2014 Archived Content

 

Cambridge Healthtech Institute’s Inaugural

PCR for Molecular Medicine

Current Applications and Future Perspectives

February 10-12, 2014 | Moscone North Convention Center | San Francisco, CA

 

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Wednesday, February 12

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee


8:00 Plenary Keynote Session (Click Here For More Details) 


9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall

10:35 Chairperson’s Remarks

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

10:40 PANEL DISCUSSION: Future Directions for PCR

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

Panelists: Christopher D. Gocke, M.D., Pathology; Director of Hematology Molecular Diagnostics and Program Director, Molecular Genetic Pathology Fellowship, Johns Hopkins University
Matthew Strain, M.D., Ph.D., Assistant Professor, Center for AIDS Research, University of California, San Diego
Bernhard Zimmermann, Ph.D., Senior Director, Research & Development, Natera, Inc.


APPLICATIONS IN PRENATAL DIAGNOSTICS  

 

11:10 Noninvasive Prenatal Diagnosis through Genetic Molecular Analysis of Circulating Trophoblastic Cells

Patrizia Paterlini-Brechot, M.D., Ph.D., Professor, Cell Biology and Oncology, University Paris Descartes Paris; Director, INSERM

Trophoblastic cells are expected to provide the optimal DNA substrate for noninvasive prenatal diagnosis (NI-PND) as they carry fetal DNA not mixed with maternal DNA, and circulate at very early terms of pregnancy. Results of a clinical validation study concerning NI-PND of hereditary genetic diseases using circulating trophoblastic cells, and of its potential extension, will be discussed.

11:40 Massively Multiplexed Single-Nucleotide Polymorphism Amplification and Sequencing to Identify Fetal Aneuploidy from Cell-Free DNA in Maternal Circulation

Bernhard Zimmermann, Ph.D., Senior Director, Research & Development, Natera, Inc.

We developed a method to multiplex, in a single reaction, tens of thousands of PCR assays targeting SNPs. Noninvasive prenatal testing based on analysis of cell-free DNA (cfDNA) is one of the most rapidly-expanding molecular diagnostics fields. I will present the most recent performance data from a commercialized version of this approach, a highly accurate noninvasive prenatal aneuploidy test. I will also discuss the potential of this approach to detect various microdeletion syndromes, which is the next major challenge
in noninvasive prenatal testing.

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


APPLICATIONS IN CANCER 

 

1:40 Chairperson’s Remarks

Mark R. Miglarese, Ph.D., CSO, GeneCentric Diagnostics

1:45 Tandem Duplication PCR: A Novel Method of Detecting Minimal Residual Disease and Minor Clones in FLT3/ITD AML

Christopher D. Gocke, M.D., Pathology; Director of Hematology Molecular Diagnostics and Program Director, Molecular Genetic Pathology Fellowship, Johns Hopkins University

The TD-PCR was initially designed to confirm ITD mutation of an amplicon, which was undetectable by capillary electrophoresis and was incidentally isolated by a molecular fraction collecting tool. Subsequently, TD-PCR detected ITD mutation in 2 of 77 patients previously reported as negative for ITD mutation by a standard PCR assay. TD-PCR can also potentially be applied to monitor minimal residual disease with high analytic sensitivity in a portion of ITD-positive acute myeloid leukemia patients.

2:15 Prediction of Lung Cancer Histological Types by RT-qPCR Gene Expression in FFPE Specimens

Mark R. Miglarese, Ph.D., CSO, GeneCentric Diagnostics

Lung cancer histologic diagnosis is clinically relevant because there are histology-specific treatment indications and contraindications. Diagnosis by standard histopathological methods can be challenging due to a variety of tumor characteristics as evidenced by less-than-ideal agreement among pathologists reviewing the same specimens. We developed a 57-gene RT-qPCR expression predictor of lung cancer histology for use on FFPE specimens. Assay performance and comparison to interpretations from traditional pathology results will be discussed.

2:45 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.

3:15 FEATURED POSTER PRESENTATION: The ALPINE Technique: Molecular Detection of Ovarian Cancer, a Proof of Concept Study

Elisabeth Maritschnegg, Department of Obstetrics and Gynecology, Medical University of Vienna

We have established a method to detect exfoliated tumor cells by performing a lavage of the uterine cavity and fallopian tubes. Genetic changes were analyzed in the lavage specimens to confirm the presence of cancer cells. The lavage procedure, called the ALPINE technique (Austrian Lavage Procedure for the Detection of Tubal Intraepithelial Neoplasms) was optimized to be performed in an outpatient setting and non-invasive manner. In 16/22 (72.7%) lavage samples of ovarian cancer patients, a mutation in a gene, included in the gene panel, was successfully detected using massively parallel sequencing. Of 18 patients, corresponding tumor tissues were available, showing the same mutation.

3:45 Refreshment Break


APPLICATIONS IN INFECTIOUS DISEASE 

4:00 Chairperson’s Remarks

Niaz Banaei, M.D., Assistant Professor, Pathology & Infectious Diseases, Stanford University

4:05 Applications of Digital PCR to Clinical Viral Load Testing

Randall T. Hayden, M.D., Director, Clinical and Molecular Microbiology, Member, Department of Pathology, St. Jude Children’s Research Hospital

Viral load testing has become integral to the care of many critically ill patients, but currently available tests suffer from marked intra-laboratory result variability and a lack of standardization. Digital PCR offers a means of direct quantitative measurement that may improve both accuracy and precision compared to other methods. This session will describe the theory behind digital PCR, as well as some initial studies evaluating its use for viral load testing.

4:35 Application of Droplet Digital PCR for the Investigation of the Latent HIV Reservoir

Matthew Strain, M.D., Ph.D., Assistant Professor, Center for AIDS Research, University of California, San Diego

The latent reservoir of HIV represents the obstacle to curing the infection with the currently highly effective antiretroviral therapy. Measuring the reservoir requires assays of rare events in a large number of cells. We have developed and applied droplet digital PCR to the assay of various species of HIV DNA and RNA transcripts. The characterization of these assays and their application to clinical studies will be discussed.

5:05 Sequencing Comes to Rescue When All Else Fails: Pathogen Detection and Identification in Clinical Samples with Broad Range PCR Amplicon Sequencing

Niaz Banaei, M.D., Assistant Professor, Pathology & Infectious Diseases, Stanford University

Clinicians frequently encounter patients with life threatening culture-negative infections. Broad range PCR combined with amplicon sequencing is a powerful tool for rapid and accurate diagnosis of culture-negative or uncultured invasive infections. In this case presentation I will describe and discuss the utility and potential pitfalls of ribosomal RNA locus sequencing for direct detection and identification of invasive bacteria and fungi from fresh and formalin-fixed, paraffin-embedded specimens.

5:35 Close of Conference Program



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