Cambridge Healthtech Institute’s Third Annual

PCR for Molecular Medicine

From Assay to FDA: Preparing PCR for Personalized Medicine

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


Polymerase chain reaction (PCR) has become increasingly cost effective, sensitive, and precise. With emphasis on personalized medicine on the rise, the need for inexpensive, reliable diagnostics will grow. Today, advances in PCR have sparked innovation, expanded research capabilities, and made the technology more clinically useful than ever. Cambridge Healthtech Institute’s Third Annual PCR for Molecular Medicine will emphasize integrated approaches for PCR, from traditional to digital, as well as next-generation sequencing. PCR for Molecular Medicine will provide a comprehensive look at PCR from assay development to FDA approval as well as insight into advanced techniques and tools for effective disease diagnosis. 

Final Agenda

Monday, March 7

10:30 am Conference Program Registration Open


11:50 Chairperson’s Opening Remarks

Chen Song, Ph.D., Research Fellow, Dana-Farber Cancer Institute, Harvard Medical School

12:00 pm Novel Approaches for Increasing Sensitivity and Specificity of Molecular Diagnostics Assays, Following Mutation Enrichment

Chen Song, Ph.D., Research Fellow, Dana-Farber Cancer Institute, Harvard Medical School

Detecting rare mutations in clinical samples and liquid biopsies requires methods having highly increased sensitivity while retaining excellent specificity. We present novel methods that provide mutation enrichment either prior to PCR or during PCR and enable established methodologies for detecting mutations at 0.1-0.01% levels or below. We present the advantages of combining a novel approach NaME (Nuclease-assisted Mutation Enrichment) or COLD-PCR with digital PCR, high resolution melting or sequencing.

12:30 Increasing Detection of Rare Cancer Mutation in Exosomes using Digital PCR

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

Individual vesicles partially reflect the content of the cells they are released from, but analysis of a large number of vesicles allows full characterization and profiling a primary tumor. Single and rare mutations may not be packaged into every vesicles and analyzing each one individually may increase sensitivity. Also, combined analysis of RNA and DNA may lead to higher sensitivity for several mutations. We used digital PCR to interrogate plasma derived vesicle for tumor mutations from brain tumor patients.

1:00 Session Break

Exiqon1:15 Luncheon Presentation I: Diagnostic microRNA Signatures for Prostate Cancer in Exosomes from Urine

Peter Mouritzen, Vice President, Research and Development, Exiqon

To develop non-invasive diagnostic tests for prostate cancer (PCa), we have applied our LNA™-based qPCR to identify diagnostic microRNAs in exosomes purified from cell free urine from non-prostate-massaged men. Sensitive and specific PCa signatures have been obtained by different combinations of the identified differentially regulated microRNAs.

1:45 Luncheon Presentation II (Sponsorship Opportunity Available)

2:15 Session Break

2:30 Chairperson’s Remarks

Jim Huggett, B.Sc. (Hons), Ph.D., Principal Scientist, Nucleic Acid Metrology, Molecular & Cell Biology, LGC

2:40 Resolving Genetic Variation from Biological and Clinical Sample Mixtures at Individual Molecule Resolution

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

“Digital” molecular assays and sequencing approaches provide high sensitivity to measure genetic variation and the presence of specific genomes. I describe a number of methods, approaches and technologies that our research group has developed that can resolve biological and clonal mixtures. Some of these approaches measure at the level of small number of individual molecules. We have used these methods to detect pathogen genomes, somatic mutations from primary tumors and genetic variation from cell free DNA. The potential of these methods for clinical application will be described.

3:10 End-Specific PCR (ES-PCR) and Helper-Dependent Chain Reaction (HDCR) for Sensitive and Specific Detection of Cancer-Derived DNA

Jason Ross, Ph.D., Research Scientist, Preventative Health Flagship, CSIRO

We have developed two PCR-based techniques particularly useful for the detection of minute quantities of target DNA within a vast excess of non-target DNA, such as in circulating tumor DNA and biopsy sample applications. We have applied these technologies, in particular, to the development of bisulfite-free DNA methylation assays to detect cancer. We have further developed this to provide a platform integrating biomarker discovery and assay development using deep sequencing.

3:40 Developing PCR Assays for Validation and Long-term Life-Cycle Management

Linda Starr-Spires, Ph.D., Director, Nucleic Acid Methods, Global Clinical Immunology, Sanofi Pasteur, Inc.

In the vaccine industry, patients enrolled in clinical trials often undergo long-term follow-up which can last as much as ten or more years. Data generated in the early days of the clinical trials must remain relevant to data generated sometimes many years later. To meet this goal, assays must developed that are very robust, undergo full validation to meet applicable regulatory requirements, and must be monitored for continued performance throughout the life of the trials. Real-life examples of the management of assays developed in-house, including manufacturing of supporting reagents, will be discussed.

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

Jesus Ching, Ph.D., CTO, Research & Development, Coyote Bioscience

A 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.

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

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

Mary Alikian, Ph.D., Senior Research Associate & Registered Principal Clinical Scientist, Imperial Molecular Pathology Laboratory; Haematology, Hammersmith Hospital, Imperial College London

10:15 E.A.C. BCR-ABL1 Assay Performance Validation by dPCR, Including a Cross Platform dPCR Comparison

Mary Alikian, Ph.D., Senior Research Associate & Registered Principal Clinical Scientist, Imperial Molecular Pathology Laboratory; Haematology, Hammersmith Hospital, Imperial College London

The presentation will describe the performance of the routine assay (called the E.A.C. assay) used for monitoring minimal residual disease (MRD) in Chronic Myeloid Leukemia (CML) on several dPCR platforms and provide a head- to-head comparison between these platforms.

10:40 Standardization on Measuring Circulating RNA

Kai Wang, Principal Scientist, Institute for Systems Biology

Circulating RNA has gained significant interest due to their potential diagnostic applications. Despite its potential, there are a number of challenges to accurately measure the levels of specific cell free RNA in circulation. To move this promising field forward, detailed documentation and optimization of laboratory protocols are encouraged which will serve as the foundation of standardization in the future.

11:00 The Role of Digital PCR in Revolutionizing the Standardization of Molecular Medicine

Jim Huggett, B.Sc. (Hons), Ph.D., Principal Scientist, Nucleic Acid Metrology, Molecular & Cell Biology, LGC

dPCR is a unique molecular method as it is able to accurately count DNA molecules and is far more reproducible than contemporary methods. These characteristics make dPCR a candidate to become a reference method that could be used to support inter laboratory performance in diagnostics settings ranging from cancer stratification to infectious disease monitoring. This presentation will discuss the outputs of two European Union funded projects (INFECT-MET and BioSitrace) which have specifically investigated the potential of dPCR to act as a reference method to support other clinical tools.

11:25 Diagnostic RAS Mutation Analysis by PCR

Ian A. Cree, Ph.D., Professor, Pathology, University Hospitals Coventry and Warwickshire; Coventry University

RAS mutation analysis is an important companion diagnostic test. Treatment of colorectal cancer with anti-EGFR therapy requires demonstration of RAS mutation status (both KRAS and NRAS), and it is good practice to include BRAF. In NSCLC and melanoma, assessment of RAS status can be helpful in triaging patient samples for more extensive testing. The presentation will discuss the role of PCR methods in providing rapid diagnostic information. 

11:50 Standardization on Measuring BCR-ABL1 Transcripts using Digital PCR-based on WHO Primary Reference Material

Hirohito Umemoto, Ph.D., Chief, OMICS Laboratory, Reference Material Institute for Clinical Chemistry Standards

Monitoring fusion transcript level is an important indicator of therapeutic response in a patient with chronic myelogenous leukemia (CML). We have established a high-resolution MRD analysis using Duplex Digital-PCR for monitoring fusion transcript level in CML. From the 3 times serial dilution assays of total RNA in K562, we confirmed that Digital-PCR value can be directly converted to IS% using the WHO primary standard equation.

12:15 pm Session Break

Applied DNA Sciences12:25 Luncheon Presentation I: PCR-Based DNA Manufacture at the Industrial Scale: DNA Diagnostics and Therapy in the 21st Century

Michael Hogan, Ph.D., Vice President, Life Sciences, Applied DNA Sciences, Inc.

We introduce PCR-based DNA manufacture to enable the gram-scale synthesis of gene-sized reagents directly from synthetic genomics, with chemical modification as needed, and with rigorous, highly-simplified purification: to support DNA diagnostics and therapeutics. Case studies will emphasize the substantial benefits of industrial scale PCR over cloning.

12:55 Luncheon Presentation II (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

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


2:00 Chairperson’s Remarks

Ian A. Cree, Ph.D., Professor, Pathology, University Hospitals Coventry and Warwickshire; Coventry University

2:10 Validating Allele-Specific PCR Somatic Mutations Tests Using NGS: From Basic Research to IVD

Eugene (Gene) Spier, Ph.D., Director, Bioinformatics, Roche Molecular Systems

Roche Molecular developed IVD test to detect somatic mutations in FFPE samples for EGFR, KRAS, BRAF, EZH2 and other oncogenes as companion diagnostics for target cancer therapies. We are adapting these tests to detect and measure somatic mutations in plasma. Allele-specific PCR can detect <0.5% mutated in normal DNA background. I will describe methods and software that enable us detect rare <0.2% somatic mutations in plasma in deep NGS re-sequencing data.

2:40 The Liquid Biopsy Approach - Integrating Both PCR and NGS Solutions for Oncology Biomarker Development

Winston P. Kuo, Ph.D., Vice President, Research & Business Development Global, Predicine

Extracellular vesicles (EVs) have been shown to carry a variety of biomacromolecules including DNA, mRNA, microRNA and other non-coding RNAs. EVs have emerged as a promising minimally invasive novel source of material for molecular diagnostics with potential clinical utility. This presentation will discuss the flexible and efficient workflow of integrating PCR and NGS of exRNA from serum sample in oncology biomarker development and their applications in therapeutic management and drug development.

3:10 Precision Oncology Applications of Integrative Multiplexed PCR Based Assays

Scott A. Tomlins, M.D., Ph.D., Assistant Professor, Pathology & Urology, University of Michigan

Precision medicine approaches require assays capable of working with small, routine pathology specimens. I will describe multiple approaches we have developed and validated, including a prostate cancer specific combined qRT-PCR and capture based DNAseq approach, as well as a pan-solid tumor multiplexed PCR based DNA and RNAseq assay. Lessons learned from assessing over 1200 specimens will be described.

Seegene3:40 “Fit-for-Workflow” Considerations for Designing Multiplex PCR Assays for SNP Detection and Target Enrichment

Young Kim, Ph.D., Lead Application Scientist, Seegene Technologies

Conventional approaches to assay development using PCR are generally limited to very few targets, which is not an ideal companion to NGS. Using examples from BCR-ABL, thrombosis, HPV genotyping, and others, we will discuss novel approaches to develop high-multiplex RT-PCR and qPCR assays that achieve high-throughput, target complexity, specificity and sensitivity.

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.

Standardization of Circulating Biomarkers

Kai Wang, Principal Scientist, Institute for Systems Biology


  • Standardization on sample preparation
  • Standardization on biomarker (panel) discovery and development processes
  • How to reduce noise
  • How to select biomarker(s)
  • How to assess the performance
  • How to verify and validate the biomarker(s) 


6:00 Close of Day

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

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

11:00 BRACAnalysis CDx: First Laboratory Developed Companion Diagnostic Approval Story

Jolette Franco, Director, Regulatory Affairs, Myriad Genetic Laboratories, Inc.

Short presentation on the PMA approval journey of a laboratory developed companion diagnostic test in conjunction with the approval of AstraZeneca’s drug Lynparza.

11:15 One Assay, Two Guvnors: Development of FDA-Approved PCR for the Clinic

Adrian Moody, Ph.D., Director & Head, Design and Development Manchester, MDx Assay Development, QIAGEN

QIAGEN’s leadership in companion diagnostics continues to grow, transforming patient care around the world. Our therascreen EGFR test is driving treatment decisions in lung cancer patients across the globe and will be used as a case study to explore the challenges of developing FDA approved PCR in the clinic.

11:30 PANEL DISCUSSION: FDA Approval of PCR- and NGS-Based Diagnostics

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


Adrian Moody Ph.D., Director, Head, Design and Development Manchester, MDx Assay Development, QIAGEN

 Additional Panelists to be Announced

This discussion will cover:

  • Reimbursement
  • Logistical considerations
  • Value perception
  • Test evidence evaluation

12:30 pm 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

Ken C.N. Chang, Ph.D., Senior Principal Scientist, Translational Biomarkers, Merck Research

2:00 Multiplexing DNA/RNA Profiling Assay Development for Patient Stratification—Case Studies: Comparing PCR to Nanostring and NGS-Based Assays

Ken C.N. Chang, Ph.D., Senior Principal Scientist, Translational Biomarkers, Merck Research

Despite of the advancement of next generation genomic profiling technologies common challenges shared by all these technologies exist including the highly fragmented nature of FFPE tissue clinical samples as well as inconsistent detection of mutations with low variant frequency that is close to the detection sensitivity. Unique strategies will be presented to address these issues in PCR-based multiplexing mutation assays, RNA profiling assays, and NGS-based mutation profiling assays.

2:30 Informatics Framework for Deriving Platform Independent Isoform-Level Expression Signatures for Multi-Class Tumor Subtyping

Ramana V. Davuluri, Ph.D., Professor & Director, Advanced Bioinformatics & Biocomputation, Northwestern University Feinberg School of Medicine

We developed novel data-mining method, called PIGExClass (platform-independent isoform-level gene-expression based classification-system), for derivation of multi-gene signature for multi-label molecular stratification of cancer patients, from exon-array or RNA-seq data. The application of this machine learning framework has led to the development of an RT-qPCR based assay for diagnosis of glioblastoma sub-types. I will discuss PIGExClass and its potential application on GBM and other cancers.

3:00 Comprehensive Analyses of Cell-Free DNA in Lung Cancer

Hatim Husain, M.D., Assistant Professor of Medicine, Division of Hematology-Oncology, University of California, San Diego

Many lung cancer patients have genomic aberrations that when targeted may provide clinical benefit to patients. We have performed PCR based analyses of urine from lung cancer patients to identify targetable EGFR mutations. These strategies to evaluate the kinetic changes in circulating tumor DNA are underway to predict who may best benefit from oncogene directed therapies. Larger studies are on-going to evaluate the clinical significance of circulating tumor DNA in urine and blood.

3:30 Detection of Osimertinib Resistant Mutations with Droplet Digital PCR

Nina Prokoph, Graduate Scientist, Translational Science, Tumor Genetics Group, AstraZeneca

Osimertinib (AZD9291) is an EGFR TKI developed to have potency against tumors harboring EGFR sensitizing and T790M resistance mutations. Next-generation sequencing of cell-free DNA detected three types of acquired EGFR C797S mutations in osimertinib-treated subjects. Here we present single droplet digital PCR assays and compare them with a multiplex assay that was developed to detect the three types of C797S resistance mutations from a single reaction.

4:00 Session Break


4:10 Chairperson’s Remarks

Tara Sigdel, Ph.D., Assistant Professor, Surgery, University of California San Francisco School of Medicine

4:15 The KSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection

Tara Sigdel, Ph.D., Assistant Professor, Surgery, University of California San Francisco School of Medicine

Noninvasive test to improve disease diagnosis and patient monitoring is a critical need. In kidney transplantation, acute rejection (AR) increases the risk for chronic graft injury and failure. We have developed a highly sensitive qPCR based test as a tool to detect high risk of AR of renal transplants. This KSORT test is able to detect AR in blood independent of age, time post-transplantation, and sample source.

4:45 Monitoring Brain Tumor Mutations from Cerebrospinal Fluids Using Digital PCR

Wenying Pan, Ph.D. Student, Bioengineering, Stanford University

Detecting tumor-derived cell-free DNA (cfDNA) in the blood of brain tumor patients is challenging, presumably owing to the blood-brain barrier. As a counterpart of blood in central nervous system, cerebral spinal fluids (CSF) can serve as an alternative “liquid biopsy” of brain tumors. We developed a method to measure cell-free DNA variants in CSF using digital PCR to characterize brain tumor mutations and monitor patients’ response to cancer therapy.

5:15 Close of Conference Program