Next Generation Dx Summit

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The isolation, sequencing and evaluation of cell-free DNA (cfDNA) for a variety of applications will be reviewed and the clinical utility of these new methods will be considered. The source of cell free DNA, methods to analyze it and use in clinical protocols will be measured against competing approaches such as circulating tumor cells. Cell free circulating DNA is being used to monitor disease recurrence, as a non invasive technique for prenatal testing and as a surrogate biomarker for cancer. Characterizing cancer based on genomic profiling of cfDNA will allow greater understanding of the biology and our ability to diagnose and treat it more effectively.

Scientific Advisory Board

Luis A. Diaz, M.D., Associate Professor, Oncology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center
Dave S. B. Hoon, MSc, Ph.D., CSI & Director, Molecular Oncology; Director, JWCI Sequencing Center, John Wayne Cancer Institute

 

 

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Recommended Pre-Conference Short Courses*

Overcoming Challenges of Working with FFPE Samples

Sample Prep Methods for Liquid Biopsy and POC Molecular Diagnostics

*Separate registration required

 

WEDNESDAY, AUGUST 20

10:30 am Registration


PLENARY SESSION: Think Tank on Next-Generation Sequencing Diagnostics

11:00 Chairperson’s Opening Remarks

11:10 Discussion: Regulatory Review of Clinical Sequencing Assays

Harry GlorikianModerator: Harry Glorikian

 

Jennifer DickeyGuest Speaker: Jennifer Dickey, RAC, Ph.D., Office of In Vitro Diagnostics, DIHD, US Food and Drug Administration

 

In November of 2013, the FDA issued the first clearances of Next Gen Sequencing- (NGS) based assays. There have additionally been a number of clinical trials approved recently that utilize NGS-based assays for patient enrollment or stratification. In light of the expanding roles that new sequencing technologies are playing in clinical decision making, this talk will focus on critical elements that FDA considers when evaluating NGS validation using the recent clearances/approvals as examples. There will also be a discussion of any new communications that FDA has issued in regard to the regulatory review of NGS- based assays. Following the discussion there will be a Q&A with the audience.

11:55 Next-Generation Sequencing in Clinical Practice: Case Reports of Clinical Utility and Reimbursement  

Elaine LyonModerator: Elaine Lyon, Ph.D., Medical Director, Molecular Genetics, ARUP

 

Case Presenters:

Andrea Ferreira-Gonzalez Andrea Ferreira-Gonzalez, Ph.D., Professor, Pathology; Director, Molecular Diagnostics Lab, Virginia Commonwealth University

 

Madhuri HegdeMadhuri Hegde, Ph.D., FACMG, Associate Professor, Human Genetics; Executive Director, Emory Genetics Laboratory, Emory University School of Medicine

 

The landscape of next-generation sequencing diagnostics is changing rapidly. Clinical laboratories are offering highly complex tests using new technologies, but face challenges in reimbursement. To be reimbursed for these tests, laboratories will need to address clinical utility as well as clinical validity. Clinical cases that demonstrate the utility of genomic oncological and inherited disease testing will be presented. Experiences with reimbursement of these tests will be discussed.

12:40 pm Enjoy Lunch on Your Own


KEYNOTE SESSION:
SEQUENCING AT THE LIMITS OF DETECTION

1:50 Chairperson’s Opening Remarks (Sponsorship Opportunity Available)

2:00 Life at the Single-Molecule Level: Single-Cell Genomics

Sunney XieSunney Xie, Ph.D., Mallinckrodt Professor, Chemistry and Chemical Biology, Harvard University

Point mutation and copy number variation in DNA can now be studied at the single-cell level by whole-genome amplification and sequencing. We will describe experiments probing the biology of meiosis and cancer, demonstrate proof of principle of selecting oocytes in in vitro fertilization to avoid miscarriage and genetic diseases and show individual CTCs can be sequenced, providing tumor genetic signatures for personalized therapy.

2:45 Genome-Wide Mapping of DNA Rearrangements in Single Cells Using DNA Template Strand Sequencing

Peter M. LansdorpPeter M. Lansdorp, M.D., Ph.D., FRSC, Scientific Director, European Research Institute for the Biology of Ageing, University Medical Center, University of Groningen; Senior Scientist, Terry Fox Laboratory, BC Cancer Research Center; Professor, Division of Hematology, Medicine, University of British Columbia

Making libraries from tiny amounts of DNA is now possible. We can generate quantitative data on DNA template strands of all parental chromosomes in a single cell using Strand-Seq, allowing mapping of sister chromatid exchange events at very high resolution and mapping of various genomic rearrangements. Its power for assembly and fine-tuning of reference genomes and characterization of diverse “cancer genomes” will be illustrated.


INTRODUCTION TO CFDNA AND BIOLOGY

3:30 Chairperson’s Remarks: Introduction and Overview

Luis DiazLuis A. Diaz, M.D., Associate Professor, Oncology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center

 

4:00 Refreshment Break in the Exhibit Hall with Poster Viewing

4:45 Detection of Circulating Tumor DNA in Early and Late-Stage Human Malignancies

Chetan BettegowdaChetan Bettegowda, M.D., Ph.D., Assistant Professor, Neurological Surgery, Johns Hopkins University School of Medicine

The development of non-invasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital PCR-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. This presentation will review the results of the study.

5:15 Circulating Tumor DNA Use for Noninvasive Analysis Of Cancer Drug Resistance Mechanisms

Muhammed MurtazaMuhammed Murtaza, MBBS, Research Assistant Professor and Co-Leader, Program in Circulating Nucleic Acids, TGen, Translational Genomics Research Institute

Cancers acquire resistance to systemic treatments through molecular evolution. This necessitates analysis of relapsed tumors to understand mechanisms of acquired resistance and to choose subsequent treatments. However, repeated biopsies are costly, invasive and confounded by spatial heterogeneity. Circulating tumor-specific DNA allows analysis of the cancer genome non-invasively. I will share proof-of-principle examples where analysis of serial plasma samples was used to assess mechanisms of drug resistance advanced solid cancer patients.

5:45 Rapid Isolation and Detection of Cancer Related Circulating Cell-Free DNA and RNA from Patient Blood and Plasma Samples

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

Circulating cell-free (ccf) DNA and ccf-RNA continue to become more widely used for cancer detection, and may ultimately allow “liquid biopsy” based diagnostics. This talk will review how we demonstrated a dielectrophoretic- (DEP) based approach that allows ccf-DNA/RNA to be isolated in 10-15 minutes directly from a small volume (25ul-50ul) of blood or plasma.

6:15 Close of Day



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