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Tuesday, September 16

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

8:00 Brainstorming Breakfast Discussion Groups

Grab a cup of coffee and join a discussion group. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.  

Table 1: Key Hurdles in Biomarker Development

Chad R. Borges, Ph.D., Assistant Professor, Chemistry and Biochemistry, The Biodesign Institute – Center for Personalized Diagnostics, Arizona State University

• How do we improve our approaches to matching clinical needs for cancer markers with analytical scientists and their platforms?
• The biospecimen procurement process: dos and don'ts
• What constitutes acceptable marker validation?
• How do we efficiently transition from discovery platforms to viable clinical platforms? When might transition not be necessary?

Table 2: Historical Samples for Biobanking

Allison Hubel, Ph.D., Professor, Mechanical Engineering and Director, Biopreservation Core Resource, University of Minnesota

• How do we define what a "historical sample" is?
• What are the most common samples that have been in storage > 10 years (tissue, plasma, serum)?
• What percentage of your repository is used for storage and what percentage of the samples are used within 30 days of collection?
• What kind of information would be helpful to have to determine whether or not a sample in storage is useful?

Table 3: Sample Annotation: Investing in the Future and the Value

Michael Liebman, Ph.D., Managing Director, IPQ Analytics, LLC

• What level of patient/sample annotation is critical?
• Can this exist in a linkable database or does it have to be embedded with the sample?
• Anonymization vs. de-identification: Creating value in the biobank and its use

Table 4: Biospecimens and Whole-Genome Sequencing: Are There New Considerations for Privacy and Data Sharing?

Geoffrey P. Lomax, Ph.D., Senior Officer, Standards Working Group, California Institute for Regenerative Medicine

• Is whole genome sequencing appropriate for "historical" samples?
• What access controls, if any (e.g., open access vs. controlled access) should be imposed on "raw" sequencing data to protect donors’ privacy interest?
• Does genomic characterization create substantial new risks to donors, families or groups? Can potential risks be effectively mitigated?

Table 5: Population-Based and Disease-Oriented Biobanking for the Biopreservation of Liquid-Based Gynecological Cell Samples

Nasrin Perskvist, Ph.D., Director and National Coordinator, Cervical Cytology Biobank, Pathology and Cytology, Karolinska Institute and BBMRI.se

• Legal and ethical aspects of a population-based and hospital-integrated biobank: How far are we willing to go?
• The process of moving from a regionally based Cervical Cytology Biobank to a national infrastructure: Is it applicable to the full scope of the population?
• Providing samples to researchers without any risk of leaving insufficient sample volumes for the care of the woman herself: Quality vs. Quantity.

Table 6: Patient-Derived Xenograft (PDX) Models of Human Cancers towards Identifying Tumor-Initiating Cells and Discovery of Patient-Specific Therapeutics

Vinagolu K. Rajasekhar, MSc, MPhil, Ph.D., Senior Research Scientist, Memorial Sloan-Kettering Cancer Center

• Why, to date, have none of the conventional biobanks for patient tumor specimens delivered on our goals for a cancer cure?
• What is the live tumor tissue banking approach and how it can help recreate the original parent tumor heterogeneity and also form a renewable tumor tissue resource?
• How does live biobanking facilitate identification of cancer stem cells and discovery of patient-specific therapeutics?
• Importance of warm autopsies, live tissue bankonomics and sustainability of viable tumor banks

Table 7: Ethical Considerations in Building Future Use Collections

Katheryn Shea, Vice President, Bioservices, Precision for Medicine

• Key considerations in creating informed consent language
• Global challenges and regulatory differences that affect designing your future use collection
• Abstract or Annotate? Generating mineable data sources

Table 8: Pediatric Participants in Biobanks

Suzanne Vercauteren, M.D., Ph.D., FRCPC, Head, Division of Hematopathology, BC Children’s Hospital and Clinical Assistant Professor, Pathology and Laboratory Medicine, University of British Columbia

• Does the opinion of children of non-consenting age matter? At what age?
• Do we need to reconsent at age of majority?
• How do we garner public support for pediatric biobanks?
• How can we improve the quantity and quality of pediatric specimens?

Table 9: Biobanking: How Can Collections Be Maximized without Dedicated Funding?

Wendell G. Yarbrough, M.D., MMHC, FACS, Professor of Surgery, Otolaryngology and Pathology; Section Chief, Otolaryngology; Co-Director, Molecular Virology Research Program; Director, Head and Neck Cancer Program, Smilow Cancer Hospital, Yale University

• Collaborations with researchers who have LN and -80oC
• Engagement of clinicians interested in the disease
• Engagement of pathologists

 

Genomics’ Role in Individualized Cancer Therapy from Assay Development to Clinical Implementation 

9:00 Chairperson’s Remarks

Colin C. Pritchard, M.D., Ph.D., Assistant Professor and Associate Director, Genetics and Solid Tumors Laboratory, Laboratory Medicine, University of Washington

9:05 Bringing Comprehensive Molecular Information into Routine Clinical Care

Josephine N. Harada, Ph.D., MBA, Director, Strategic Alliances, Foundation Medicine, Inc.

Oncology has experienced a recent paradigm shift toward thinking about cancer as a disease of the genome. Next-generation sequencing has furthered our understanding of cancer biology and let us more comprehensively characterize the genomic alterations in an individual patient’s cancer. This profiling approach enables precision medicine in clinical cancer care. Its widespread use could provide more treatment options and enable more rapid accrual to ongoing and planned trials of agents targeting pathways under study, thereby continuing to advance precision medicine.

9:35 Successful Implementation of Precision Medicine in Clinical Cancer Care: The UW Experience

Colin C. Pritchard, M.D., Ph.D., Assistant Professor and Associate Director, Genetics and Solid Tumors Laboratory, Laboratory Medicine, University of Washington - Biography 

Genomic sequencing technology for diagnostic testing is especially promising for cancer patients, both for hereditary cancer risk assessment and for tumor-based sequencing for precision cancer therapy. Since 2011, the UWMC genetics lab has offered clinical assays for precision medicine in clinical cancer care that harness genomic next-generation sequencing. We will review considerations related to clinical implementation of this technology and cover gene panels currently in clinical use for cancer patients and their families at UW and SCCA.

 

10:05 Next-Generation Applications for Personalised Genomics: from CARTaGENE to the Clinic

Philip Awadalla, Ph.D., Professor, Faculty of Medicine, University of Montreal; Director, CARTaGENE

CARTaGENE was developed to produce an internationally competitive, cohort-based biobank facilitating the emergence of new and novel research projects. As a result, these investigations will generate new healthcare knowledge for and about Québec, Canada and the international community. By acting as a springboard, scientists can expand their research questions by investigating the genomic, metabolomic, epigenomic and environmental control points of complex chronic disorders and related quantitative traits. My own research program has exploited the deep clinical and phenotypic data collected from over 40,000 participants to discover novel genomic factors associated with disease and quantitative traits.

10:35 Coffee Break in the Exhibit Hall with Poster Viewing

11:15 Development and Validation of a Clinical Trial Patient Stratification Assay that Interrogates 27 Mutation Sites in MAPK Pathway Genes

Ken C. N. Chang, Ph.D., Clinical Assay Development and Outsourcing Lead, Clinical Biomarkers and Diagnostics, Merck & Co., Inc. - Biography 

A custom-designed Single Nucleotide Primer Extension (SNPE) multiplexing mutation assay was developed and analytically validated as a clinical trial assay for more than 30 specific mutations among three targeted RAS/RAF oncogenes. We used next-generation sequencing to resolve discordant calls between the SNPE mutation assay and Sanger sequencing. We also applied a triplicate rule to reduce potential false positives and false negatives, and proposed special considerations for clinically significant level of mutations including pre-defining a cut-off percentage for each mutant and wild-type.

11:45 Integrating Laboratory and Clinical Informatics for Next-Generation Sequencing Assays

Noah Hoffman, M.D., Ph.D., Assistant Professor, Laboratory Medicine, University of Washington - Biography 

Next-generation sequencing assays, like human germline and somatic mutations surveys and deep sequencing of mixed bacterial populations, introduce significant complexity to the laboratory and healthcare system. To manage this complexity, our laboratory has invested heavily in staff and infrastructure to support data analysis, interpretation and clinical reporting. We will discuss challenges encountered related to quality control, data management, case signout and reporting into electronic medical records, and describe approaches for addressing these challenges within the UW Medicine healthcare system.

12:15 pm Close of Session

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

 

Deciphering Cancer’s Complexity Takes
Multidisciplinary Integration 

2:00 Chairperson’s Remarks

Sui Huang, M.D., Ph.D., Professor, Institute for Systems Biology

2:05 Glycan “Node” Analysis for Detecting and Monitoring Cancer

Chad R. Borges, Ph.D., Assistant Professor, Chemistry and Biochemistry, The Biodesign Institute – Center for Personalized Diagnostics, Arizona State University - Biography 

Cancer biologists have known for many years that tumor cells display abnormal glycan structures. Dr. Borges has developed a technique to quantify glycan structural characteristics in blood serum that provides a completely new angle by which to leverage glycans as markers to identify and classify cancer. Results from studies of lung cancer and several other different types of cancer will be presented.

2:35 Integrative Genomic Analysis of Gastric Cancer

Kai Wang, Ph.D., Principal Scientist, Computational Biology and Precision Medicine, Pfizer Oncology - Biography 

Gastric cancer is a heterogeneous disease with diverse molecular and histological subtypes. We performed comprehensive genomic profiling in a large cohort of gastric cancers for integrative genomic analysis. Our data revealed subtype-specific genetic, epigenetic perturbations and unique mutational signatures. We identified previously known (TP53, ARID1A and CDH1) and new significantly mutated driver genes. These findings illustrate a multidimensional and comprehensive genomic landscape that highlights the molecular complexity of gastric cancer and provides a roadmap to facilitate genome-guided personalized therapy.

3:05 Selected Oral Poster Presentation: Development of Statistical Process Control Parameters for Tissue Quality in a Pregnancy-Related Biorepository

Donald O. Chaffin, Laboratory Manager, Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), Seattle Children's Hospital

It is vital that specimens obtained though biobanks preserve a level of quality consistent with research needs. Several factors can impede this goal: the heterogeneous nature of starting materials, artifacts introduced by collection, processing and storage and the often destructive nature of test regimes. It is a requisite that specimens are robustly characterized against a set of normative values which can determine suitability for use and that the effects of post-collection events are known and remain “in control” with respect to these values. We present the quality control regimen for placental tissue collected by the GAPPS repository, a pregnancy-related biobank, with a cohort of over 1540 women. This regimen sets the expectation for achievable quality levels with the current protocols and allows evaluation of collection design changes to increase quality and lower variance. The use of statistical process control methods described here assure consistent specimen quality and can drive future improvement in methods of collection.

3:20 Refreshment Break in the Exhibit Hall with Poster Viewing

4:00 Complex Cell Response to Therapy as Basis for Therapy Resistance in Cancer Cells: “What Does Not Kill Me Makes Me Stronger”

Sui Huang, M.D., Ph.D., Professor, Institute for Systems Biology - Biography 

Current cancer research operates with the tacit assumption that our understanding of cancer cell behavior is established, and all that is needed is to identify new molecular targets and target them. But as single-cell analysis and new theories reveal, beyond this paradigm exists the realm of complex adaptive systems dynamics, endowing cancer cells with the unfathomable ability to act collectively as a population to mount an evasive response to treatment, allowing non-killed cells to become even more malignant.

 

5:15 Close of Day

 

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