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Digital PCR Conference - Day 2


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2013 Archived Content

 

TUESDAY, OCTOBER 8


MINORITY TARGET DETECTION 

8:25 am Chairperson's Remarks

8:30 Molecular Analysis of Liquid Biopsies in Biomarker Driven Clinical Research

Filip Janku, M.D., Ph.D., Assistant Professor, Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center

Discovery of oncogenic mutations in the tumor tissue led to the identification of distinct therapeutic targets and major novel drug discoveries, which were quickly translated into patient care. However, mutation analysis is not always feasible due to a limited amount of available tumor tissue. DNA from other sources such as plasma or urine from individuals with cancer offers an easily obtainable, low-risk, and inexpensive source of biologic material for mutation analysis and personalized medicines applications.

9:00 Early Detection of Somatic Mutations in Circulating Tumor DNA

Nickolas Papadopoulos, Ph.D., Professor, Oncology; Director, Translational Genetics, Ludwig Center for Cancer Genetics & Therapeutics, Sidney Kimmel Comprehensive Cancer Center

Most tumors are incurable because they become symptomatic at a late stage. Early detection of cancer, before symptoms appear, at a stage curable by surgery, holds great promise for decreasing the death rate of cancer. Somatic mutations are specific biomarkers that reveal the presence of cancer when present in circulating tumor DNA. The number of circulating tumor DNA molecules with somatic mutations is very low compared to that of DNA molecules with wild type sequence and requires very sensitive methods for their detection. Here we discuss our efforts for developing such methods and studies for their validation.

9:30 Droplet-Based Microfluidics as a Tool for Personalized Medicine

Valerie Taly, Ph.D., Group Leader/CNRS Researcher, Université Paris-Descartes

To demonstrate the pertinence of droplet-based microfluidics to overcome clinical oncology challenges, the results of 2 studies will be presented. When the first one addresses our ability to detect minoritary subclones in colorectal tumors and to understand the impact of these subclones on responses and survival of patients treated by anti-EGFR therapies, the second one aims at demonstrated the possibility to detect circulating tumor DNA in plasma of patients with advanced colorectal cancers.

10:00 Coffee Break with Exhibit and Poster Viewing

10:30 BEAMing and Droplet Digital PCR Analysis of Mutant IDH1 mRNA in Glioma Patient Serum and Cerebrospinal Fluid Extracellular Vesicles

Leonora Balaj, Ph.D., Researcher, Massachusetts General Hospital, Harvard Medical School

Here, we describe a novel approach that uses BEAMing droplet RT-PCR (EV-BEAMing), as well picodroplet digital PCR, to interrogate mRNA sequences contained within EVs from serum and CSF of glioma patients. Using both assays, we were able to reliably detect and quantify mutant and wild-type IDH1 transcripts in CSF of patients with gliomas. EV-BEAMing and picodroplet dPCR from EV's represent a valuable new strategy for cancer diagnostics, which can be applied to a variety of biofluids and neoplasms.

11:15 Circulating Tumor DNA Testing for the Stratification and Monitoring of Cancer Patients

Philipp Angenendt, Ph.D., CTO, Inostics GmbH

Previous mutation detection assays have not been sufficiently specific, sensitive, or quantitative for the assessment of the clinical utility of circulating nucleic acids in oncology. Newly developed technologies based on digital PCR provide a high sensitivity and at the same time allow quantification of the fraction of mutant to normal DNA molecules. One of these approaches applied by Inostics is the BEAMingTechnology. Several studies have been performed using BEAMingshowing thattesting of circulating tumor DNA is a novel approach to improve cancer patient management. Inostics will present its clinical testing experience using the BEAMing technology.

11:45 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

 

COPY NUMBER VARIATION 

1:10 Chairperson's Remarks

David Dodd, Ph.D., Postdoctoral Fellow, Corey Lab, University of Texas, Southwestern

MolecularMD1:15 pm Absolute Quantification of EGFR Activation and Resistance Mutations by Droplet Digital PCR in Circulating Nucleic Acids

Sabita Sankar, Ph.D., Associate Director, Scientific Affairs, MolecularMD

Selection of treatment, monitoring disease progression and providing early detection of treatment failure associated with acquired resistance to first generation EGFR inhibitors poses several challenges because of limited access to post-treatment tumor tissue. MolecularMD has addressed these challenges by developing and optimizing droplet digital PCR assays that quantify both EGFR activating and resistance mutations in circulating, cell-free DNA.

1:30 Sponsored Presentation (Sponsorship Opportunity Available)

1:45 Digital PCR Assessment of Clinically Actionable Variants in Human Disease

Hanlee P. Ji, M.D., Assistant Professor, Medicine, Division of Oncology, Stanford University School of Medicine

Digital PCR technologies provide an extremely rapid and readily accessible approach to query clinically relevant genetic variation. First, the strengths of this technology enable the assessment of archival and degraded clinical samples with exquisite sensitivity and specificity. Second, digital PCR enables the temporal assessment of clinically relevant genetic variation, and is providing a wealth of information about disease progression. Namely, we are increasingly able to track the presence, expansion and disappearance of pathogenic genetic variants in cancer, infectious diseases and other human diseases over the course of time. This longitudinal component of disease-related genetic variation provides biological insight and has enormous potential for highly informative diagnostics.

2:15 High-Resolution Chromosome Mapping for 22q11.2 Deletion Syndrome Using Digital PCR

Vicki Hwang, Graduate Student Researcher, Biochemistry and Molecular Medicine, University of California at Davis

22q11.2 Deletion Syndrome (22q11DS)is characterized by a wide range of clinical manifestations. Caused by a deletion on chromosome 22, up to 60 genes can behemizygously deleted, many of which have been proposed to be important players. As the position of the breakpointshas not been thoroughly investigated, we have used droplet digital PCR (ddPCR)to examine the deletion endpoints in 60 22q11DS subjects.The characterization of the extent of the deletion is necessary for our understanding of the broad spectrum of phenotypes observed in this syndrome.

2:45 Why Millions of Droplets Matter with Digital PCR

Andrew Watson, Chief Commercial Officer, RainDance Technologies, Inc.

Digital PCR allows researchers to visualize and count changes that were previously unattainable due to technological limitations. This presentation will cover recent developments at RainDance Technologies and why millions of droplets produce superior results.

3:15 Refreshment Break with Exhibit and Poster Viewing

 

ABSOLUTE QUANTIFICATION 

Life_Technologies4:00 Expanding PCR Toolbox - The QuantStudio 3D System for Absolute Quantification, CNV Analysis and Mutation Detection

Stephen Jackson, Ph.D., Associate Director, Product Applications, Genetic Analysis, Life Technologies

 

4:30 Quantitative Multiparameter Analysis of Single Cells Using Microfluidically Generated Emulsions

Richard A. Mathies, Ph.D., Professor, Chemistry, University of California, Berkeley

Bulk analysis of cell populations obscures differences among individual cells. Microfluidic systems allow for rapid generation of uniform emulsions that enable high-throughput analysis of populations with single-cell resolution. I present several microfluidic methods for interrogating cell variability at the DNA and RNA levels as well as investigating the impact of genetic variability on cell phenotype.

5:00 Digital Quantitation of Therapeutic Target RNAs in Mammalian Cell Nuclei

David Dodd, Ph.D., Postdoctoral Fellow, Corey Lab, University of Texas, Southwestern

Accurate determination of the amount of a given RNA within a cell is necessary to gain a full understanding of an RNA's function and regulation. Here we compare Droplet Digital PCR (ddPCR) with more traditional qPCR for this task. Results reveal insights into the design of experiments using ddPCR and show that ddPCR can be a robust tool for identifying the number of RNA species inside of cells.

5:30 Problem-Solving Breakout Discussions

TABLE 1: Sources of Error when Measuring Nucleic Acids Using Digital PCR?

Moderator: Jim Huggett, B.Sc. (Hons), Ph.D., Science Leader, Nucleic Acid Metrology, Molecular & Cell Biology, LGC

  • Variance
  • Bias
  • Absolute quantification/rare variant detection
  • Need for controls/calibration

TABLE 2: Detecting Latent HIV Reservoirs with dPCR

Moderator: Douglas D. Richman, M.D., Director, Center for AIDS Research; Distinguished Professor, Pathology and Medicine; Florence Seeley Riford Chair in AIDS Research, University of California, San Diego

  • Assaying rare events in a large number of cells
  • Developing assays for various species
  • Characterizing assays
  • Retrieving clinically relevant data

TABLE 3: dPCR to Query Clinically Relevant Genetic Variations

Moderator: Hanlee P. Ji, M.D., Assistant Professor, Medicine, Division of Oncology, Stanford University School of Medicine

  • Assessing degraded clinical samples with exquisite sensitivity and specificity
  • Temporal assessment of clinically relevant genetic variation
  • Tracking pathogenic genetic variants in cancer, infectious diseases and other human diseases

TABLE 4: Tools for Analyzing Liquid Biopsies

Moderator: Filip Janku, M.D., Ph.D., Assistant Professor, Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center

  • Why use plasma or urine as a sample source?
  • Digital PCR as a tool for analysis of liquid samples
  • Mutation analysis and personalized medicines applications

6:30 Close of Day

 

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