2014 Archived Content

Cambridge Healthtech Institute’s Inaugural
Circulating Cell-Free DNA
Advancing Non-Invasive Diagnostics
Part of the 21st Annual Molecular Medicine Tri-Conference

February 13-14, 2014 | Westin St. Francis | San Francisco, CA


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Friday, February 14

8:00 am Morning Coffee


NEW APPROACHES AND FINDINGS 

8:25 Chairperson’s Remarks

Mitch Raponi, Ph.D., Senior Director, Molecular Diagnostics, Clovis Oncology

8:30 Rapid Detection of Cancer-Related Circulating Cell-Free (CCF) DNA Directly from CLL Patient Blood

Michael J. Heller, Ph.D., Professor, Bioengineering and Nanoengineering, University of California, San Diego

We now demonstrate a dielectrophoretic (DEP)-based approach that allows ccf-DNA biomarkers from chronic lymphocytic leukemia (CLL) patients to be isolated in less than 10 minutes directly from a small volume (20ul) of unprocessed whole blood. The use of DEP devices for rapid isolation of ccf-DNA directly form a small volume of blood has considerable potential as a noninvasive point-of-care (POC) approach for the detection of incipient, residual, and recurrent cancer.

9:00 Nanotechnology Enhanced Analysis of Methylation and Integrity Index of Circulating Tumor DNA

Jeff Tza-Huei Wang, Professor, Mechanical Engineering & Biomedical Engineering, Sidney Kimmel Comprehensive Cancer Center, Institute for NanoBioTechnology, Johns Hopkins University

This talk describes a streamlined DNA methylation detection platform that utilizes silica super paramagnetic particles to improve the processing of circulating DNA in serum/plasma and quantum dots to enhance methylation detection. In addition, a microfluidic single molecule detection platform for analyzing the integrity index of circulating DNA as a potential cancer marker is also discussed.

9:30 Circulating Cell-Free MicroRNAs as Biomarkers

Muneesh Tewari, M.D., Ph.D., Human Biology, Fred Hutchinson Cancer Research

10:00 FEATURED POSTER PRESENTATION: Towards the Implementation of a Portable Magnetoresistive Point-of-Care System for Cell-Free DNA Detection in Cancer Diagnosis

Tomás Dias, Ph.D. Candidate, Bioengineering, MIT Portugal Program, Instituto Superior Tecnico

In this work, we investigate the use of a novel and portable device based on the use of 30 magnetoresistive (MR) sensors in a microarray-like format for the assessment of cfDNA integrity. ALU repeats of 115 bp (representative of total cfDNA) and of 247 bp (representative of tumor DNA) were analyzed in order to assess the functionality of the system. ALU115 and ALU247 were first targeted for Polymerase Chain Reaction (PCR) after a step of cfDNA extraction from plasma donor samples. During the reaction, a biotin and a 5’ phosphate group were incorporated per newly synthesized fragment allowing thereafter to generate single-stranded targets upon a digestion step with lambda exonuclease. By means of a streptavidin-biotin interaction, the generated targets were labeled with streptavidin-coated superparamagnetic nanoparticles (Micromod, 250 nm) and consequently hybridized with complementary probes previously immobilized on top of two separated columns of 15 MR sensors each. The stray field originated from the magnetic particles, after the application of an external magnetic field, allows to infer the number of captured analytes on top of the sensors. Analyte concentrations in the picomolar range were detected making this approach suitable for the detection of low copy number targets originated from blood samples of cancer patients. In future work, we envision to exploit the 30 sensing sites of the microarray platform for the multiplex detection of different targets for the combined identification of decisive biomarkers in cancer diagnostics.

10:30 Coffee Break with Exhibit and Poster Viewing


ALTERNATE APPLICATION AREAS FOR CFDNA 

11:00 Sequencing of Plasma DNA for the Diagnosis of Infection and Rejection in Organ Transplantation

Iwijn De Vlaminck, Ph.D., Researcher, Quake Lab, Stanford University

In this talk, I will present results of our efforts to develop DNA-sequencing based diagnostics of both rejection and infection in organ transplantation. We have analyzed cell-free DNA in plasma samples from a large cohort of transplant recipients (>700 samples, >100 transplant recipients). We find that donor-derived cell-free DNA is an informative marker of rejection. An analysis of non-human derived sequences reveals strong interactions between the virome and immune strength.

11:30 Cell-Free DNA: A Noninvasive Monitoring Tool for Renal Injury

Minnie Sarwal, M.D., FRCP, DCH, Ph.D., Professor, Pediatrics and Transplant Nephrology, CPMC; Director, The BIOMARC Program for Personalized Medicine, CPMCRI, Sutter Health Care

Organ transplantation is the treatment of choice for patients with end stage organ failure. The donor organ in the recipient body experiences several immune and non-immune related insults. Improved immunosuppressive drugs and surgical techniques and procedures have helped in the short-term outcome in terms of graft survival, however in the absence of effective and specific methods of monitoring of transplanted organ the long-term outcome is still far from satisfactory. Currently available methods are far from optimal as they are either not specific or are invasive. This reality has inspired several groups to look for more effective and semi- or noninvasive methods of diagnosis of transplant injury. CfDNA has been considered as a diagnostic biomarker for different health issues including transplant injury. Urinary dd-cfDNA after renal transplantation has patient specific thresholds and reflects the apoptotic injury load of the donor organ. Serial monitoring of urinary dd-cfDNA can be a surrogate sensitive but non-specific biomarker of acute injury in the donor organ.

12:00 pm Prognostic Utility of Cell-Free DNA in Sepsis: Basic and Translational Studies

Dhruva Dwivedi, Ph.D, Research Associate, Department of Medicine, Division of Hematology, David Braley Research Institute, Thrombosis and Atherosclerosis Research Institute (TaARI), McMaster University

Sepsis remains a major cause of morbidity and mortality in ICU patients. Our studies focus on the mechanistic links between cell-free DNA, blood coagulation, and inflammation. My presentation will highlight findings from in vitro studies as well as translational studies in septic patients and mouse models of sepsis.

12:30 Close of Symposium



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