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CAMBRIDGE HEALTHTECH INSTITUTE’S SECOND ANNUAL 

Quantitative Digital Detection TechnologiesQUANTITATIVE DIGITAL DETECTION TECHNOLOGIES   

DIGITAL DETECTION WITH PCR, MICROFLUIDICS, AND SINGLE CELL TECHNOLOGIES 


PART OF THE PRECISION DIAGNOSTICS SUMMIT 
JUNE 17-18, 2014 | HILTON BACK BAY | BOSTON, MASSACHUSETTS

Advances in microfluidics and nanofabrication have led to the manufacture of technologies capable of utilizing hundreds to millions of small-scale partitions. Digital enumeration, whether it is done through digital PCR, microfluidics, or next-generation sequencing, is finding growing utility in both basic research and clinical applications. By allowing for detection of nucleic acids at higher resolution and lower target levels, digital detection technologies have the ability to identify diseases earlier in progression, providing an advantage for diagnostics and preventative medicine. Cambridge Healthtech Institute’s Second Annual Quantitative Digital Detection Technologies conference will cover digital PCR, microfluidics, and single-cell analysis and how these technologies are best used in clinical research. The evolution of qPCR to a more digital format as well as the role that next-generation sequencing will play will also be discussed. Special focus will be given to clinical translation and future trends driving the field.
 


 

Final Agenda


TUESDAY, JUNE 17

12:00 pm Conference Registration


SAMPLE PREP INTEGRATION INTO DIGITAL DETECTION WORKFLOW 

1:00 Chairperson’s Remarks

1:05 PLENARY KEYNOTE: Sample Preparation Considerations for Digital Technologies

N Reginald BeerN. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and Nanotechnologies, Lawrence Livermore National Laboratory

Digital PCR provides extremely accurate quantification as compared to traditional standard curve methods but pre-detection processing remains pivotal. Critical factors such as sample preparation, sample homogeneity, reaction volume measurements, thermal cycler uniformity, template GC content and methylation can all effect data quality. In this talk we will discuss the benefits of digital technologies as well as steps to ensure accurate measurement. Attention will be given to future trends driving the field and moving out of the lab and onto the bench.

1:35 How To Choose The Right Assay On The Right Platform: A Clinical Diagnostic Laboratory PerspectiveElizabeth Duffy HynesElizabeth Duffy Hynes, Laboratory Manager for Clinical Development, Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Genetic MedicineClinical diagnostic and research laboratories may have similar fundamental criteria for evaluating instruments, technologies, and platforms, but there are additional facets and layers of stringency that need to be considered when in a clinical setting. At a technical level,  assays have to have the best possible sensitivity and specificity scores and cutting-edge technologies should be proven to meet or exceed gold standard metrics, or current standard of care. Routine laboratory operations considerations, such as cost,  hands on time, ease of use, and turn-around-time, among others must also be evaluated. Of course, these factors must be carefully balanced with proven clinical utility in order to provide the highest quality healthcare service to patients and their physicians. Experiences and decision making processes of the Laboratory for Molecular Medicine will be discussed.

2:05 Session Break


ADVANCES IN DIGITAL DETECTION 

2:35 KEYNOTE PRESENTATION: Single Molecule Detection for Ultrasensitive Analysis

David R. WaltDavid R. Walt, Ph.D., Robinson Professor of Chemistry, Howard Hughes Medical Institute Professor, Tufts University

Counting single molecules is the ultimate method for making measurements. Biological molecules are of particular interest because these molecules exist at levels of 1-1000 molecules per cell, beyond the sensitivity of most analytical methods. Methods for counting individual molecules are being developed that enable the enumeration of individual molecules. Some of these methods are simple to implement and will facilitate new discoveries as well as revolutionize clinical diagnostics.

 Life_Technologies3:05 Sensitive Detection of Hematopoietic Chimerism using Chip-Based Digital PCR 

Stephen Jackson, Ph.D., Associate Director, Product Applications, Life Science Solutions, Life Technologies

Hematopoietic chimerism occurs in leukemia samples when cells from bone marrow donor and recipient are present in the recipient's bone marrow at the same time.  Increasing chimerism is associated with increased risk of relapse after transplant.  Digital PCR (dPCR) provides an ideal mechanism for quantifying genetic chimerism.  In this study, we show how chip-based dPCR facilitates quantification of hematopoietic chimerism.  Furthermore, we show that its extreme sensitivity can detect chimerism in samples earlier than qPCR, facilitating earlier. 

3:35 Refreshment Break with Exhibit and Poster Viewing

4:15 Absolute Quantification by Droplet Digital PCR versus Analog Real-Time PCR

Muneesh Tewari,Muneesh Tewari, M.D., Ph.D., Associate Professor, University of Michigan

Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased 37–86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer.

4:45 PANEL: Future Directions in Digital Biology

Panelists: Daniel T. Chiu, Ph.D., A. Bruce Montgomery Professor, Chemistry; Endowed Professor, Analytical Chemistry; Professor, Bioengineering, University of Washington, Seattle
Stephen Jackson, Ph.D., Associate Director, Product Applications, Life Science Solutions, Life Technologies

Muneesh Tewari, M.D., Ph.D., Associate Professor, University of Michigan

5:15 Reception in the Exhibit Hall with Poster Viewing

6:15 Close of Day


WEDNESDAY, JUNE 18

7:30 am Registration and Morning Coffee


MICROFLUIDIC PLATFORMS 

8:30 Chairperson’s Remarks 

Bruno Ping, Laboratory Manager, Royal Surrey County Hospital

8:35 SD Chip for Digital Biological Measurements

Daniel T. ChiuDaniel T. Chiu, Ph.D., A. Bruce Montgomery Professor, Chemistry; Endowed Professor, Analytical Chemistry; Professor, Bioengineering, University of Washington, Seattle

This presentation describes a very simple and robust microfluidic device for digitizing samples into a large array of discrete volumes; we called this the SD (Self Digitization) Chip. As a demonstration of the utility of SD Chip, we describe digital nucleic acid amplification, including digital PCR and digital isothermal amplification.

9:05 Precise Quantitation of Nucleic Acids with the RainDrop™ Digital PCR System

Darren LinkDarren Link, Co-Founder and CTO, Raindance Technologies, Inc.





Meso Scale9:35 Breaking the fg/ml Barrier with Ultrasensitive Immunoassays

Pankaj Oberoi, Ph.D., Vice President, Commercial Assay, Meso Scale

MSD’s MULTI-ARRAY® electrochemiluminescence technology is used extensively to measure low levels of proteins in biological and clinical samples. We developed a next-generation assay format that is 100 to 1000 times more sensitive than the current limits of ELISA technology. We will present the ability to measure sub-fg/ml levels of cytokines and other biomarkers on established MSD® instrumentation. These new assays allow quantitation of previously unmeasurable baseline samples and have the capability of being multiplexed, allowing for the preservation of precious samples. These assays allow for the measurement of previously undetected biomarkers and could lead to the development of the next set of high sensitivity companion diagnostics and clinical assays. 

10:05 Coffee Break with Exhibit and Poster Viewing


SINGLE CELL ANALYSIS METHODS 

10:35 All-Optical Electrophysiology for High-Throughput Single-Cell Analysis

Adam CohenAdam Cohen, Ph.D., Professor, Departments of Chemistry and Chemical Biology; Physics Investigator, HHMI

The electrical firing patterns of neurons are the primary functional readout of their physiological state, in health and disease. But these firing patterns have been notoriously difficult to study: manual patch-clamp measurements are too slow to be used in screening, and multielectrode arrays only provide low-resolution aggregate information. We developed a system for all-optical electrophysiology, in which light pulses stimulate and record electrical activity in neurons. This system provides functional data in wild-type and disease model neurons with a throughput and information content unmatched by any other technology.

11:05 Live Single-Cell Functional Phenotyping in Droplet Nanoliter Reactors

Tali (Tania) KonryTali (Tania) Konry, Ph.D., Assistant Professor, Pharmaceutical Science, Northeastern University

Here we describe a nano-liter droplet microfluidic-based approach for stimulation and monitoring of surface and secreted markers of live single immune dendritic cells (DCs) as well as monitoring the live T cell/DC interaction. This nano-liter in vivo simulating microenvironment allows delivering various stimuli reagents to each cell and appropriate gas exchanges which are necessary to ensure functionality and viability of encapsulated cells. Thus live cell stimulation, secretion and surface monitoring can be obtained simultaneously in distinct microenvironment, which previously was possible using complicated and multi-step in vitro and in vivo live-cell microscopy, together with immunological studies of the outcome secretion of cellular function.

11:35 Quantitative Single Cell and Single Molecule Proteomics for Clinical Studies

Keith WillisonKeith Willison, Ph.D., Chair, Chemical Biology; Professor, Chemistry, Imperial College London

We have developed a label free, microfluidic antibody capture chip platform called the MAC chip to quantify precisely the copy numbers of several proteins from a single cell in a multiplexed single assay format. We are extending the capability of the MAC chip devices in order to count proteins in circulating tumour cells (CTCs) isolated from biopsies of cancer patients undergoing chemotherapy. We hope to discover biomolecular signatures which correlate with intrinsic biological properties of tumour cells and clinical outcomes during treatment.

12:05 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own


PROBLEM-SOLVING CASE STUDIES 

1:00 Chairperson’s Remarks

Tali (Tania) Konry, Ph.D., Assistant Professor, Pharmaceutical Science, Northeastern University

CANCER 

1:05 HER-2 Testing by Digital PCR: Challenges and Opportunities

Bruno PingBruno Ping, Laboratory Manager, Royal Surrey County Hospital

With increased financial pressures on molecular diagnostic laboratories to perform more testing in a cost effective manner, the advent of digital PCR is potentially the perfect opportunity to introduce cost savings in the lab without compromising patient quality. In our research, we looked at HER-2 testing as a proof of principle model, in a cohort of Her-2 amplified and non-amplified cases and then extrapolated potential lab savings based on an alternative testing algorithm.

1:35 Quantification of Plasma miRNAs Using Digital PCR for Lung Cancer Diagnosis

Feng JiangFeng Jiang, M.D., Ph.D., Associate Professor, Department of Pathology, University of Maryland School of Medicine

To evaluate the utility of digital PCR for analysis of miRNAs in lung cancer diagnosis, we first determined dynamic ranges and sensitivities of digital PCR for measuring plasma miRNAs. We then used digital PCR to quantify plasma miR-21-5p and miR-335-3p in lung cancer patients and controls. Our data suggest that digital PCR is a robust tool for quantitative assessment of plasma miRNAs in lung cancer diagnosis.


GENETICS 

2:05 Analysis of Germline and Somatic Genome Variation Using Integrated NGS and PCR-Based Technology

Alexej Abyzov, Ph.D., Division of Biomedical Statistics and Informatics (BSI), Department of Health Sciences Research (HSR), Mayo Clinic

This presentation will report on our work investigating genome variants that affect brain development and function. We study germline variants as well as somatic variants using both tissue culture models and primary tissue samples. For these purposes we use combinations of next-generation sequencing based approaches, targeted-capture and whole-genome, respectively, as well as PCR based methods such as standard PCR, qPCR and digital droplet PCR.


INFECTIOUS DISEASE 

2:35 Universal Digital High Resolution Melt for Rapid Bacterial Identification in Polymicrobial Infections

Stephanie FraleyStephanie Fraley, Ph.D., Burroughs Wellcome Fund Fellow, Emergency Medicine and Infectious Disease, The Johns Hopkins School of Medicine

A key challenge in clinical diagnostics and biomarker research involves the ability to quantitatively and accurately profile heterogeneous biological samples for detection of numerous and even unexpected genotypes. We have developed Universal Digital High Resolution Melt (U-dHRM), a molecular diagnostic approach that overcomes critical limitations to accomplish rapid, high-content, broad-based detection of individual genotypes within heterogeneous samples. We apply this identify bacterial pathogens in polymicrobial infections.

3:05 Close of Quantitative Digital Detection Conference