Digital PCR Conference: Technologies and Tools for Precision Diagnostics - Day 1



Register by August 14 & SAVE up to $350!

Polymerase chain reaction (PCR) is an invaluable tool for nucleic acid detection and quantification. As a staple in diagnostics labs, PCR has continued to evolve with scientific need, the latest iteration being digital PCR (dPCR). dPCR increases sensitivity, specificity, and in many cases allows higher throughput. Cambridge Healthtech Institute’s Fourth Annual Digital PCR conference will continue to highlight the importance PCR advances for clinical diagnostics. As always, this event gathers technology providers, early adopters, and platform newcomers to network and discuss digital PCR’s capabilities, limitations, and future applications. This year, key focus will be placed on the technology behind dPCR, interfacing between dPCR and NGS, and emerging technologies and areas of study. Other topics to be addressed include solutions for processing difficult samples and increasing sample throughput, working with extracellular DNA, and guidelines and best practices for digital detection.

Program Advisors

Jim Huggett, B.Sc. (Hons), Ph.D., Science Leader, Nucleic Acid Metrology, Molecular & Cell Biology, LGC
N. Somanath Bhat, Ph.D., Senior Research Scientist, Bioanalysis Group, Department of Industry and Science, National Measurement Institute, Australia


TOPICS INCLUDE:

  • Technology considerations:
    Chips and droplets
  • Validation and reference standards
  • Digital PCR data analysis
 
  • Interfacing dPCR and NGS
  • Absolute quantification
  • Copy number variation
  • Minority target detection
 

FEATURED SPEAKERS:


Alexandra Whale, Ph.D., Senior Researcher, Molecular and Cell Biology Team, Science and Innovation Division, LGC Group

 

Filip JankuFilip Janku, M.D., Ph.D., Assistant Professor, Investigational Cancer Therapeutics (Phase I Program), MD Anderson Cancer Center

 

Valerie TalyValerie Taly, Ph.D., Group Leader, CNRS Researcher, UMR S1147, University of Paris Descartes, CNRS

 

Recommended Short Courses*

Digital PCR: A Technology Primer

Alexandra Whale, Ph.D., Senior Researcher, Molecular & Cell Biology, LGC Group

Single Cell Analysis Technologies: Ready and Able

Michael Masterman-Smith, Ph.D., Senior Scientist, Cynvenio Biosystems, Inc.


*Separate Registration Required



TUESDAY, NOVEMBER 3


DAY 1: TECHNICAL ASPECTS OF DIGITAL PCR

7:30 am Registration and Morning Coffee

8:25 Chairperson’s Opening Remarks

N. Somanath Bhat, Ph.D., Senior Research Scientist, Bioanalysis Group, Department of Industry and Science, National Measurement Institute

 

TECHNOLOGY CONSIDERATIONS: FROM CHIPS AND DROPLETS TO MULTIPLEXING

8:30 Introduction Crystal Digital PCR

Dangla RemiRémi Dangla, Ph.D., President and Co-Founder, Stilla Technologies

Stilla Technologies unveils its unique tool for high precision genetic analysis: Crystal digital PCR. Taking advantage of groundbreaking microfluidic advances, Crystal digital PCR relies on a single consumable to perform on-chip PCR in monolayer droplet arrays. This innovative approach increases multiplexing capacities in digital PCR and is readily amenable to large-scale, high-throughput clinical studies, thanks to a simple and fast workflow.

9:00 Whole Genome Amplification Using Droplet Digital MDA

Minsoung RheeMinsoung Rhee, Ph.D., Postdoctoral Research Fellow, Biological Science and Technology, Sandia National Labs

We demonstrated for the first time that whole genome amplification by MDA can be performed in picoliter emulsion droplets, resulting in improved performance over corresponding reactions carried out at conventional microliter scale. De novo assembly of E. coli genome sequences from our droplet MDA and conventional tube MDA has revealed that droplet MDA showed more uniform coverage for all length of the genome and ~>99% of specific amplification.

9:30 Rapid Detection of Rare Biomarker in Blood Using Integrated Comprehensive Droplet Digital Detection

Dong-Ku KangDong-Ku Kang, Ph.D., Assistant Research Scientist, Sue and Bill Gross Stem Cell Research Center, Pharmaceutical Sciences & Biomedical Engineering, University of California, Irvine; Co-Founder and CSO, VeloxBiosystems

Rapid and sensitive diagnosis remains a major unmet challenge in food industry and medical applications. In this presentation, I will discuss a new technology called “Integrated Comprehensive Droplet Digital Detection Technology” (IC 3D) that is able to rapidly (1-2 h) and selectively detect rare pathogens/or rare biomarkers from milliliters (mLs) of complex media (e.g., unprocessed whole blood) at single-cell sensitivity in a one-step, homogenous, and culture-free reaction. This platform technology also has the potential to introduce a new paradigm in rapid detection for various diseases including cancer (targeting circulating tumor cells), neurological disorder (e.g., Alzheimer’s disease), and infectious diseases (e.g., Lyme disease, HIV, and Ebola).

10:00 Coffee Break with Exhibit and Poster Viewing


VALIDATION AND REFERENCE STANDARDS
USING dPCR

10:45 Digital PCR for DNA Reference Materials

Somanath BhatN. Somanath Bhat, Ph.D., Senior Research Scientist, Bioanalysis Group, Department of Industry and Science, National Measurement Institute

Accurate, reliable and reproducible quantification of nucleic acids is vital for many diagnostic applications and in routine laboratory testing. Digital PCR has the potential to not only improve quantitative nucleic acid analysis, but also to be considered as a reference method for certification of nucleic acid reference materials (RMs). This presentation will discuss how this technology was applied to characterize DNA RMs and discuss factors affecting reliability of the results.

11:15 The Potential Role of Enumeration by dPCR in Clinical Measurement: The Example of KRAS SNPs

Alexandra Whale, Ph.D., Senior Researcher, Molecular and Cell Biology Team, Science and Innovation Division, LGC Group

Unlike qPCR, dPCR does not require a calibration curve for quantitative analysis as the partitioning required to perform the technique enables DNA to be directly counted, or enumerated. This characteristic is fairly unique and opens a number of possibilities when considering clinical measurement, either through direct measurement using dPCR or in its use to support other methods, like qPCR, through the quantification of reference materials. This talk will discuss the work of the European Metrology Research Programme funded project Bio SITrace (http://biositrace.lgcgroup.com/) which is investigating the accuracy of dPCR when measuring rare single nucleotide polymorphisms in cell free DNA.

11:45 Sponsored Presentation (Opportunity Available)

12:15 pm Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:00 Session Break


DIGITAL PCR DATA ANALYSIS

1:25 Chairperson’s Remarks

Alexandra Whale, Ph.D., Senior Researcher, Molecular and Cell Biology Team, Science and Innovation Division, LGC Group

 

1:30 Data Analysis of Droplet Digital PCR with Generalized Linear Mixed Models

Oliver ThasOliver Thas, Ph.D., Professor, Biostatistics, Ghent University (Belgium) and University of Wollongong (Australia)

Target quantification with ddPCR depends heavily on the Poisson assumption. We demonstrate how Generalized Linear Mixed Models (GLMM) can be used for the data-analysis. GLMM is very flexible and allows for analyzing many designs, including dealing with replicates, run or plate effects and one or more references. The method can be used for absolute quantification, CNV and gene expression, and it allows for standard error and confidence interval calculation and hypothesis testing.

2:00 HistoMosaic Detects G12V KRAS in CRC Tissue by in situ PCR in a Microfluidic Matrix

Emil KartalovEmil Kartalov, Ph.D., Assistant Professor, Pathology, Keck School of Medicine, University of Southern California

We present the experimental proof of principle of HistoMosaic - a novel technique for in situ genetic analysis of cancer tissue sections. HistoMosaic offers a high-throughput, low-cost, high-sensitivity means of detection and localization of rare mutations conferring drug resistance to cancer tissue, while the morphological information is preserved and co-registered with the genetic information. This ability would allow proper stratification of cancer patients, so the right drug is given to the right patient. HistoMosaic also has wide applicability in fundamental research and drug development.

2:30 Sponsored Presentation (Opportunity Available)

3:00 Refreshment Break with Exhibit and Poster Viewing


INTERFACING NGS AND dPCR

3:30 Mutation Detection in Multiple Biopsy Types from Advanced Tumors by NGS and Digital PCR

Errin L. LagowErrin L. Lagow, Ph.D., Senior Scientific Liaison, Asuragen, Inc.

Targeted NGS permits detection of low-frequency somatic mutations in tumor biopsies, but call confidence may require independent assessment. Multiple biopsy types from advanced tumors were analyzed with the Quantidex™ PanCancer Panel, designed, developed, and cGMP-manufactured by Asuragen, and with digital PCR. Low frequency mutations were identified in FFPE tissue and confirmed in matched frozen tissue. Digital PCR demonstrated high utility for resolving discordant calls for samples with low frequency mutations.

4:00 Copy Number Variations: Digital PCR, NanoString and Next-Generation Sequencing

Reinhold PollnerReinhold Pollner, Ph.D., Director, Clinical Trial Assay Development, Genoptix, Inc., a Novartis company

A variety of different technologies can be utilized to determine copy number variations in clinical samples. My presentation will focus on how three digital technologies - digital PCR, NanoString and Next-Generation Sequencing are used to determine copy number variations in clinical trial samples for patient stratification or exploratory purposes.

4:30 Challenges and Strategies for Accurate Quantification of NGS Libraries with Digital PCR

Peter SchweitzerPeter Schweitzer, Ph.D., Director, Genomics Facility, Institute of Biotechnology, Cornell University

One critical step in producing high quality DNA sequence data in a timely and cost efficient manner is accurately quantifying Illumina sequencing libraries. Digital PCR (dPCR) offers several advantages over real-time PCR. One significant challenge is accurately performing the large dilution required and I’ll describe an internal reference developed to correct for variability during dilution. I’ll also describe our experiences with dPCR assays for Illumina libraries using several different platforms.

5:00 Welcome Reception with Exhibit and Poster Viewing

6:00 Close of Day



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