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Register by Friday, March 16 and Save up
to $200!
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Pre-Conference Short Courses (SC)*:
Tuesday, April 10
SC1: Using Classical Statistics & Experiment Design to Reduce
Noise in Your Next Microarray Experiment
Thomas J. Downey Jr., President & CEO, Partek, Inc.
Microarray data contains treatment and/or phenotype effects
embedded in a sea of technical and biological noise. This workshop
will demonstrate how to use proven statistical methods of experiment
design and data analysis to reliably identify biological effects of
interest while controlling and removing noise due to biological and
technical nuisance effects. Attendees will learn how to employ
completely randomized block designs to isolate and remove batch
effects due to processing batches, etc. clearly revealing the signals
from the biological factors of interest. In addition to p-values,
estimates of ratios and fold-changes will be examined from a
statistical perspective. The techniques will be demonstrated using
gene expression, copy number, exon, and ChIP-on-Chip regulation
studies.Attendees will learn how to apply and interpret statistical
techniques such as analysis of variance (ANOVA) -including mixed
linear models and linear contrasts, multiple test corrections, and
principal components analysis.
SC2: Grid Technology in Tissue-Based Diagnosis
Klaus Kayser, M.D., Ph.D., Director of UICC Telepathology Consultation Center, Charite Berlin
Juergen Goertler, Ph.D., IBM DeepComputing
2 pm - 5 pm
SC3: Laser Capture Microscopy – Optimizing Results
* Separate Registration Required
Wednesday, April 11
7:30 Registration and Morning Coffee
8:30 Opening Introductions
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Keynote Presentations:
8:40 The Rosetta Stone of Cancer Genomics & Proteomics
James L. Wittliff, Ph.D., M.D. hc, Professor of Biochemistry &
Molecular Biology, James Graham Brown Cancer Center, University of
Louisville
9:20 Preanalytical Variables in the Analysis of Biomarkers for
Clinical Trials
Scott D. Patterson, Ph.D., Senior Director, Medical Sciences, Amgen
Inc.
Much can be learned from the careful examination of analytes from
samples collected from clinical trials. For example, PK:PD responses
can be modeled to help guide dose-ranging studies. However, collected
human tissue samples should be considered as responding to their
perturbed environment until they are rendered incapable of doing so.
Understanding what can happen to the analytes of interest in the
period from collection of the tissue to analysis is critical to
generating robust data.
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10:00 Coffee Break
Issues with Tissues
10:35 Emergent Technology for Proteomic Biomarker Discovery from
Formalin-Fixed Paraffin-Embedded Tissue
Brian L. Hood, Ph.D., Research Scientist, Clinical Proteomics
Facility, University of Pittsburgh Cancer Institute
Formalin-fixed paraffin-embedded (FFPE) tissues are often
overlooked for mass spectrometry-based tissue biomarker discovery
investigations as they are considered intractable to standard
proteomic methods of analysis. We have recently developed a simple
methodology for efficient extraction of unmodified peptides from FFPE
tissue and incorporated this novel technology in a comprehensive
tissue biomarker discovery workflow. This emergent tissue disease
biomarker discovery workflow will be discussed in the context of its
application to cancers of the prostate, head and neck, and breast.
11:05 The Use of Fresh Human Tissue in Drug Discovery Research
James Eliason, CSO, Research and Development, Asterand, Inc.;
Associate Professor, Barbara Ann Karmanos Cancer Institute, Wayne
State University
Genomic and proteomic techniques have increased the importance of
human tissue in drug discovery research. Much focus has been made on
use of snap frozen tissues, but fresh tissues play an important role
as well. Fresh viable tissues not only can be used for proteomic and
genomic studies but provide the basis for functional studies that test
the efficacy and toxicity of lead compounds.
11:35 Emerging Platforms (Sponsorship Available)
12:05 Lunch Workshop or Lunch on your own
1:30 Accelerating the Development of Targeted Therapeutics with
Tissue Microarrays
John Reilly, Ph.D., Research Fellow, Merck & Co, Inc. Sponsored
by (applied Imaging Logo)
Identification of patient populations likely to respond to a
particular compound is a key issue in clinical
development for oncology indications. Combining cancer tissue
microarrays, immunohistochemistry and automated image analysis allows
rapid assessment of target activation in clinical samples to
facilitate preclinical and clinical development of targeted therapies.
2:00 New Developments in Technology (Sponsorship Available)
2:30 Histological Staining Methods Preparatory to Laser Capture
Microdissection Significantly Affect Detection of mRNAs in
Microarray Hybridization
J. Frederic Mushinski, Ph.D., Senior Investigator, Laboratory of
Genetics, Center for Cancer Research, National Cancer Institute, NIH
To study the contribution of staining methods to degradation of
results from GEP of LCM samples, we subjected pellets of the mouse
plasmacytoma cell line TEPC1165 to direct RNA extraction and to
parallel frozen sectioning for LCM and subsequent RNA extraction. We
used microarray hybridization analysis to compare GEP of RNA from cell
pellets with that of RNA from frozen sections that had been stained
with hematoxylin and eosin (H&E), Nissl Stain (NS), and for
immunofluorescence (IF) as well as with the plasma cell-revealing
methyl green pyronin (MGP) stain. The MGP-stained samples showed the
least introduction of mRNA loss, followed by H&E and
mmunofluorescence. Inclusion of RNAase inhibitor in aqueous staining
solutions appears to be important in protecting RNA from loss of gene
transcripts.
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3:00 Meet-the-Experts
Brainstorming discussion groups moderated by experts in the area.
Attendees are invited to choose the table according to their main
interest; however, they may switch between roundtables. We emphasize
that this roundtable discussion is for an interactive exchange among
scientists and is not meant to be, in any way, a corporate or product
discussion
Topics moderated:
Table 1: The Importance of Protein Partitioning and
Fractionation: Enrichment before Downstream Analyses
Host: Jerry Feitelson, Ph.D., Manager, Strategic Marketing,
Proteomics Business Unit, Beckman Coulter, Inc.
- "To partition or not to partition? That is the
question."
- Specificity & reproducibility?
- Methods for high capacity proteome fractionation
- Digging into the proteome using these tools. How deep can you
go?
Table 2: Gel Based Proteomic versus Peptide Labeling Proteomic
Host: Sunny Tam, Ph.D., Director of Proteomic Fractionation Group,
Research Associate Professor, UMMS Proteomic Consortium, University of
Massachusetts Medical School
- Pros and cons of 2D gel versus iTRAQ
- What are the expected outcomes of the two approaches?
- What are the future improvements for the two approaches?
Table 3: Biorepositories/HIPAA/IRB
Host: James L. Wittliff, Ph.D., M.D. hc, Professor of Biochemistry
& Molecular Biology, James Graham Brown Cancer Center, University
of Louisville
Table 4: Influence of Sample Collection Parameters on Functional
Assays
Host: Scott D. Patterson, Ph.D., Senior Director, Medical Sciences,
Amgen Inc.
- Which analytes change rapidly following collection?
- What realistic controls can be put in place?
- Validity of ex vivo stimulation as oppose
Table 5: RNA Amplification and Labeling for Array Profiling
Host: Christoph Adams, Ph.D., Research Area Manager/Epigenetics,
Life Sciences Division, Invitrogen Corporation
- Normalizing RNA sample input
- What constitute proper internal controls for array
normalization?
- When is RNA amplification a good idea?
- How many microRNAs are there in humans?
Table 6: Fresh versus Frozen Tissue in Drug Discovery
Research
Host: James Eliason, CSO, Research and Development, Asterand, Inc.;
Associate Professor, Barbara Ann Karmanos Cancer Institute, Wayne
State University
Table 7: Sample Collection and Processing, a Pivotal Stage of
Transcript Profiling
Host: Eric R. Fedyk, Ph.D., Senior Scientist II, Drug Safety
Evaluation, Millennium Pharmaceuticals, Inc.
- When to collect and store samples frozen versus formalin-fixed
and paraffin-embedded?
- Isolate subpopulations of leukocytes or store whole blood?
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Biomarker Discovery
4:30 Molecular Profiling of Colon and Breast Cancer: Novel
Clinical Diagnostics
Dr. Yixin Wang, Group Director, Discovery Research and Pharma
Biomarker Support, Veridx/OCD, Johnson & Johnson
The development of the traditional cancer diagnostic markers has
been largely disappointing and is clearly not able to meet the needs
in cancer patient care. One reason is that highly heterogeneous
specimens from cancer patients require multiple markers to produce a
clinically useful assay. DNA microarray technology is widely used to
classify tumors into clinically relevant subtypes in research
laboratories. The technology provides a potential solution for cancer
diagnostics. However, few microrray derived cancer markers have been
adopted in clinical practice. This presentation will review some of
the opportunities and challenges facing the development of cancer
molecular diagnostics. In addition, a couple of clinical studies that
aimed to identify molecular markers for colon and breast cancer
prognosis will be discussed.
5:00 Better Microarray Spots Using Continuous Flow Spotting
Techniques
Bruce Gale, Ph.D., Assistant Professor, Mechanical Engineering,
University of Utah
A microfluidic platform for manufacturing protein, lipid, and cell
arrays has been developed that produces spots with less than a 5% CV
between spots, making microarrays a more quantitative tool. In
addition, these systems have shown the ability to concentrate proteins
from crude samples on spots without expensive purification steps,
significantly reducing the cost of custom protein microarrays. These
same systems have been shown to be able to deposit cells, lipid
bilayers, and sequential chemistries on a single spot with high
quality.
5:30 End of Day One
Thursday, April 12
8:30 Chairperson’s Opening Remarks
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Keynote Presentations:
8:40 Step 1: Harvest Tissue; Step 2: Prepare Template
Michael Brownstein, M.D., Director of Functional Genomics, Craig
Venter Institute
Investigators who are new to the field of functional genomics are
put off by the apparent difficulties inherent in labeling probes,
hybridizing and washing arrays, and analyzing results. This is
perfectly appropriate, but assuming that preparing nucleic acids for
one’s studies is trivial, would be incorrect. Attention to detail
and quality control are essential and different applications demand
different templates. I will give examples of the latter and describe
novel amplification methods that allow experiments to be done today
that were impossible to imagine a few years ago.
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9:20 Robust Data, Robust Algorithms: From Preanalytical
Variability to Bioinformatic Analysis
Dr. Stephen R. Master, Assistant Professor, Department of Pathology
and Laboratory Medicine, University of Pennsylvania Health System
Several recent studies have demonstrated the importance of
controlling preanalytical variability during sample collection for
genomic and proteomic assays. Further, both preanalytic and analytic
variation can have a profound impact on the ultimate outcome of highly
multiplexed diagnostic tests. We will discuss sources of this
variation as well as the importance of choosing appropriate
bioinformatic analyses in in order to maintain test quality.
10:00 Grand Opening Refreshment Break in The G.O.T. Summit
Exhibit Hall
Gene Expression from Fixed Tissues
11:00 Chairperson’s Remarks
11:05 Gene Expression Profiling from Difficult Samples such as
FFPE
Gianfranco de Feo, Ph.D., Senior Director, Customer Solutions,
NuGEN Technologies
Access to biologically and clinically relevant samples for the
discovery, refinement, and validation of gene expression signatures
reflecting clinical phenotypes has been hindered by the inability to
generate high quality gene expression results from the most readily
available tissue sources, formalin fixed, paraffin embedded tissues.
NuGEN technologies has recently developed a linear, isothermal, and
robust amplification approach to perform whole transcript
amplification from very small amounts of total RNA (below 5ng input).
This technology will not only allow researchers to perform splice
variant analysis, but will also allow for the use of degraded RNA
samples, such as RNA isolated from FFPE sources, in expression
experiments.Data demonstrating the performance of the technology,
including sensitivity, linearity, dynamic range, and differential
expression accuracy will be shown. In addition, data demonstrating the
performance of the approach to clinically relevant samples such as RNA
isolated from FFPE tissue sources will also be shown.
11:35 Measurement of Gene Expression from Fixed Tissue: qNPA
Validation of Biomarkers for Diffuse Large-B-Cell Lymphoma
Bruce Seligmann, Ph.D., Chairman & CSO, HTG, Inc.
Measurement of gene expression from fixed tissue using the lysis
only qNPA multiplexed ArrayPlate assay measures the total RNA in the
tissue including the "in situ" cross-linked mRNA. It is
sensitive (using only 1/4th of a tissue slice), gives equivalent
quantitative results as measurement from fresh or frozen tissue, and
gene expression levels correlate with their protein product biomarkers
measured in situ by immunohistochemistry. Three independent studies
using snap frozen tissue had identified non-overlapping sets of
biomarker genes, for a total of 36 putative biomarkers. All 36 were
measured plus cell lineage genes. The validation of a biomarker set
and correlation to therapeutic response and survival outcome will be
reported.
These results demonstrate that archives of fixed tissue can now be
easily mined for biomarker and target validation. Safety studies,
clinical development, and diagnostic assays can be performed using
fixed tissue without changing current tissue storage practice, to get
gene expression results that correlate to protein biomarkers without
any pre-qNPA sample prep.
Featured Presentation:
12:05 Functional Proteomics for Target and Biomarker Discovery
Joshua LaBaer, M.D., Ph.D., Director, Harvard Institute of
Proteomics
12:45 End of Conference
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