are sex-related differences in cardiovascular disease and heart
                                                                                                  failure in humans, including age of onset, initial manifestations, and drug responses. These
3:45     Pathogen Surveillance and

                                                                                                  differences may be reflective of differential gene and protein expression. Gene expression
         Discovery in Acute and Chronic Disease

                                                                                                  profiles in the heart were examined in both male and female rats at three different ages.
W. Ian Lipkin, M.D., John Snow Professor of                                                       The sex difference was much greater at 21 weeks compared to 8 weeks and 78 weeks. Few
Epidemiology, Professor of Neurology and Pathology , Columbia University                          common differentially expressed genes at different ages indicated that the sex difference
Advances in nucleic acid technologies have revolutionized microbiology by facilitating rapid,     is age-specific. These results may provide insights into sex- or age-related cardiovascular
sensitive pathogen surveillance and differential diagnosis of infectious diseases. Implemen-       diseases and drug responses.
tation of these technologies will enable effective intervention and reveal unappreciated links     10:00 Solution Showcase (Sponsorship Available)
between infection and chronic diseases. I will review various assay platforms and describe a
staged strategy for microbiological-diagnostics.                                                  10:15 Coffee Break in the Exhibit Hall
                                                                                                  11:00 Challenges to Patenting Microarray Inventions
                                                                                                  Les Overman , Ph.D., Attorney, Patent & Trademark , Heller Ehrman LLP
4:15     Cytogenetic Stability and Molecular Profiling of Clinical Stem                            Current USPTO practices and new and proposed rules, recent court decisions, and pend-
         Cell Products                                                                            ing legislation are conspiring to make the process of securing and defending patent rights
Robert Deans, Ph.D., Senior Vice President, Regenerative Medicine,                                much more challenging now and in the future. The business of Microarray technology is
                                                                                                  particularly sensitive to these legal changes. Scientists need to know how these changes
Athersys, Inc .                                                                                   will affect research activities and business developers need to know how these changes will
Production of adult stem cells for clinical use requires extensive safety testing, and dem-
                                                                                                  affect financing, licensing and litigation risk. This presentation will address these concerns
onstration that biological potency is retained over significant population doublings in
                                                                                                  for stakeholders in the Microarray technology area.
expansion. We have utilized chromosomal SNP analysis to augment karyotypic stability
measurements, and transcriptional profiling and gene methylation analysis to demonstrate           11:30 Programmable Submicrolitre Lab-on-a-Chip for Molecular
equivalency of early and late expansion products. Use of differential profiling strategies                Diagnostic Applications
has allowed discovery of novel marker sets which distinguish primitive from more mature
adult stem cell types.                                                                            Stefan Thalhammer, Ph.D., Institute of Radiation Protection, GSF - National
                                                                                                  Research Center for Environment and Health
4:45     Standardisation and External Quality Controls for Gene                                   Here we present an acoustic driven free programmable multifunctional biochemical lab-
         Expression Measurements in the Clinic: Lessons from BCR ABL                              on-a-chip. By combining different platform elements, like microdissection-, nanofluidic-
                                                                                                  and detection-modules, the lab-on-a-chip can be adapted to question- and patient-specific
         Dosage in the Tyrosine Kinase Inhibitors Era
                                                                                                  cytogenetic and forensic applications. In contrast to many common available lab-on-a-chip
Jean Gabert, Professor, M.D., Ph.D., Biochemistry & Molecular Biology,                            approaches, the fluidic handling is done on a planar surface of the lab-on-a-chip. Minute
University Hospital, Marseille                                                                    amounts of biochemical fluids are confined in ‘virtual’ reaction chambers and ‘virtual’ test
Standardisation and external quality controls are part of the routine in clini-                   tubes in the form of free droplets. The droplets, fluidic tracks and reaction sites are de-
cal biochemistry since years. International standards and external quality con-                   fined at the chip surface by a monolayer chemical modification of the chip surface. Surface
trol rounds are absolutely warranted for any new biological marker for its world-                 acoustic waves are employed to agitate and actuate these little virtual test tubes along
wide use in the clinic. Taking the measurement of BCR ABL transcripts (M-BCR) as                  predetermined trajectories. Well-defined analyses, controlled in the submicrolitre regime,
a model, we developed freeze dried cells that can be sent worldwide at room tem-                  can be quickly and gently conducted on the lab-on-a-chip
perature. During, the meeting will be reported our efforts in this field at the regional,
national and international levels.                                                                12:00 pm Simultaneous Detection and Definitive Identification of Up-
                                                                                                           per Respiratory Pathogens Using Resequencing Microarrays
5:15 Reception in the Exhibit Hall
                                                                                                  Matthew Lorence, Ph.D., Vice President, Marketing and Sales,
6:30 End of Day                                                                                   Tessarae, LLC
                                                                                                  TessArae’s Resequencing Pathogen Microarray (RPM) simultaneously detects and identifies
                              TUESDAY, MAY 20                                                     hundreds of strains of viral and bacterial pathogens.
                                                                                                  Unlike PCR and immunoassays that employ a surrogate marker for detection (e.g. fluo-
7:45 am - 6:00 pm Registration Open                                                               rescent signal), RPM results are the nucleotide sequences of pathogen-specific signatures
7:45     Morning Coffee or Breakfast Workshop (Sponsorship Available)                              that distinguish between known and previously unknown variants, as well as detecting co-
                                                                                                  infecting pathogens.
                          APPLIED MICROARRAYS                                                     Epidemiological analysis of such sequence variants enables monitoring of newly intro-
                                                                                                  duced, circulating, and commensal organisms within defined populations. A clinical study
                                                                                                  of 424 respiratory specimens demonstrated superior sensitivity and specificity, with zero
8:25     Chairperson’s Remarks                                                                    false positives, compared to benchmark microbial cultures and PCR tests and identified
8:30     Genomewide Dissection and Predictive Modeling of                                         thirteen novel H3N2 influenza strains. RPM provides single-specimen, single-test, same-
         Complex Traits                                                                           day results for real-time global epidemiology.
Marco F. Ramoni , Ph.D., Assistant Professor, Division of Health Sciences                         12:30 End of Conference
and Technology Harvard Medical School and Massachusetts Institute of
Technology                                                                                                                            Media Partners:
Complex traits are the result of the interaction of multiple genetic factors. Genomewide
association studies give us the opportunity to query virtually all of the variations in an
individual, but our analytical methods focus on analyzing one SNP at a time. Learn how to
identify the complex multigenic profiles underpinning two common diseases - stroke and
asthma - and to develop prognostic models able predict the risk of an individual based on
his genetic variations.

9:00     Genotyping of Pooled DNA on Affymetrix Microarrays
Tomas Drgon , Ph.D., Staff Fellow, Molecular Neurobiology , NIDA, NIH
I will discuss advantages and disadvantages of pooled DNA genotyping in clinical and basic
research in human genetics. I will discuss the sources of error, from clinical ascertainment,
to pool construction, analysis and replication. I will also discuss selected methods for analy-
sis of pooled genotype data such as Principal Component Analysis, Hierarchical Clustering
and Monte Carlo modeling.
9:30      Analysis of Sex- and Age-Related Differences in Heart of Rat
Strain Fisher 344 Using Oligonucleotide Microarrays
Tao Han, Ph.D., Staff Scientist, Systems Toxicology, National Center for

                           Summit – At – A – Glance                                                  Sponsorship & Exhibit
                                          Microarrays in               Proteomic
                                                                                               Sponsorship Information
                                            Medicine                SamplePreparation
                    7:00 am – 6:00 pm                  Registration Open                      Custom designed sponsorship programs enable you to com-
                                                                                              petitively position your company as a leader in the industry,
                    8:10 – 9:40                      Keynote Presentations                    while collecting quality leads. Sponsored presentations al-
                    9:40 – 10:25         Grand Opening Coffee Break in Exhibit Hall           low your company to educate leading scientific and execu-
Monday, May 19

                    10:25 – 12:00          Data Analysis               Optimization           tive decision-makers on your latest technology or solution.
                                               Luncheon Technology Workshops                  Sponsorships Include:
                    12:00 – 1:25
                                                    (Sponsorship Available)                   Embedded Agenda Presentation – Speak to a captive
                                         Models to Predict                                    audience! This Sponsorship includes a podium presenta-
                    1:25 – 3:00                                          Biomarkers
                                            Responses                                         tion given during the scientific agenda, onsite branding,
                    3:00 – 3:45                 Networking Refreshment Break                  cooperative marketing efforts, and more.
                                           Stability and                                      Breakfast or Luncheon Workshop - These workshops
                    3:45 – 5:15                                      Protein Analysis
                                          Standardization                                     include presentation time with a Q&A session over break-
                    5:15 – 6:30                     Reception in Exhibit Hall                 fast or lunch. CHI will provide the room and AV and will
                    7:45 am – 6:00 pm                  Registration Open                      promote workshop attendance onsite.
                    8:30 – 10:15        Applied Microarrays          Morning Session          CHI can also work with you to customize an Invitation-Only
                    10:15 – 11:00                  Networking Coffee Break                    VIP Dinner, or Networking Reception. Please call for details.
Tuesday, May 20

                    11:00 – 12:35         Data Analysis               Tissue Proteomics
                    12:35                              End of Conferences
                                                                                               Exhibitor Information
                                         Genomic Sample              Proteomic Tools for      WHY EXHIBIT?
                                           Preparation                   Diagnostics
                                                                                              • Demonstrate your expertise to top decision-makers
                    1 pm – 1:55 pm                      Registration Open
                                                                                                representing biotech, academic research institutions,
                    1:55 – 3:30              Isolation               Protein Microarrays
                                                                                                national labs, and clinical research organizations.
                    3:30 – 4:15                 Networking Refreshment Break
                                                                                              • Dedicated time from the conference program for del-
                    4:15 – 6:00           Amplification               Proteomics as a Tool
                                                                                                egates to view posters and exhibits.
                    6:00                             End of Conference Day
                                                                                              • Market your technology/products/services to all delegates.
                    7:30 am                              Morning Coffee
                    8:30 – 10:00                     Keynote Presentations                    • Identify new business leads.
                    10:00 – 10:45                 Coffee Break in Exhibit Hall                • Perfect platform to introduce a new product.
Wednesday, May 21

                    10:45 – 12:10        Morning Session               Morning Session        • The Exhibit Hall is strategically located near the session
                    12:15 – 1:30          Luncheon in Exhibit Hall, sponsored by CHI            rooms to allow delegates to easily view your
                                                                                                demonstration and meet you face-to-face.
                                                                   Biomarkers in
                    1:30 – 2:30
                    2:30-3:00                  Networking Refreshment Break
                                                                                               For sponsorship and exhibit details,
                                         Optimization for
                    3:00 – 5:00                                   Protein Analysis             contact Suzanne Carroll at 781-972-5452
                    5:00                            End of GOT Summit

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❒ Microarrays in Medicine AND Genomic Sample Preparation                                                                                         tical technology, business, and therapy markets. Keep abreast
❒ Microarrays in Medicine AND Proteomic Tools for Diagnostics                                                                                    of the latest advances in pharmaceutical R&D, their potential
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