Cambridge Healthtech Institute’s Second Annual 

Genomic Sample Prep and Biospecimen Science

Assuring Development of Robust and Accurate Omics Assays

February 16-18, 2015 | Moscone North Convention Center | San Francisco, CA
Part of the 22nd Annual Molecular Medicine Tri-Conference

 

Personalized medicine is based on the analysis of inter-patient differences at the molecular level through the measurement of biomarkers. Biomarkers are detected in human biospecimens that represent samples for particular molecular tests. A systematic approach is necessary for quality assessment of biospecimens as well as for their appropriate pre-analytical processing both in research and in clinical laboratory. Novel genomic sample preparation technologies have the ability to significantly increase sensitivity and specificity of a test that is run on a heterogeneous sample or a sample that contains a low concentration of analyte. Cambridge Healthtech Institute’s Second Annual Genomic Sample Prep and Biospecimen Science conference is designed to bring together leading industry and academia experts in biospecimen science and molecular diagnostics to discuss major challenges and latest advances in sample preparation for advanced genomic technologies as well as biospecimen management and quality assurance.


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Monday, February 16

10:30 am Conference Program Registration


STANDARDIZING SAMPLE QUALITY AND PREANALYTICAL PROCESSING

11:50 Chairperson's Opening Remarks

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

12:00 pm Pre-Analytical Variation in Human Biospecimens: The Ultimate “Sample Preparation” Challenge for Diagnostics

Carolyn Compton, M.D., Ph.D., Professor, School of Life Sciences, Arizona State University

This talk will be focused on pre-analytical, process-related variables that may have significant effects on biomolecular composition and quality of samples. Rigorous adherence to standards under a quality management system that includes documentation of process steps and recording of deviations from protocol is required to control, document, or eliminate random and unknown pre-analytical variation in samples. Especially for complex diagnostic analyses, reproducibility and clinical validity cannot be achieved without assurance of the provenance of the specimens being tested. The biomarker qualification program of the Center for Drug Evaluation and Research at the Food and Drug Administration emphasizes the need to document the biospecimen quality of diagnostic biomarkers used for drug development, and the Center for Devices and Radiologic Health has similar requirements for approval of diagnostic devices. It is imperative that the diagnostics development community address the need for standardized processes and fit-for-purpose biospecimens to accelerate the delivery of accurate, reproducible, clinically relevant molecular diagnostics for precision medicine.

12:30 Comparison of Various Preanalytical Strategies in Molecular Testing for Infectious Diseases

David R. Hillyard, M.D., Medical Director, Molecular Infectious Diseases, Arup Laboratories

Molecular infectious disease testing places unique demands on pre-analytic methods for organismal disruption, nucleic acid release, purification, and concentration. For both high-throughput core platforms and the increasing number of near point-of-care devices, nucleic extraction is a key pre-analytic step for good test performance. This presentation will review both currently available and emerging approaches to pathogen nucleic acid extraction, and issues relevant to its integration with downstream amplification and analysis technologies.

1:00 Session Break


FFPE vs. FROZEN SAMPLES

1:15 Luncheon Presentation I: Recovery and Analysis of FFPE Derived Pure Tumor Cells Using the DEPArray System: Enabling Molecular Profiling and NGS Applications

Farideh Z. Bischoff, Ph.D., Executive Director, Scientific Affairs, Silicon Biosystems

Silicon Biosystems has combined the ability to manipulate individual cells using DEPArray™ technology. Molecular testing of FFPE tissue can often be compromised due to specimen size, heterogeneity, and presence of normal cells. The DEPArray™ platform enables identification and recovery of pure cell populations of interest from these complex, heterogeneous samples that are now amenable to downstream molecular profiling and NGS.

1:45 Luncheon Presentation II (Sponsorship Opportunity Available)

2:15 Session Break

2:30 Chairperson’s Remarks

2:40 National Cancer Institute Resources to Guide Fit-For-Purpose Biospecimen Collection and Utilization

Helen Moore, Ph.D., Branch Chief, Biorepositories & Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute

The National Cancer Institute has led the way in developing Best Practices for Biospecimen Resources, sponsoring new research in Biospecimen Science, and building groundbreaking research biospecimen collections including postmortem biospecimens for the NIH GTEx program. New projects to build evidence-based best practices for frozen and FFPE tissues will be described.

3:10 Overcoming Challenges of Working with FFPE Sample.

W. Fraser Symmans, M.D., Professor & Director, Research Operations, Pathology, UT MD Anderson Cancer Center

This presentation will discuss several important issues, such as: RNA detection in cancer tissues stored in FFPE samples; Profiling microRNA expression; FFPE DNA quality control and its correlation with NGS data; Understanding pre-analytic effects on RNA gene expression

3:40 Transformative Systems Pathology: Moving Omics to Clinics

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

We will discuss latest advances in proteomic cancer biomarker discovery, cancer genome sequencing, and metabolomic discovery in human disease. We will highlight that ultra-rapid tissue biobanking and preservation in the frozen state are critically important for faithful physiome preservation in next gen diagnostics and specimen-driven molecular clinical trials.

4:10 Standardizing Molecular Pathology with Fully Automated Nucleic Acid Isolation from FFPE and FF Tissue 

Guido Hennig, Ph.D., Senior Global Scientific Affairs Manager, BU Molecular Global Marketing, Siemens Healthcare Diagnostics

Molecular analysis in FFPE/FF tissue is important in retrospective biomarker studies, biobanking and molecular pathology. The discussed Siemens Tissue Preparation System (TPS) fully automates and standardizes extraction of high quality DNA and RNA from any tissue for PCR and sequencing applications.  

4:25 Sponsored Presentation (Opportunity Available)

4:40 Break and Transition to Plenary Session

5:00 Plenary Session

6:00 Grand Opening Reception in the Exhibit Hall with Poster Viewing

7:30 Close of Day


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Tuesday, February 17

7:00 am Registration and Morning Coffee

8:00 Plenary Session

9:00 Refreshment Break in the Exhibit Hall with Poster Viewing


NOVEL TECHNOLOGIES

10:05 Chairperson's Remarks 

David R. Hillyard, M.D., Medical Director, Molecular Infectious Diseases, Arup Laboratories


10:15 KEYNOTE PRESENTATION: New Technologies for Diagnostics 

Ronald W. Davis, Ph.D., Professor of Biochemistry and Genetics, Director, Stanford Genome Technology Center, Stanford University

The need to interrogate an expanding number of clinical biomarkers including host and pathogen nucleic sequence using tests that are rapid, accurate, and cost effective is a fundamental challenge for laboratory medicine. Advances in electronics, chemistry, fabrication, and informatics, allow for development of new test formats with dramatically improved performance and cost profiles. This presentation will highlight emerging technologies for detection and characterization of protein and nucleic acid biomarkers.


NGS ASSAYS: PREANALYTICAL CONSIDERATIONS, ASSAY DEVELOPMENT AND VALIDATION

11:15 Development and Validation of Clinical NGS tests: the Requirements and the Challenges Presented by the Various Clinical Applications

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

The use of NGS in clinical laboratories has come of age. NGS tests for different sub-specialties (e.g., Infectious Diseases, Genetics, Oncology, etc.) involve a wide variety of clinical targets with varying requirements for sample preparation, sequence target size, target enrichment, depth of coverage, data analysis and clinical reporting. My presentation will focus on the requirements for the various tests and the challenges for developing and validating these tests for use in CLIA certified clinical laboratories.

11:45 A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

Kamlesh Patel, Ph.D., Manager, Advance Systems Engineering and Deployment, Sandia National Labs

DNA sequencing is advancing at an unprecedented rate, but sample preparation methods rely on manual bench-top processes, which are labor-intensive. The introduction of fast, low-throughput sequencers warrants a need to automate these protocols. We report on our work to integrate novel digital microfluidic technology to automate DNA library preparation workflows for characterization of novel and emerging pathogens from clinical samples.

12:15 pm Session Break

12:25 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

1:25 Refreshment Break in the Exhibit Hall with Poster Viewing


NGS ASSAYS CONTINUEd

2:00 Chairperson's Remarks 

Jamie L Platt, Ph.D., Vice President, Genomic Solutions, Molecular Pathology Laboratory Network, Inc.

2:10 Validation Challenges for Panels and Exomes

Josh Deignan, Ph.D., Associate Director, UCLA Molecular Diagnostics Laboratories, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA

Guidelines for the validation of molecular diagnostic tests have existed for some time, but guidelines for NGS testing have only recently emerged. Moreover, the approach required for the validation of a NGS mutation panel is different than the one required for an exome sequencing test, both of which are now offered clinically at UCLA. This talk will discuss our experiences with the validations of these two types of NGS tests.

2:40 FDA-Approved Versus LDT-Based NGS Systems: Preanalytical Issues and Validation

Jamie L Platt, Ph.D., Vice President, Genomic Solutions, Molecular Pathology Laboratory Network, Inc.

As NGS technologies have matured and their utility in clinical diagnostics has been embraced, the evolution of RUO-based Laboratory Developed Processes (LDPs) to FDA-Cleared In Vitro Diagnostic Tests has followed. The major considerations around Preanalytical issues for these two categories of systems will be compared and discussed. In addition, the key validation or verification challenges will be contrasted and discussed within the context of a CLIA Lab experience using both types of systems. The objective of the presentation is to provide sufficient information, drawn from experience, to enable labs to choose the path that best suits their environment, goals and objectives.

3:10 PANEL DISCUSSION: Comparing Major NGS Instruments: Technical Differences, Application Preferences

Moderator: Jamie L Platt, Ph.D., Vice President, Genomic Solutions, Molecular Pathology Laboratory Network, Inc.

Selecting the NGS platform or platforms that best address the pre-analytical and technical considerations of the assay objectives given the specific environment can be a challenging undertaking. Platform throughput, chemistry, and error modality vary greatly and are tightly tied to overall assay performance. This discussion will focus on the strengths and capabilities of the different commercially available NGS platforms from the perspective of users with experience on multiple platforms.

3:40 A Novel Method for Efficient and Hands-Free Purification of Circulating, Cell-Free DNA (ccfDNA) from Human Plasma

Douglas Horejsh, Ph.D., Senior Research Scientist, Promega Corporation

The Promega Maxwell® RSC circulating DNA kit allows parallel purification of ccfDNA from 1-16 plasma samples. This method purifies high-quality DNA suitable for use in qPCR and NGS. The absence of pre-processing steps improves reproducibility and lowers risk of contamination.

Sample Minded 

3:55 Can You Handle a Million Tests per Year? Transitioning from Clinical Trials to a Validated, High-Throughput Diagnostics Operation

Daniel Steenblik, Vice President of Technology and Operations, Engineering, sampleminded

We will discuss the challenges of transitioning a lab from clinical trials to a high throughput diagnostic organization. How we employ a simple and sleek mission critical LIS, including tablets, monitoring and workflow metrics to capture quality indicators, while maintaining traditional LIS/LIMS functionality.

4:10 Mardi Gras Celebration in the Exhibit Hall with Poster Viewing


5:00 Breakout Discussions in the Exhibit Hall
This interactive session provides attendees an opportunity to choose a specific discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion.


NGS Assay Development and ValidationModerators: Martin Siaw, Ph.D., Associate Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute
Josh Deignan, Ph.D., Associate Director, UCLA Molecular Diagnostics Laboratories, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA

Topics to be discussed:
• NGS clinical test requirements – panels vs exomes/genomes
• Development and validation of germline clinical NGS tests
• Development and validation of somatic clinical NGS tests

Microfluidic DNA Library for NGSKamlesh Patel, Ph.D., Manager, Advance Systems Engineering and Deployment, Sandia National Labs

Topics to be discussed:
• State-of-the-art in DNA preparation technologies
• Reducing  bias in library prep
• Prep methods for targeted vs whole genome sequencing

RNA Sequencing: Assay Development, Major Applications and MoreKai Wang, Ph.D., Principle Scientists, Institute of Systems Biology 

Topics to be discussed:
• Pro and con of NGS based RNA sequencing.
• NGS platform selection.
• Issues associated with NGS data analysis
• Impact of sample preparation and contamination on data quality

6:00 Close of Day


Day 1 | Day 2 | Day 3 | Download Brochure 

Wednesday, February 18

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Plenary Session Panel

9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


BEST BIOSPECIMEN AND BIOPREPOSITORY PRACTICES

10:35 Chairperson's Remarks 

Andrew Brooks, Ph.D.,COO and Director,Technology Development, Technology, RUCDR Infinite

10:45 Preparing Research Samples for Future Use: Innovative Methods for Assessing Functional Quality Control and Biobanking Best Practices

Andrew Brooks, Ph.D.,COO and Director,Technology Development, Technology, RUCDR Infinite

Variable DNA sample quality and the lack of standardized sample tracking in biorepositories perpetuates sample ID errors caused by mishandling during sample collection, storage or use. The RUCDR finds that greater than 98 percent of biorepository errors occur from issues during sample collection and are not errors in sample processing once they arrive at the biorepository. Sample qualification and verification prevents erroneous use of misidentified samples in downstream experiments and also ensures high-quality data from samples being analyzed.

11:15 Practical Approaches to Expanding Biorepository Representation: Innovative Tissue Print Technologies for Collecting High Quality Snap-Frozen Specimens for Biomarker Research

Sandra M. Gaston, Ph.D., Director, Molecular Biomarkers Research Laboratory,Pathology and Laboratory Medicine, Tufts Medical Center Assistant Professor of Pathology, Tufts University School of Medicine

Most human tissue samples obtained from clinical biopsy and surgical resections are only secondarily considered as research specimens, and any plan to collect tissue for research must put first priority on patient care. Remnant tissues obtained from fresh surgical specimens are the mainstay for biorepositories that provide high quality snap-frozen samples for research, but many critical areas of a surgical resection and most diagnostic biopsies cannot be easily “divvied up” before the tissue is submitted for processing as a formalin-fixed paraffin embedded (FFPE) specimen.

11:45 Sponsored Presentations (Opportunities Available)

12:15 pm Session Break

12:25 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


RNA TESTING AND SAMPLE TO RESULT TECHNOLOGY

1:40 Chairperson's Remarks 

Andrew Goldsborough, Ph.D., CEO, RNA Stability, RNAssist Ltd

1:50 Circulating RNA - Is it a Blessing or a Curse?

Kai Wang, Ph.D., Principle Scientists, Institute of Systems Biology

Cell free circulating RNA has attracted a great deal of attention in recent years as specific physiopathological conditions have been linked to varying concentrations of various RNA species. However, there are a number of challenges in accurately assessing levels of specific circulating RNA sequence. Standardized sample preparation protocols and new measurement approaches are clearly needed. In the meantime caution should be exercised when interpreting circulating RNA based results.

2:20 Human Cerebrospinal Fluid (CSF) miRNA Analysis: Critical Factors in Sampling Preparation and Detection

Wang-Xia Wang, Ph.D., Senior Scientist, Sanders-Brown Center on Aging, University of Kentucky

Human cerebrospinal fluid (CSF) microRNAs (miRNAs) have been proposed as potential biomarkers for disease conditions, specially, neurodegenerative diseases; however, technical challenges related to RNA sample preparation and detection has hindered the establishment of reproducible miRNA signatures. This talk will focus on the overview of technical aspects of CSF RNA sample preparation and detection, and will discuss the recent advance including several commercially developed extracellular miRNA/RNA sample preparation and analysis platforms..

2:50 RNAssist Fixative and Stabilizer for Immunohistochemistry and the Recovery of High Quality RNA, DNA and Proteins

Andrew Goldsborough, Ph.D., CEO, RNA Stability, RNAssist Ltd

The RNAssist reagent has been developed to efficiently fix tissue samples whilst preserving RNA, DNA, proteins as well as tissue histology for IHC analysis. It does not contain alcohol or formaldehyde, has very low volatility and is biodegradable. RNA stabilisation is superior to both standard fixatives and dedicated RNA stabilisation solutions. Results will be shown demonstrating RNA, DNA and protein stabilisation, and IHC in RNAssist fixed tissues.

3:20 Extending The Reach Of Molecular Diagnostics: Sample-To-Result Infectious Disease Tests

Barry Lutz, Ph.D., Research Assistant Professor, Department of Bioengineering, University of Washington

We are developing tests for DNA and RNA that can be performed outside conventional laboratory settings. All steps from sample preparation to visual readout are carried out automatically without an instrument. Data collection by a cell phone will allow transmission of results to a healthcare provider and medical record. Project goals include commercializable tests as well as broad platform capabilities for future tests. We are also collaborating to develop simplified drug resistance tests based on detection of single-base mutations in HIV and other infectious diseases.

3:50 Refreshment Break


ENABLING CANCER RESEARCH
AND DEVELOPMENT

4:00 Chairperson's Remarks 

Michael J. Heller, Ph.D., Professor, Nanoengineering & Bioengineering, University of California San Diego

4:10 Isolation of DNA/RNA Biomarkers and the Quest for Liquid Biopsy Cancer Diagnostics

Michael J. Heller, Ph.D., Professor, Nanoengineering & Bioengineering, University of California San Diego

The isolation of circulating cell free (ccf) DNA and ccf-RNA directly from blood and/or plasma remains a complex and time consuming procedure, which is impeding process toward liquid biopsy and point of care (POC) cancer diagnostics. We have now demonstrated the rapid isolation and detection of ccf-DNA/RNA from a number of different hematological and solid tumor samples.

4:40 Antibody Validation to Prevent Error

David L. Rimm, M.D., Ph.D., Professor, Pathology; Executive Director, Translational Pathology; Director, Yale Pathology Tissue Services, Yale University

Antibodies are an extremely broadly used and valuable tool, both in discovery research, translational research and in the clinic. However, some of the data produced and published in the literature is flawed, or misleading due to non-specificity or cross-reactivity. Here we will look at the use of antibodies, both in the research and clinical setting and show how lack of rigorous validation can produce flawed data. We will also provide guidelines for antibody validation that can be used to avoid flawed, but publishable results.

5:10 Managing Quality in Biorepository Operations to Support Translational Research- Experiences of the OHSU Knight BioLibrary

Devon Kelly, Director, OHSU Knight BioLibrary, Knight Cancer Institute, Oregon Health and Science University

Methods by which human research specimens are consented, collected, stored and distributed varies greatly from repository to repository. This variation is a large contributing factor in the ability of researchers to generate high-quality data from specimens acquired from multiple repositories into a single research project. Therefore, it is important to manage the quality of biobanking activities to maximize the utility of banked specimens collected for future research projects. Experiences in assessing and standardizing practices across a large cancer repository network will be discussed.

5:40 Close of Conference Program



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