The Science of BioBanking - Day 3

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8:30am Morning Coffee

Interrogating the Biospecimen – Tools and Platforms 

8:45 am Chairperson’s Opening Remarks

8:50 Extrinsic and Intrinsic Controls for Measurement of Protein Analyte Concentrations in Tissue Slides

Allison Welsh, Ph.D. Candidate, Department of Pathology, Yale University School of Medicine

Measurement of protein on slides by traditional immunohistochemistry has historically been a highly subjective process.  Now tools are available for accurate measurement that use standardization methods and result in reproducibility that is similar to that seen in ELISA assays or flow cytometry.  This lecture will describe the use of the AQUA method for automated analysis and illustrate findings that have been elusive using traditional immunohistochemistry.  This method is especially important in that it can sense and potentially adjust for the problems of pre-analytic variation often seen in specimens in paraffin archive biobanks.

9:20 Genomic Evolution, Progression and Metastasis in Breast Tumors

James B. Hicks, Ph.D., Research Professor, Genetics, Cold Spring Harbor Laboratory

The genomic evolution of solid tumors can traced by copy number profiling at genome level and tracked spatially through the tumor itself. The discussion will focus on the application of ‘next-generation’ high-throughput sequencing methods to assay genomic copy number and epigenetic variation (DNA methylation) in tumors, including the evolution of tumors at the single cell level.

9:50 Mass Spectrometric Analysis of Proteins from FFPE- or OCT-Embedded Tissues

Hui Zhang, Ph.D., Assistant Professor, Pathology & Clinical Chemistry, Johns Hopkins
University School of Medicine

Formalin-fixed-paraffin-embedded (FFPE) tissues and OCT-embedded tissues, archived with pathological and clinical information processed by universal standard methodology, are used worldwide in hospitals and tissue banks, and present a rich resource of specimens for biomarker discovery. Mass spectrometric analysis of proteins isolated from FFPE-embedded or OCT-embedded tissues from specific disease are likely to detect proteins and protein post-translational modifications as clinically relevant protein markers for disease diagnosis. We have tested the feasibility and established a workflow for proteomic analysis FFPE- or OCT-embedded tissues using mass spectrometry.

10:20 Morning Coffee Break with Exhibit and Poster Viewing

11:00 Biosensing in Thermal Space: Multiplexed Highly Sensitive Detection of Multiple Biomarkers Using Phase Change Nanoparticles

Ming Su, Ph.D., Assistant Professor, NanoScience Technology Center, Department of Mechanical, Materials, Aerospace Engineering, University of Central Florida

Although many biomarkers have been identified with certain specificity to detect cancers at early stage, it is clear that no individual biomarker is ideal to distinguish lethal cancers from indolent ones due to lack of tumor specificity. This talk will describe a new biosensing technique, i.e., biosensing in thermal space, where a series of composition-encoded solid to liquid phase change nanoparticles will be modified with a series of ligands, and used for in vitro detection of multiple biomarkers. The presence and concentration of each biomarker will be derived from the melting peak and fusion enthalpy of according nanoparticles. The multiple sensing results will be used to distinguish lethal cancers from indolent cancers by using pattern recognition technique.  

11:30 CometChip: High-Throughput DNA Damage Analysis

David M. Weingeist, Engelward Laboratory, Biological Engineering, MIT

In collaboration with Sangeeta Bhatia, the Engelward Lab has developed a high-throughput version of the single cell gel electrophoresis “comet” assay. Cells are arrayed in microwells in order to fully automate imaging/analysis and enable a 96-well format for simultaneous assaying of multiple cell types, drugs, or other conditions. Given its sensitivity, robustness and versatility, it is anticipated that this new technology will help to advance studies of chemical toxicology.

12:00 pm Close of Morning Session

12:15 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 

Closing Case Study Combined Session: BioBankers and BioUser Partnerships 

This session brings together scientists who use biospecimens for research (“biousers”) with operation managers who collect and store the biospecimens (“biobankers”).
Biobankers and biousers elaborate on the characteristics of their working relationship as they address the following issues:

• How does this partnership work?
• What are the bottlenecks?
• What does each member bring to the table?
• What does each member need from the other?
• Ultimately, what are the scientific results?

1:30 Chairperson’s Opening Remarks

1:35 Yale University Co-Presentation

Alexander Vortmeyer, Ph.D., Director, Fresh and Frozen Tissue Procurement and Distribution, Yale University

Tobias Carling, M.D., Ph.D., Assistant Professor, Surgery; Director, Yale Endocrine Neoplasia Laboratory, Yale University School of Medicine

Diseased and normal control human tissues are an invaluable resource for diagnostic procedures and research. Traditional pathologic procurement techniques cause partial bio-chemical destruction of tissues, while research interests frequently require optimal biochemical preservation. Modifications of traditional procurement techniques are proposed for the benefit of both research analysis and molecular diagnostic evaluation.

2:30 Quintiles Co-Presentation

Barbara E. Glazer, MT(ASCP), Director, Pre-Analytical Services, Global Central Laboratories, Quintiles

Karl Kammerhoff, MBA, Associate Research Scientist, Discovery Medicine & Clinical Pharmacology, Research & Development, Bristol-Myers Squibb

Collaboration is key in developing the partnership between the biobanker and the biouser. This session explores what each party contributes to the relationship and how the
requirements of the individual parties contribute to the end result. Consideration will be given to initial collection of the biospecimen, training of collection sites, anonymization,
data provision, among others. What are the bottlenecks that can occur, and ultimately, how does all of this translate to quality scientific results?

3:35 Refreshment Break – Last Chance for Poster and Exhibit Viewing

4:00 Millennium Presentation
Samples, Assays and Data: Bio-Repository Practices to Maintain Sample Integrity, Enable Genomic Testing, Data Integration and Utility for Translational Medicine

Erik Koenig, Senior Manager, Molecular Technologies, MILLENNIUM: The Takeda Oncology Company

With the increase in outsourcing in the Bio-Pharmaceutical industry, biorepositories are required to coordinate sample tracking, sample testing and retesting within and throughout several laboratories. Biorepository practices, from Millennium: The Takeda Oncology Company, to maintain sample integrity throughout outsourced genomic testing to support translational medicine will be discussed.

4:40 The Broad Institute Co-Presentation

Kristin Ardlie, Ph.D., Director, Biological Samples Program, The Broad Institute of MIT and Harvard

Jordi Barretina, Ph.D., Research Scientist, Cancer Program, The Broad Institute of MIT and Harvard

5:20 Conference Wrap-up

5:30 Close of Conference