Cambridge Healthtech Institute’s Third Annual 

Genomic Sample Prep and Biomarker Assay Development

DNA/RNA Extraction, NGS Assays, Liquid Biopsy, Antibody Validation, & More

March 7-9, 2016 | Moscone North Convention Center | San Francisco, CA
Part of the 23rd International Molecular Medicine Tri-Conference


The final goal of any assay development is to assure its intra- and inter-laboratory reproducibility and accuracy. This goal can be reached by innovative assay development and its careful validation. Appropriate and novel sample preparation is a pivotal part of assay development and validation that guarantees its repeatability and robustness. Novel 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 Third Annual Sample Prep and Diagnostics Assay Development 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 omics technologies as well as development and validation of NGS and other novel diagnostics assays.

Final Agenda

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Monday, March 7

10:30 am Conference Program Registration Open


11:50 Chairperson’s Opening Remarks

Robert Daber, Ph.D., Vice President, Genomics Operations and Development, Laboratory Medicine, Bio Reference Laboratories

12:00 pm Eliminating Barriers to Precision Diagnostics: Cost, Content, Turn-Around Time and Sample Size

Robert Daber, Ph.D., Vice President, Genomics Operations and Development, Laboratory Medicine, Bio Reference Laboratories

Next Generation Sequencing has tremendous potential for disrupting routine clinical practice in many areas of medicine. As many health care practices look to build precision medicine programs, access to clinical NGS testing for every patient is currently limited by several challenges. We have set out to build an oncology diagnostics program that reduces or eliminates these barriers by building assays that are cost effective, provide fast turn around time, work with low levels of FFPE DNA input and is focused on content that reduces the incidence of unclear variants.

12:30 Emerging Sample Prep Technologies for Genomics Applications

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

Non-invasive prenatal testing, solid tumor profiling, liquid biopsy, and other tests all require special consideration not only for specimen characteristics, but also for the detected variant types. In clinical applications, the amount of specimen can be highly limited and the quality can be variable. The challenges of recovering adequate DNA and RNA will be discussed within in the context of these applications and some emerging sample prep technologies that may address these issues will be highlighted.

1:00 Session Break

1:15 Luncheon Presentation I to be Announced


1:45 Luncheon Presentation II (Sponsorship Opportunity Available)

2:15 Session Break


2:30 Chairperson’s Remarks

Robert Daber, Ph.D., Vice President, Genomics Operations and Development, Laboratory Medicine, Bio Reference Laboratories

2:40 Assessment of FFPE Samples for Success in NGS

Helen Fernandes, Ph.D., Director, Molecular Pathology, Pathology & Laboratory Medicine, Weill Cornell Medical College

This presentation will discuss several important issues, such as: Identification of DNA variants and RNA fusions in FFPE tissue; FFPE DNA quality control and its correlation with NGS data; and understanding pre-analytic variables for obtaining optimal results in NGS assays.

3:10 Quantitative Comparison of Biomarkers by IHC vs mRNA Using a Nearly Point of Care Cancer Biomarker Platform

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

The measurement of tissue biomarkers is a challenge in the US, but much more so in less developed countries. Some drugs, like Tamoxifen are inexpensive and effective but need a companion diagnostic test. This work will describe the comparison of a low cost, mRNA based platform for measuring Estrogen Receptor and other tissue biomarkers with immunohistochemistry and quantitative immunofluorescence.

3:40 NGS Applications with FFPE Samples: No Longer a Pipedream

Andrew J. Hollinger, Application Scientist, Broad Genomics Platform, Broad Institute.

The Genomics Platform at the Broad Institute has initiated a number of projects to explore QC of FFPE samples upstream of NGS applications resulting in development of protocols and processes that provide insight into likelihood of success for various NGS processes. This has been enabled in large part by the vast number of samples and large collections of FFPE samples that have been processed to date. Here we discuss our approach to preserving usage of nucleic acid from these limited sample types, high-throughput processing, DNA and RNA QC metrics to estimate likelihood of success, and NGS metrics of interest when working with FFPE.

Siemens4:10 Standardizing Molecular Pathology with Fully Automated DNA and RNA Extraction from
Formalin-Fixed, Paraffin-Embedded (FFPE) and Fresh Frozen (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.

Beckman Coulter Life Sciences4:25 Presentation to be Announced

4:40 Refreshment Break and Transition to Plenary Session

5:00 Plenary Keynote Session 

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

7:30 Close of Day

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Tuesday, March 8

7:00 am Registration Open and Morning Coffee

8:00 Plenary Keynote Session

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


10:05 Chairperson’s Remarks

P. Mickey Williams, Ph.D., Director, Molecular Characterization & Clinical Assay Development Laboratory (MoCha), Frederick National Laboratory for Cancer Research

10:15 Preparing a Multi-Analyte NGS Assay for Use in Clinical Studies for Cancer

P. Mickey Williams, Ph.D., Director, Molecular Characterization & Clinical Assay Development Laboratory (MoCha), Frederick National Laboratory for Cancer Research

NGS offers a powerful tool for assessment of molecular defects found in cancer. The utilization of NGS is becoming common practice in clinical laboratories. This complex technology requires a new level of analytical performance testing and validation. This discussion will focus on approaches used for analytical validation of the NGS clinical assay used for treatment selection in the NCI-MPACT study.

10:45 Developing and Validating Assays for Population Scale Clinical Sequencing

William Biggs, Ph.D., Head, Sequencing Operations, Human Longevity, Inc.
Over the past few years advances in several key areas has effectively set the stage for a revolution in utilization of genetic information in routine medical care. A dramatic reduction in the cost of both sequencing and distributed computing together with improvements in algorithmic machine learning methods are enabling the population scale genetic analysis required to identify complex genetic relationships of diagnostic, prognostic or predictive utility. Together with a shift towards value-based patient care these advances are driving a shift in emphasis from the treatment of disease to maintaince of health. In a effort to drive this shift Human Longevity Inc. has built one of the largest genome sequencing facilities in the world. In this presentation we'll describe experience gained while building this facility over the past year.

11:15 Development of a Clinical Cell-Free Circulating Tumor DNA Assay for Cancer Molecular Profiling

Geoff Otto, Ph.D., Senior Director, Molecular Biology & Sequencing, Foundation Medicine

Profiling circulating tumor DNA (ctDNA) for the genomic alterations (GA) driving oncogenesis promises to provide insight into cancer biology, inform therapy selection when conventional biopsies are unobtainable and enable monitoring of response to therapy. A clinical, NGS-based ctDNA assay was developed; highly accurate detection of GA was analytically validated; and clinical utility investigated from patient-matched FFPE and blood samples across lung, breast and colon cancer at different disease stages.

11:45 Approaches to High Efficiency Nucleic Acid Extraction and Purification from Diverse Sample Types for NGS-Based Pathogen Detection

David R. Hillyard, M.D., Professor, Pathology, University of Utah; Director, Molecular Infectious Disease Testing, Arup Laboratories

Rapid and efficient preparation of well-purified nucleic acids from diverse sample types has increasingly become a critical component of diagnostic testing. Applications such as infectious disease and circulating cell free genetic testing also demand great test sensitivity and may require extraction from larger sample volumes. This presentation will review both currently available and emerging approaches to nucleic acid extraction, and issues relevant to its integration with downstream amplification and analysis technologies for highly multiplexed targeted and NGS-based pathogen detection.

12:15 pm Session Break

NanoString12:25 Luncheon Presentation to be Announced

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


2:00 Chairperson’s Remarks

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

»» 2:10 KEYNOTE PRESENTATION: New Diagnostic Technology with Advances in Electrical Engineering

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

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. At Stanford we came up with nanoplasmonic electrical fieldenhanced resonating device, which addresses all these impediments on a single platform. Application of this and other new technologies to address unmet needs of clinical diagnostic testing and research will be discussed.

2:40 Mobile Phone-Based Imaging, Sensing and Diagnostics Technologies

Aydogan Ozcan, Ph.D., Electrical Engineering Department, Bioengineering Department, California NanoSystems Institute, University of California, Los Angeles

In this presentation I will discuss some of the emerging applications and the future opportunities/challenges created by the use of mobile phones and other consumer electronics devices as well as their embedded components for the development of next-generation imaging, sensing, diagnostics and measurement tools through computational photonics techniques.

3:10 PANEL DISCUSSION: Advancing Laboratory Medicine through Innovation

Moderator: David R. Hillyard, M.D., Professor, Pathology, University of Utah; Director, Molecular Infectious Disease Testing, Arup Laboratories

Over the last 5 decades, laboratory medicine has witnessed a remarkable wave of innovations that transformed the field from a peripheral to a central player in healthcare delivery. These advances enabled the introduction and performance of new tests on a large scale, some in a decentralized setting, in an accurate and a precise manner, thus leading to better diagnosis, more accurate prediction of disease prognosis, and improved patient management. This discussion features two prominent thought leaders who dedicated their work to adoption of the most innovative and cutting edge technology to advance laboratory medicine.

3:40 DEPArray Technology for Single Cell Precision in Oncology: From Research to Clinical Application

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

DEPArray is an innovative technology capable of sorting and isolating 100% pure single or pooled cells through a digitally controlled dielectrophoretic field. The DEPArray system offers the potential for pre-analytical cell-type purification for downstream molecular analysis, which is a major step forward for precision medicine.

4:10 St. Patrick’s Day Celebration in the Exhibit Hall with Poster Viewing

5:00 Breakout Discussions in the Exhibit Hall

These interactive discussion groups are open to all attendees, speakers, sponsors, & exhibitors. Participants choose a specific breakout 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.

Future of Portable Sequencing for Real-Time Diagnostics

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

  • Discuss the the current state-of-the-art of the technology and current limitations
  • Explore the diagnostic landscape in search of the right applications for portable sequencing
  • Predict how diagnostics would change with this technology 5 years from now.

NGS Assay Development and Validation

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

  • NGS clinical test requirements – panels vs exomes/genomes
  • Development and validation of germline clinical NGS tests
  • Development and validation of somatic clinical NGS tests

6:00 Close of Day

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Wednesday, March 9

7:00 am Registration Open

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

8:00 Plenary Keynote Session Panel 

10:00 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


10:50 Chairperson’s Remarks

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

11:00 Nanopore DNA Strand Sequencing in Basic Biology & Medicine

Mark Akeson, Ph.D., Professor, UC Santa Cruz Genomics Institute & Biomolecular Engineering Department, University of California, Santa Cruz

Nanopore DNA strand sequencing was conceived by Deamer, Branton, and Church over twenty years ago. I will discuss key academic experiments that lead to successful nanopore reads of individual DNA strands, and the subsequent implementation of the commercial Oxford Nanopore ‘MinION’. This device is well suited to point of care use due to its portability and direct reads of genomic DNA absent copying. It has been employed in West Africa for Ebola sequencing, and is slated for experiments on the International Space Station.

11:30 Nanopore Sequencing for Real-Time Pathogen Identification

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

As recent outbreaks have shown, effective global health response to emergent infectious disease requires a rapidly deployable, universal diagnostic capability. We will present our ongoing work to develop a fieldable device for universal bacterial pathogen characterization based on nanopore DNA sequencing. Our approach leverages synthetic biofunctionalized nanopore structures to sense each nucleotide. We aim to create a man-portable platform by combining nanopore sequencing with advance microfluidic-based sample preparation methods.

12:00 pm Centrifugal Microfluidic Sample Preparation for Genomics and Bio-Analytical Applications

Teodor Veres, Ph.D., Functional Nanomaterials Group Leader, Life Sciences Division, National Research Council of Canada

We have developed a new centrifugal microfluidic platform based on the integration of regulated pressure and programmable valving systems that offer the interesting prospect to decouple basic microfluidic functions from specific material properties, channels dimensions and fabrication tolerances, surface treatments, or on-chip active components, thus promoting integration of complex assays on simple and low-cost microfluidic cartridges. I will discuss the use of this microfluidic platform for targets isolation, nucleic acids and protein extraction for genome sequencing molecular diagnostics applications.

12:30 Session Break

12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:10 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


1:50 Chairperson’s Remarks

Kai Wang, Ph.D., Principal Scientist, Institute for Systems Biology

2:00 Tethered Lipoplex Nanoparticle (TLN) Biochips For Extracellular Vesicles Based Early Disease Diagnosis and Prognosis

L. James Lee, Ph.D., Helen C. Kurtz Chair, Chemical & Biomolecular Engineering, Ohio State University

Circulating extracellular vesicles (EVs) is currently the major focus of non-invasive early disease detection and prognosis. We show that biochips using tethered lipoplex nanoparticles (TLNs) containing molecular beacons can capture cell-derived EVs from body fluids, and identify encapsulated microRNAs/mRNAs and EV surface membrane protein targets with very small sample size (~20 uL blood for 2 targets) and higher sensitivity than qRT-PCR. We will present TLN applications to cancer and non-cancer diseases.

2:30 Measurement of exRNA: Quantitative Studies of Small RNA-seq

David Galas, Ph.D., Principal Scientist, The Pacific Northwest Diabetes Research Institute

A wide range of RNA molecules exist in various body fluids outside of cells and represent potentially important biological information. RNA-seq has is a powerful detection technology, but flawed as a measurement technology. We and others have systematically studied issues like sequence-specific bias, length effects and other phenomena as they are affected by variations in RNA-seq protocols, and will discuss the results.

3:00 Best Practices for Fusion Detection by Targeted RNA Sequencing: Pre-Analytical Considerations, Assay Validation and More

Robert D. Daber, Ph.D., Director, Research and Development and Sequencing Operations, Bio-Reference Laboratories

This presentation will discuss challenges and benefits of NGS based targeted RNA sequencing in the detection of gene fusion events, including, nucleic acid isolation, sample preparation and downstream data processing. There are a number of specific challenges related to RNA sequencing, standardized quality control metrics both before and after library prep are clearly needed.

3:30 Sponsored Presentation (Opportunity Available)

4:00 Session Break

4:10 Chairperson’s Remarks

Gregory Richmond, Ph.D., Principal Scientist, Ibis Biosciences, Abbott

4:15 Validation of Integrated Workflows and Reagents for RNA Sequencing from Blood: A Specific and Sensitive Solution for Research and Clinical Diagnostics Applications

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

Here we report the validation of an end-to-end workflow for RNA-Seq analysis from human whole blood that integrates whole blood sample preservation, automated isolation of total RNA and target specific RNAseq library creation. A three arm study was designed to address several assay performance parameters including intra-assay precision (repeatability), inter-assay precision (reproducibility), and assay sensitivity.

4:45 Sample Prep Challenges for Bloodstream Infection Assays

Gregory Richmond, Ph.D., Principal Scientist, Ibis Biosciences, Abbott

We describe a sample preparation system that provides for the rapid detection and identification of bacterial and Candidal nucleic acid directly in whole blood specimens from patients with suspected bloodstream infections. A cellular lysis method and DNA purification system were designed for processing 5 ml of whole blood. A novel sample prep approach removed high levels of inhibiting human DNA prior to target detection. The system provides for rapid and sensitive molecular detection of diverse agents of these clinically important infections in approximately 6h.

5:15 Clinical Development of Gene Expression Signatures

Joel S. Parker, Ph.D., Director, Bioinformatics, Lineberger Comprehensive Cancer Center, Assistant Professor, Department of Genetics, University of North Carolina at Chapel Hill

Gene expression signatures have been used extensively for subtype discovery and classification in cancer research. Subtyping provides a global view of tumor biology, and expression subtypes are typically associated with clinical features. Successful translation of this information requires a clinically actionable hypothesis, model development, validation in a representative cohort, and a reproducible and accurate measurement technology. These challenges and resulting decisions will be reviewed in the context of Prosigna™ assay development, as well as the more recently developed PREDICT-AR™

5:45 Close of Conference Program

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