Cambridge Healthtech Institute’s Second Annual

PCR for Molecular Medicine

Integrating Approaches for Clinical Success

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

 

Polymerase chain reaction (PCR) is a staple in diagnostic labs worldwide with applications ranging from cancer to infectious diseases. Today, advances in PCR have sparked innovation, expanded research capabilities, and made the technology more clinically useful than ever. Cambridge Healthtech Institute's Second Annual PCR for Molecular Medicine will emphasize integrated approaches for PCR, from traditional to digital. PCR for Molecular Medicine will provide a comprehensive look at PCR in both the research and clinical setting as well as insight into advanced techniques and tools for effective disease diagnosis.

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Monday, February 16

10:30 am Conference Program Registration


KEYNOTE SESSION

11:50 Chairperson’s Opening Remarks

12:00 pm Are There Limits to the Performance and Speed of PCR?

Carl T. Wittwer, M.D., Ph.D., Professor, Pathology, University of Utah

By increasing primer and polymerase concentrations, high yield, efficient and specific PCR can be performed in less than 30 seconds with short products. With cycling overhead reduced to less than one second, product size and the polymerase extension rate determine depressors. Will advances in this foundational technology ever stop?

12:30 Pathogen Detection by Proximity Ligation Assay

Stephen Bustin, BA(Mod), Ph.D., FSB, Professor, Molecular Medicine, Faculty of Medical Science, Anglia Ruskin University

Detection of pathogen-specific proteins can be physiologically more relevant than detection of nucleic acids and is more sensitive than ELISAs or lateral flow devices. We describe the development of proximity ligation assays (PLA) targeting Aspergillus spp and Clostridium difficile, allowing earliest possible diagnosis of infectious or toxin-producing microorganisms.


1:00 Session Break

1:15 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

2:15 Session Break


FDA-APPROVED PCR IN THE CLINIC

2:30 Chairperson’s Remarks

Carl T. Wittwer, M.D., Ph.D., Professor, Pathology, University of Utah

2:40 Lab Quality Point-of-Care: 15 Minute Sample-to-Result Nucleic Acid Test for Strep A

Shuqi Chen, Ph.D., Vice President, Point-of-Care R&D, Roche Molecular System, Inc.

Point-of-care testing must combine speed, ease-of-use, and accuracy to make patient care more efficient. cobas® Strep A is a nucleic acid test performed on the cobas® Liat that detects Strep A in only 15 minutes. Studies show that this molecular test, when used by untrained operators at the point-of-care, delivers accurate results compared to gold-standard culture, and significantly higher sensitivity compared to rapid antigen-based tests.

3:10 How Film Array Almost Killed Its Creators: Overcoming Regulatory and Developmental Challenges with an Integrated Product Team

Kirk M. Ririe, CEO & Founder, BS, BioFire Defense

The FilmArray diagnostic platform from BioFire offers hospital laboratories an easy-to-use syndrome-focused approach. FilmArray tests for dozens of viral, bacterial, or other pathogens in a one-hour test. Three panels are now CE and FDA-cleared with more in the pipeline. Together with our new partners at bioMérieux, we are making a difference in patient care. How did a small team in Salt Lake City do this?

3:40 Extended Q&A with Session Speakers: Preparing for FDA Approval

Moderator: Carl T. Wittwer, M.D., Ph.D., Professor, Pathology, University of Utah

Panelists: Shuqi Chen, Ph.D., Vice President, Point-of-Care R&D, Roche Molecular System, Inc.

Kirk M. Ririe, CEO & Founder, BS, BioFire Defense

4:10 One-Step PCR System as a Genetic BioSensor in Molecular Medicine 

Sabrina Li, CEO, Coyote Bioscience Company

Coyote Bioscience is dedicated to making break-through innovations in molecular diagnostics that brings complex clinical testing directly to the patient. We would like to introduce our novel method of one-step gene test without nucleic acids extraction. The system can be as fast as 10min from blood sample to the result, and thus can be used as a Genetic Biosensor in Molecular Medicine.

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


TECHNOLOGY AND ASSAY ADVANCES

10:05 Chairperson’s Remarks

Kirk M. Ririe, BS, CEO & Founder, BioFire Defense

10:15 MTIDx: Multiple Target Identification Diagnostics

Hong Cai, Ph.D., CEO, Mesa Tech International, Inc.

Rapid identification of highly infectious disease is crucial for early forecast and effective medical countermeasures. Mesa Tech International, Inc. (MTI) seeks to reduce the complexity and cost of nucleic acid-based molecular diagnostics (MDx) via the MTIDx, Multiple Target Identification Diagnostics, a disposable, sample-to-result platform that integrates all requisite steps of a NA-based diagnostic test while retaining of the simplicity of the lateral flow immunoassay format familiar to most POC clinicians.

10:45 Implementation and Transition of Digital PCR from Discovery Applications to Clinical Diagnostic Tools

Andrew Brooks, Ph.D., COO, RUCDR Infinite Biologics, Rutgers Universit.

The use of digital PCR technologies is rapidly evolving for a number of applications. As the technology transitions from being used as discovery tool to diagnostic applications there are many components and benchmarks that need to be established in order to accomplish these goals. This talk will look address the operational considerations for such a transition.

11:15 Not All Primers Are Created Equal: Priming Efficiency Bias Uncovered by NGS

Jian Han, Ph.D., Faculty Investigator, iCubate, HudsonAlpha Institute for Biotechnology

TM-based primer design software has been used for over 30 years. However, if the same primer is subject to different TM evaluation equations, the obtained value could be 8-10 degrees different! We have designed a simple experiment to measure DNA polymerase bias. From these results, a mathematical model of the bias was developed and utilized in a software to guide primer design. This PPI (polymerase preference index) method can be used to improve PCR success rates.

11:45 Standardization Considerations for Circulating Cell-Free DNA Analysis

Alison Devonshire, Ph.D., Science Leader, Nucleic Acid Metrology, LGC Genomics

Cell-free DNA (cfDNA) is becoming an increasingly popular analyte to measure cancer progression, donor organ rejection or prenatal foetal genotype. However the reproducible measurement of cfDNA is associated with a number of challenges because of its low concentration and biological variability. This talk will outline means of assessing extraction efficiency and fragment size bias and quantifying yield. Digital PCR and its role in the development of QC materials for assessing methodological performance and ensuring data comparability will be discussed.

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


PCR FOR PATIENT STRATIFICATION

2:00 Chairperson’s Remarks

Andrew Brooks, Ph.D., COO, RUCDR Infinite Biologics, Rutgers University

2:10 Digital PCR for Patient Monitoring and Stratification in Clinical Trials

Reinhold Pollner, Ph.D., Director, Clinical Trial Assay Development, Genoptix Medical Laboratory, a Novartis Company

My presentation will focus on how digital PCR is used in the validation of clinical trial assays with respect to patient monitoring and stratification in a CLIA/CAP laboratory setting. A variety of different applications of digital PCR will be discussed ranging from the determination of DNA copy numbers in FFPE samples, absolute quantitation of a transgene in whole blood and bone marrow samples, identification of a fusion gene at the mRNA level in FFPE specimens, and rare allele detection using circulating tumor DNA.

2:40 Evaluation of EGFR Mutations in Plasma from NSCLC Patients: Utility in Managing Patients on TKI Therapy

Chris Karlovich, Ph.D., Principal Scientist, Molecular Diagnostics, Clovis Oncology

We are utilizing blood-based molecular testing in patients who have become resistant to first generation tyrosine kinase inhibitors with the goal of enabling subsequent therapy without need for repeat lung biopsy. The utility of plasma-based EGFR mutational analysis will be described in the context of CO-1686, a novel third-generation TKI that selectively inhibits the EGFR activating and T790M resistance mutations in NSCLC patients.

3:10 NGS-Assisted DNA-Based Digital PCR for the Detection and Quantification of Residual Disease in CML Patients with Undetectable BCR-ABL1 Transcripts

Mary Alikian, MSc, Clinical Scientist, Imperial Molecular Pathology, Imperial College

The presentation will describe a DNA-based method of detecting and quantifying low levels of BCR-ABL1 positive disease that improves on previous methodologies in two key areas: Identifying the patient-specific genomic BCR-ABL1 fusion junctions using targeted next generation sequencing allowing the rapid generation of high-performing DNA based qPCR assays. The second area is: Use of a DNA-based approach by optimizing the technique for use on a digital PCR (dPCR) platform, which provides absolute molecular quantification without the need for standard curve.

Bio-Rad3:40 Sponsored Presentation

Speaker to be Announced

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

5:00 Breakout Discussions in the Exhibit Hall

6:00 Close of Day


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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


APPLICATION CASE STUDIES

10:35 Chairperson’s Remarks

Chris Karlovich, Ph.D., Principal Scientist, Molecular Diagnostics, Clovis Oncology

10:45 PANEL DISCUSSION: Future Directions for PCR

Panelists: David Godler, Ph.D., Senior Research Fellow, Cyto-molecular Diagnostics Research and Victorian Clinical Genetics Services; Head, The FMR1 Related Disorders Group, Murdoch Children’s Research Institute, Royal Children’s Hospital

Stephanie I. Fraley, Ph.D., Assistant Professor, Bioengineering, University of California San Diego Johns Hopkins

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


GENETIC DIAGNOSTICS

11:45 An Automated Genetic Analysis Instrument That Boasts High Multiplexing Capabilities and Low Hands-On Time

Hanyoup Kim, Ph.D., Senior Scientist, Canon U.S. Life Sciences, Inc.

The development of an automated genetic analyzer instrument using liquid handling robots and pre-loaded custom reagent plates to run multiplexed genotyping panels on proprietary microfluidic cartridges is described. The microfluidic cartridge that rapidly amplifies and detects via high-resolution melting provides a simple, flexible test workflow. The instrument allows panels of >20 genetic targets to be tested sequentially on a single sample under different PCR conditions, while reducing hands-on time.

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

1:40 Chairperson’s Remarks

Mary Alikian, MSc, Clinical Scientist, Imperial Molecular Pathology, Imperial College

1:50 Droplet Digital PCR and Methylation Specific Quantitative Melt Analysis – Applications in Fragile X Related Disorders and Beyond

David Godler, Ph.D., Senior Research Fellow, Cyto-molecular Diagnostics Research and Victorian Clinical Genetics Services; Head, The FMR1 Related Disorders Group, Murdoch Children’s Research Institute, Royal Children’s Hospital

The first part of the talk will focus on a droplet digital PCR method for absolute quantification of FMR1 RNA toxicity. The second part will focus on a novel FMR1 methylation test utilizing combination of real-time PCR and high resolution melt, named methylation specific quantitative melt analysis or MS-QMA. The presentation will cover applications of both methods in Fragile X Related Disorders in multiple cohorts.


INFECTIOUS DISEASE

2:20 Universal Digital High-Resolution Melt: A Rapid Molecular Approach for Accurately Resolving Mixed Infections

Stephanie I. Fraley, Ph.D., Assistant Professor, Bioengineering, University of California San Diego Johns Hopkins

Nucleic acid amplification with universal primers against microbial nucleic acids can achieve broad-based amplification, but resolving a mixture of amplified sequences, resulting from background contaminating DNA or polymicrobial infections, has proven to be a major challenge for rapid molecular diagnostics. We developed Universal Digital High Resolution Melting, a single microbe sensitive, rapid, and broad-based diagnostic technology to overcome these limitations and have demonstrated its utility in the context of diagnosing bacteremia.

2:50 “Salvage Microbiology” and the Infectious Diseases Physician

Robert A. Bonomo, M.D., Chief, Medical Service, Louis Stokes Cleveland VA Hospital; Vice Chair, Veterans Affair, Medicine, University Hospital Case Medical Center

The timely and accurate diagnosis of pathogens is critical to choosing appropriate therapy and for informing antimicrobial stewardship measures. In many cases, bacterial cultures are unrevealing due to improper handling of samples, previous use of antibiotics, or low colony counts. We present a case series describing how PCR coupled with electrospray ionization mass spectrometry (PCR/ESI-MS) can be used to guide choices for therapy.We illustrate how unsuspected pathogens can be discovered, thereby improving decisions for therapy and increasing our understanding of disease processes.

3:20 Evaluation of Manufacture and QC Controls for PCR Components Used in Molecular Diagnostic Assays

Doug Storts, Ph.D., Head, Nucleic Acid Technologies, Promega Corporation

PCR-based molecular diagnostic assays rely on high quality reaction components to yield robust and reliable results. Gain a better understanding of the impact that PCR component manufacture and QC controls have on molecular diagnostic assay design and performance.

3:35 Sponsored Presentation (Opportunity Available)

3:50 Refreshment Break

4:00 Chairperson’s Remarks

G. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana Farber and Harvard Medical School

4:10 HIV RNA Detection and Quantification by Nucleic Acid Testing-PNA Enzyme Linked Assay (NAT-PELA) for Viral Load Assays

Daniel Appella, Ph.D., Senior Investigator, LBC, NIDDK, NIH

This presentation will demonstrate how to engineer peptide nucleic acids (PNAs) to detect HIV RNA at levels competitive with standard PCR assays. Since PNA is resistant to degradation by enzymes, diagnostic devices using PNA probes are very stable. With the proper PNA probes, standard ELISA platforms can be used to directly detect HIV RNA and may be used to quantify viral load in plasma at clinically useful levels.


CANCER

4:40 Single-Tube Enrichment of Mutations in Cancer Gene Panels Using COLD-PCR Prior to Targeted Amplicon Resequencing

G. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana Farber and Harvard Medical School

Targeted re-sequencing of mutations in cancer-relevant genes provides opportunities for fine-tuning cancer therapy and treatment follow-up, by examining mutations in tumors and bio-fluids. We present a new adaptation of COLD-PCR, fast-TT-COLD-PCR, via which mutations in numerous amplicons are first enriched in a single-tube reaction, prior to targeted re-sequencing. Modified nucleotides are employed in the reaction to enable detection of all mutations. Using this approach, sub-clonal mutations of 0.01-0.1% abundance are first converted to clonal mutations and then detected via NGS.

5:10 Evaluation of Biofluid Derived Extracellular Vesicles in Brain Tumors

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

Extracellular vesicles (EVs) are lipid rafts released by all cells. They end up in biofluids where they can be captured and further characterized. Their cargo represents a molecular snapshot of the primary tumor, and have great potential to report these molecular changes over time. We have isolated EVs from plasma and CSF of patients with brain tumors, and have shown that they are a powerful source of genetic changes present in the primary tumor.

5:40 Close of Conference Program



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