Advances in

November 17-18, 2009 Crowne Plaza Philadelphia, City Center

Philadelphia, PA

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Technologies. . . Transcripts. . . Therapies

Gene Expression Profiling

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Keynote PresentationLooking to the Future — Regulations, Standards, Quality, and Clinical TrialsElizabeth Mansfield, Ph.D., Director, Personalized Medicine Staff, Office of In Vitro Diagnostic Devices, CDRH/FDA

Featured PresentationNew Approaches Towards Characterizing Noncoding RNA’s and Their Roles in Health and DiseaseAllen Nicholson, Ph.D., Professor, Biology and Chemistry, Temple University

Session Topics Include• Technologies...Transcripts...Therapies• SingleCellGeneExpressionProfiling• ProfilingGeneExpressionfromTissue• DefiningandUtilizingBiospecimenswithanEyeforFit-For-Purpose

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Lead Sponsoring Publications:Premier Sponsor:

Conference Short Course*Using Automation to Set-up a Successful

Research Laboratory: From BioSample to Meaningful Biological Results

Course Instructors:Nicholas Ilasi, M.Sc., Business Analyst

Petar Stojadinovic, Professor, National University, Corporate Trainer, AutomationTrainer and New Horizons

MONDAY, NOVEMBER 16, 2009

5:00-5:30 pm Early Conference Registration

5:30-6:30 Welcome Reception in the Exhibit Hall

TUESDAY, NOVEMBER 17, 2009

7:00 am Conference Registration

7:30 am Breakfast Presentation (Sponsorship Opportunity) and Morning Coffee

8:15 Java and Jive Break-out Discussion GroupsGrab a cup of coffee and join a facilitated discussion group focused around specific themes. This unique session allows conference participants to exchange ideas, experiences, and develop future collaborations around a focused topic.

DEFINING AND UTILIZING BIOSPECIMENS WITH AN EYE FOR FIT-FOR-PURPOSE

(Combined session with The Science of Biobanking meeting)

9:00 Chairperson’s Remarks

KEYNOTE PRESENTATION

9:05 Looking to the Future – Regulations, Standards, Quality, and Clinical Trials

Elizabeth Mansfield, Ph.D., Director, Personalized Medicine Staff, Office of In Vitro Diagnostic Devices, CDRH/FDA

9:50 Defining Biospecimen Quality Within the Fit-For-Purpose Paradigm

Stephen M. Hewitt, M.D., Ph.D., Chief, Tissue Array Research Program and Applied Molecular Pathology Laboratory, National Cancer Institute, NIH

10:20 Networking Coffee Break, Poster & Exhibit Viewing

11:00 Translational Research Working Group Developmental Pathway For Biospecimen-Based Assessment Modalities

Speaker to Be Announced

11:30 Standards and ControlsGeraldine Thomas, Ph.D., Professor, Molecular Pathology, Department of Histopathology, Imperial College of LondonThere is a huge variety in the use to which human material can be put for scientific studies. However, biobanks must ensure that the material they supply is fit-for-purpose, or they will encourage the “garbage in, garbage out” principle. Samples from biobanks should be demonstrated to be pathologically what they say they are, and of a suitable quality for downstream scientific protocols. A number of simple procedures that permit the biobanker to document the quality of their collected samples will be discussed.

12:00 Close of Session

12:15 Luncheon Presentation Sponsored by Gene Signature’ Focused Expression Analysis: Enabling the Assessment of Pathways, Disease States & Biomarker Sets, from Samples Including Single Cells

Jon Sherlock, Ph.D., TaqMan Array Product Manager, Consumables, Applied BiosystemsWith increasing biological knowledge and understanding scientists can now consider experimentally assessing and interrogating entire pathways,

Biology is not static–neitherarethetoolsandtechnologiesthatsupportgenomicdiscoveryforbasicandpharmaceuticalresearch.Geneexpressionprofilingispreferred,providingcommonlanguageforfindingrelationshipsbetweenhealthanddisease;geneticchangesasaresultoftherapy;markersfortoxicologyanddrugsafety;andeven

potentiallyleadingtopersonalizedmedicine.Additionally,itmaybepossibletocapturetheserevealingexpressionprofileswithasfewasathousandtranscripts.Learnfromseasonedandsavvyresearcherswhosharetheirexperiencesusingthelatestgenomictechnologiesforpiecingtogetherthebiologicalpuzzleofhealthanddisease.

SHORT COURSESSUNDAY, NOVEMBER 15, 2009

1:00 – 2:00 pm Short Course Registration

2:00 – 5:00 pm SC1 - Pre-Conference Short Course* Scientific & Technical Considerations for Developing & Managing Biobanking Protocols

The biospecimen research protocol is the cornerstone of any research utilizing precious biological samples and serves as a crucial tool to support both large and small biobanking programs. The management of biorepository protocols is one of the largest and most important considerations when calculating costs in biobanking programs today, putting sustainable quality operations of biospecimen resources at risk. While often overlooked, proactive management and design of biobanking protocols can dramatically improve & address critical issues helping most programs achieve the quality required for serving their community. This workshop will present an in-depth overview and discussion of the following topics:

• RecommendedPracticeforProtocolDevelopment• ConsiderationsforEvidence-basedProtocolDesign• FactorsrelatedtoDownstreamAnalysis• OperationalStrategiesforManagementofEndUserProtocols• GuidelinestoOptimizeIRBReview• IssuesRelatedtoCulling&DisasterPlanningandFinancial

Considerations&CostUseCases

Who Should Attend?Biospecimen Resource Directors, Lab Managers, Technicians, Scientists & Biobank End Users, Regulatory & Informatics Professionals and Policymakers & Grant Writers/Managers

Course Instructors:Andrew Brooks, Ph.D., Director, Bionomics Research & Technology Center, Rutgers UniversityLisa Miranda, President, Biobusiness Consulting Inc.; Former Technical Director, TTAB Core Facility, University of Pennsylvania

TUESDAY, NOVEMBER 17, 2009

5:30 – 8:30 pm SC2 - Short Course* Using Automation to Set-up a Successful Research Laboratory: From BioSample to Meaningful Biological Results

Researchlaboratoriesarecomprisedofindividualautomatedsystemsthat should allow seamless access from samples, to reagents, to runs, throughtoresults.Researchscientistsneedtobeabletosecurebiologicsamples (storage, processing and retrieval) and run experiments on the selectedinstrumentalplatforms(microrrays,qPCR,digitalPCR).Alwayskeeping in mind new conditions/instrumentation lead to new protocols as the genomics field matures. This balancing act is comprised of successful utilization of precious resources including biosamples, reagents, instrumentation,andbrainpower.Embracingthesechallengesandresultingchanges must be done with tight control over budgets to maximize return on investment because there is a high standard set for maximizing value and minimizing waste. Topics to be covered include:

• Robotics(whatyoureallyneedandwhatyoucandowithout)• LIMsandELN/LIMS/Inventory• IT

Who Should Attend?Lab managers, technicians, and scientists from biobanks and gene expression laboratories whose top priority is biological results through successful laboratory automation.

Course Instructors:Nicholas Ilasi, M.Sc., Business AnalystPetar Stojadinovic, Professor, National University; Corporate Trainer, AutomationTrainer and New Horizons

*Separate registration required

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or evaluating whole gene classes, biomarker sets or disease states rather than studying single genes. To this end Applied Biosystems have developed>150TaqMan® Gene Signature Arrays for human, mouse and rat in 384-well micro fluidic card and 96-well plate formats. Together with tools enabling single cell amplification and data analyses these provide scientists with a powerful system for biological investigations. Specific examples of the pluripotency gene signature from single embryonic stem cells and the lipidomics gene class will be discussed.

PROFILING GENE EXPRESSION FROM TISSUE (Combined session with The Science of Biobanking meeting)

2:00 Chairperson’s Remarks

2:05 Tackling Technical Barriers to Achieve High Fidelity Gene Expression Data from Formalin-Fixed Paraffin-Embedded Clinical Tissues

Jun Luo, Ph.D., Assistant Professor, Department of Urology, Johns Hopkins HospitalFormalin-fixationandparaffin-embedding(FFPE)isastandardpathologicalprocedure commonly applied to clinical specimens in preparation for pathological evaluation. This procedure however inevitably compromises genomicanalysis,limitingtheutilityofclinicalFFPEspecimens.DissectingthevarioustechnicalvariablesduringtheFFPEprocedurethatcontributetoinferiorRNAqualitywillhelptoimprovethequalityofmoleculardataderivedfromFFPEspecimens.Inaddition,anumberofprospectivemeasures that are relatively easy to implement should be taken to improve theprocessing,storage,andtheutilityofFFPEspecimensformolecularanalysis.

2:35 Comparison of Quantity, Quality, and Microarray Performance of RNA Extracted from Formalin-Fixed Paraffin-Embedded and Unfixed Frozen Tissue Samples

Marshall S. Scicchitano, M.S., Manager, Molecular Pathology, Department of Safety Assessment, GlaxoSmithKlineArchived pathology specimens used for retrospective analyses are typically preservedasformalin-fixedparaffin-embedded(FFPE)tissue.FormalinfixedtissueshavebeenpreviouslyshowntoyieldcompromisedRNAcomparedwiththatobtainedfromfrozentissue.Inordertoassessandcompareunfixed,frozenRNAandFFPERNAqualityandperformanceonanAffymetrixplatform,RNAwasisolatedfromLPS-stimulatedhumanbonemarrowstromalcellsandeithersnap-frozenorFFPERNAintegritywasqualitativelyassessedandcomparedbetweenfrozenandFFPEsamples using the Agilent 2100 Bioanalyzer. Affymetrix quality control parameters were assessed and compared for each of these samples. Additionally,differentiallyregulatedgeneswereanalyzedwithIngenuityPathwayAnalysissoftwareforcomparisonofoutputdatabetweenfrozenandFFPEsamples.

3:05 Technology Presentation (Sponsorship Opportunity)

3:20 Networking Refreshment Break, Poster & Exhibit Viewing

4:00 Elucidating Lung Cancer Subtypes Using Genomics Technologies

George Vasmatzis, Ph.D., Molecular Medicine, Mayo Clinic Cancer CenterOurdataderivedfromLaserCaptureMicrodissected(LCM)tumorsand other public lung cancer expression profiles show a high degree of heterogeneity in these tumors. Because of variability in therapy response, more targeted therapies are being developed specific to lung cancer subtypes.Developingapanelofgenesthatcoulddistinguishlungcancersubtypes in poorly differentiated tumors or in small biopsy specimens would be helpful in the management of patients with lung cancer.

4:30 Effects of Sample Processing Time on PBMC Gene Expression Patterns from JIA Patients

Michael Barnes, Ph.D., Director, Cincinnati Biobank; Pathology, Cincinnati Children’s HospitalManygeneexpressionstudiesutilizeFicollisolatedperipheralbloodmononuclearcells(PBMC)asasourceofRNA.Priortocommencementofa multi-center longitudinal study of patients with juvenile idiopathic arthritis

(JIA),theeffectofprocessingtimewasevaluatedusingAffymetrixU133plus2.0 GeneChips®. Gene expression differences were identified and the trends were confirmed in a group of over 300 experimental samples allowing selection of an acceptable window for sample processing. The talk will discuss lessons learned from this project and the effect of processing time on the quality and outcome of translational research that utilizes microarray technology to study gene expression.

5:00 Close of Day

5:30 – 8:30 pm Short Course 2* Using Automation to Set-up a Successful Research Laboratory: From BioSample to Meaningful Biological Results

*Separate registration required

WEDNESDAY, NOVEMBER 18, 2009

7:30 am Breakfast Presentation (Sponsorship Opportunity) and Morning Coffee

TECHNOLOGIES. . . TRANSCRIPTS . . . THERAPIES8:10 Chairperson’s Remarks

FEATURED SPEAKER

8:15 New Approaches Towards Characterizing Non-Coding RNA’s and Their Role in Health and Disease

Allen Nicholson, Ph.D., Professor, Biology and Chemistry, Temple UniversityThediversefunctionsofnon-coding(nc)RNAsincellularandviralgeneexpressionandregulationrivalthoseofproteins.NewtechnologiesareaddressingthechallenginggoalsofidentifyingncRNAs,determiningtheir roles in health and disease, and suggesting new therapeutic approaches. Specific studies will be presented that either analyze the ncRNAcomponentofcellulartranscriptomesorthatcharacterizediseasesinvolvingncRNAsandtheirpotentialtreatmentstrategies.

9:00 Application of Gene Expression Profiling in Discovery and Early Development to Identify and Characterize the Toxic Profiles of Compounds

Wayne Buck, Ph.D., Cellular Molecular & Exploratory Toxicology, Abbott LaboratoriesGene expression profiling can help predict the toxic properties of compounds and identify novel molecular biomarkers of toxicity early in the discovery process. However, the optimal implementation and positioning ofthesemoleculartechniquesinanorganizationcanbechallenging.Inthis presentation, using specific examples, we will illustrate how these emerging techniques can be successfully used in vitro and in vivo to identify compounds with an acceptable toxicologic profile and novel biomarkers of toxicity.

9:30 Examining CNS Gene Expression in Isolated Sleep Circuits

Christopher Winrow, Ph.D., Director, Psychiatry, Merck Research LaboratoriesA circuit-based analysis of brain regions is complicated by the spatial and cellulardiversityoftheCNS.Combininglasercapturemicrodissectionwithtranscriptome-wide profiling enabled detection of significant changes in sleep/wake regulating nuclei between night and day in preclinical species.

10:00 Networking Coffee Break, Poster & Exhibit Viewing

10:45 Genetic Tools to Study Gene Expression During Bacterial Pathogen Infection

Jay Zhu, Ph.D., Assistant Professor, Microbiology, University of Pennsylvania School of MedicineThe astonishing flexibility and adaptability of the bacterial cell has enabled

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many pathogenic species to freely transition between dramatically different environmental conditions. The transcriptional changes that underlie this ability can determine the success of the pathogen in the host. We will use Vibrio cholerae as a primary example to introduce a number of genetic techniques that have been devised to examine the transcriptional repertoire of bacteria in vivo during infection.

11:15 Evaluating Quality in a Multicenter Gene Expression Microarray Study

Kellie Archer, Ph.D., Assistant Professor, Department of Biostatistics, Virginia Commonwealth UniversityMulticentermicroarraystudiesareincreasingtoensureanadequatenumber of samples will be procured, particularly when the phenotype being studied is rare. The quality of hybridized microarrays is dependent uponthequalityoftheextractedRNA,whichinturnisdependentuponthequalityofthesourcetissuesamples.Inthispresentation,proceduresundertaken to evaluate quality of samples submitted for inclusion in a multicentermicroarraystudy,fromRNAisolation,tocDNAsynthesisandIVTlabeling,tohybridizationwillbedescribed.

11:45 Increased Expression of Desmoglein 2 in Malignant Skin Carcinomas: A Tissue- and RNA-Microarray Based Study

M G. Mahoney, Ph.D., Associate Professor, Department of Dermatology and Cutaneous Biology, Thomas Jefferson UniversityDesmoglein2(Dsg2),atransmembranecadherinofthedesmosomalcell-cell adhesion structure, is downregulated with epithelial differentiation. WerecentlydemonstratedthatoverexpressionofDsg2inepidermalkeratinocytes deregulates multiple signaling pathways associated with increased growth rate, anchorage-independent cell survival, and the developmentofskintumors.Usingtissuemicroarrays,weshowadramaticupregulationofDsg2expressionincertainhumanepithelialmalignancies including basal cell carcinomas, squamous cell carcinomas, carcinomas of sebaceous and sweat glands and adenocarcinomas. Dsg2expressionwascompletelyabsentinmalignantfibrosarcomasandmelanomas.Thus,wehaveidentifiedDsg2asapotentialnovelmarkerforepithelial-derived malignancies.

12:15 pm Close of Morning Session

12:30 pm Luncheon Presentation (Sponsorship Opportunity) or Lunch on Your Own

TECHNOLOGIES . . . TRANSCRIPTS . . . THERAPIES (continued)2:00 Chairperson’s Remarks

2:05 Mapping Transcriptome-wide Functional Protein-RNA Interactions in the Mouse Brain

Donny Licatalosi, Ph.D., Postdoctoral Associate, Laboratory of Molecular Neuro-oncology, Rockefeller University

2:35 Development and Validation of Molecular Signatures Predicting Risk of Recurrence and Survival of Human Breast Carcinoma Patients

Sarah A. Andres, M.S., Department of Biochemistry & Molecular Biology, University of LouisvilleTheHumanGenomeProjectprovidedopportunitiestodevelopprecisetestsforcancerdiagnostics,therapyselectionandmonitoring.Fromanalyses of various microarray studies, genes expressed in human breast cancercellsprocuredfromde-identifiedtissuesectionsbyLCMandgenespredicted in adjacent stromal cells were identified, whose expression appearsrelatedtoclinicaloutcome.Molecularsignaturesconsistingofsubsets of candidate genes predicted breast cancer recurrence and overall survival in multivariate Cox proportional hazards models. Collectively, results suggest that these genes may form the basis for developing clinical laboratory tests to predict clinical outcome of breast cancer.

3:05 Networking Refreshment Break, Final Poster & Exhibit Viewing

SINGLE CELL GENE EXPRESSION PROFILING3:30 Novel Gene Knockdown Models for Studying

Reprogramming in the Early EmbryoMylene W. M. Yao, M.D., Assistant Professor, Department of Obstetrics and Gynecology, Stanford University School of MedicineComparedtotheembryonicstemcell(ESC)generegulatorynetwork,littleis known about the dynamic gene network that directs reprogramming intheearlymammalianembryo.WehavefoundthatESCpluripotencyregulators,suchasOct4,havenovelandcriticalfunctionsinthefirstfewdays of development, when both maternal and embryonic transcripts may be present. We established models of gene-specific knockdown bymicroinjectingmorpholinosanddiscoverednovelOct4functionsinpost-transcriptional regulation by global gene expression profiling and large-scalesemi-quantitativeRT-PCR(RT-qPCR)atthelevelofthesingle-embryo. This experimental strategy is being applied to deconstruct the dynamic gene network that regulates development, reprogramming and cell fate decisions.

4:00 Single Molecule Sequencing for Unbiased Views of Gene Expression from Small Numbers of Cells

John Thompson, Ph.D., Senior Director, Genomic Research, Helicos BiosciencesDeepsequencingofcDNAsfromavarietyofbiologicalsystemshasprovided gene expression data that spans a much broader linear range than possible with hybridization-based methodologies as well as providing information about previously unannotated transcription units and splice sites. Though sequencing technologies are much better at quantitating the transcriptome than hybridization-based technologies, many still suffer from the need for ligation and amplification steps that can bias the quantitative outcomes. Single molecule sequencing, in contrast, is able to provide quantitative information without the need for either amplification or ligationandtheconcomitantbiasestheycanintroduce.Furthermore,thesimple sample preparation and low sample needs allow the use of very small numbers of cells for starting material. Advances in reducing sample requirements and demonstrating the broad range of samples that can be addressed by single molecule sequencing will be described.

4:30 Current-Generation High-Throughput Sequencing: Deepening Insights into Mammalian Transcriptomes

Benjamin Blencowe, Ph.D., Professor, Banting and Best Department of Medical Research, Molecular Genetics, Center for Cellular and Biomolecular Resaerch, University of Toronto (tentative)

5:00 Close of Meeting

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SPONSORSHIP AND EXHIBIT INFORMATIONSponsorsandExhibitorswillenjoyfacilitatednetworkingopportunitieswith200internationalscientistsandexecutives.Enhancebusinessdevelopmentandleadgeneration initiatives by presenting and exhibiting your expertise to this hard to reach market.

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To customize your sponsorship or exhibit package, contact:Angela Parsons, VP, Business Development, 781-972-5467, aparsons@healthtech.com

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Advances in

Gene Expression ProfilingTechnologies. . . Transcripts. . . TherapiesNovember 17-18, 2009 Crowne Plaza Philadelphia City Center Philadelphia, PA

Present a Poster and Save $50!CambridgeHealthtechInstituteencouragesattendees to gain further exposure by presenting their work in the poster sessions.

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