2014 Archived Content

Cambridge Healthtech Institute’s Inaugural

Biospecimen Science and Sample Prep

Enabling Sample-Centered Precision Medicine

February 10-12, 2014 | Moscone North Convention Center | San Francisco, CA


Day 1 | Day 2 | Day 3 | Download Brochure 

Tuesday, February 11

7:00 am Registration and Morning Coffee

8:00 Plenary Keynote Session (Click Here For More Details) 

9:15 Refreshment Break in the Exhibit Hall with Poster Viewing


10:25 Chairperson’s Remarks
Martin Siaw, Ph.D., Associate Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute  

10:30 NGS-Based Clinical Assays: Building Castles in the Air

Jamie L. Platt, Ph.D., Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute

While applying NGS in the clinical setting may seem like “building castles in the air” to some, the utility of NGS assays can be enormous when built on a strong foundation. The foundation of sample prep will readily prove the validity of “garbage in, garbage out”. Examples of sample prep issues from commercially available NGS tests will be introduced.

11:00 Optimized Sample Handling and Target Enrichment Strategies for Challenging Clinical Samples

Bill Biggs, Ph.D., Director, Clinical Sequencing, Broad Institute of MIT and Harvard

The desire to access valuable clinical FFPE samples using advanced molecular techniques such as next-generation sequencing methods in an efficient and productive manner represents an ongoing challenge for most clinical laboratories. At the Clinical Research Sequencing Platform (CRSP) within the Broad Institute methods have been developed, optimized and implemented which allow for the ready and routine access of FFPE samples for such NGS-based analyses as Whole Exome Sequencing and Targeted Re-sequencing. These processes and methods allow for exceptional data to be obtained from even the most challenging of FFPE samples where low yield (≤ 100ng) or age (> 5 yrs) can confound analytical processes.

11:30 Automation of Sample Preparation for Clinical NGS: The Requirements and the Challenges Presented by the Various Clinical Sample Types

Martin Siaw, Ph.D., Associate Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute

Sample preparation is an important component of any molecular testing that is being done in clinical laboratories. With the increasing use of NGS for clinical testing comes the need to process increasingly larger numbers of patient samples. Automation of sample preparation should be considered to be critical to the workflow of diagnostic tests involving the use of NGS. My presentation will focus on the requirements and challenges for CLIA-certified clinical laboratories.

12:00 pm Better Annotation Needed at Various Points in the Sequencing Process to Avoid Reporting Errors due to Pseudogenes and High Repeat Genomic Regions

Patricia Mueller, Ph.D., Chief, Molecular Risk Assessment Laboratory, Newborn Screening and Molecular Biology Branch, DLS, Centers for Disease Control and Prevention (CDC)

Outside of clinical genomic sequencing centers, there is a general lack of awareness of the problems in NGS caused by the large number of pseudogenes in the human genome. Current estimates exceed 19,000 pseudogenes. Current standard enrichment methods do not reliably distinguish between highly homologous functional and pseudogenes. Better annotation is needed at different points in the sequencing process, including reference sequences, hybrid-capture arrays, PCR primer design software, and data-analysis software to help those designing tests and analyzing data to avoid reporting errors.

12:30 Session Break

12:40 Luncheon Presentation I: Seven Steps to the Sample Life: Best Practices for Clinical Trial Sample Management

Mark. A Collins, Ph.D., Director, Marketing, BioFortis, Inc.

The increased interest in biomarker-based studies necessitates a new rigor and sophistication in sample and sample related data management within the clinical trial context. In addition many trials occur across geographies, are increasingly externalized with multiple stakeholders and generate large amounts of data, which is putting existing software systems, infrastructures and processes under considerable pressure. Using case studies, attendees will learn emerging best practices for clinical trial sample and data management.

1:10 Luncheon Presentation II

(Sponsorship Opportunity Available)

1:40 Refreshment Break in the Exhibit Hall with Poster Viewing


2:15 Chairperson’s Remarks

Michael H.A. Roehrl, M.D., Ph.D., Director, UHN Program in BioSpecimen Sciences, University of Toronto

2:20 Use of Clinical Genetic Specimens to Support Clinical Drug Development

Peter Shaw, Ph.D., Senior Principle Scientist, Clinical Pharmacogenomics, Merck & Co., Inc.

Many pharmaceutical companies maintain biorepositories of clinical specimens consented for and collected during clinical trials. This presentation will address common uses of biorepository samples to support clinical drug development, and will highlight challenges in specimen collection that impact ultimate utility of the specimen.

2:50 Biospecimen Sample Integrity and Validation of Biomarkers in Clinical Trials

Lokesh Agrawal, Ph.D., Program Director, Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute

3:20 Best Practices for Management of Clinical Specimens to Support Clinical Drug Development

George Y. Tokiwa, Ph.D., Associate Principal Scientist, Clinical Genetics, Merck Sharp & Dohme Corp.

Pharmaceutical companies maintain biorepositories of clinical specimens collected during clinical studies that are consented for future biomedical research. This presentation will focus on best practices to address the end to end clinical specimen management activities required to support optimal and compliant use of the specimens.

3:50 When Worlds Collide: Sharing A Vision for an Integrated Clinical Trial Management System

Bruce Pharr, Vice President, Product Marketing Laboratory Systems, Remedy Informatics

Mr. Pharr will discuss data strategies to facilitate a more efficient flow of information enterprise-wide between disparate, yet key players in life sciences research and healthcare—such as clinical trial teams, hospitals, labs, biobanks, and others—in order to deliver on and advance the promise of personalized medicine.

4:20 Valentine’s Day Celebration in the Exhibit Hall with Poster Viewing  

5:20 Breakout Discussions in the Exhibit Hall

TABLE: Biobanking Considerations in Translation Research
Cary D. Austin, M.D., Ph.D., Pathologist, Department of Pathology, Genentech, Inc.  

  • Biospecimen quality control indicators: which are most useful?
  • Fit-for-purpose approaches to use of archived biospecimens
  • Budgeting for procurement: leveraging project-driven versus biobank-driven funding

TABLE: Biospecimen Considerations in Biomarker-Driven Clinical Trials 
Peter Shaw, Ph.D., Senior Principle Scientist, Clinical Pharmacogenomics, Merck & Co., Inc. 

  • Ability to consent for genome wide studies as part of main study consent (mandatory)
  • Approaches to successful voluntary consent language to allow for genome wide studies in large multi-national studies
  • Future prospects for generating whole genome sequence data from banked samples as routine practice, with storage and retrieval of banked data as important (or more important?) that storing and retrieving the banked sample  

TABLE: Sample Prep Challenges for NGS-Based Clinical Assays:
Jamie L. Platt, Ph.D., Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute 

  • Limited sample availability and sampling bias
  • ccfDNA, FFPE and difficult sample types
  • Unmet sample prep automation needs

TABLE: The Value of an Integrated Clinical Trials Management System that Facilitates Collaboration Both in and Outside of the Organization:
Wessam Sonbol, Product Manager, Clinical Research & Informatics, Remedy Informatics 

  • What should an integrated system look like?
  • What are the obstacles standing in the way of developing and launching an integrated clinical trials management system?
  • What obstacles might stand in the way of adoption of such a system amongst healthcare and life sciences professionals?

6:30 Close of Day

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