Next Generation Dx Summit

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The unthinkable is now possible. Next-generation sequencing (NGS) has evolved rapidly, reducing costs and making cancer genome sequencing more routine. Traditional approaches requiring bulk DNA or RNA from multiple cells only provide global information on average states of cell populations without resolving genomic differences in heterogeneous tumors. But now, whole-genome amplification (WGA) and NGS advances enable analyses of single cells to detect variations in individual cancer cells and dissect tumor evolution. Thus, single-cell sequencing will improve oncology by detecting rare tumor cells early, monitoring circulating tumor cells (CTCs), measuring intra-/intertumor heterogeneity, guiding chemotherapy and controlling drug resistance – all aiding cancer diagnosis, prognosis and prediction and leading to individualized cancer therapy.


 

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Recommended Pre-Conference Short Courses*

NGS Data Analysis – Determining Clinical Utility of Genome Variants

NGS as a Diagnostics Platform

*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.

3:30 Molecular Characterization of Circulating Tumor cells: Opportunities and Challenges

Denis Smirnov, Associate Scientific Director, US Biomarker Oncology, Janssen R&D US

Molecular characterization of circulating tumor cells (CTCs) offers a unique opportunity  to dynamically monitor metastatic process so optimal therapy regimens can be developed and applied in clinic.  Potential and challenges of molecular characterization of CTCs will be discussed. 

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


SINGLE-CELL ANALYSIS:
FROM DIAGNOSIS TO THERAPY

4:40 Chairperson’s Remarks

James Hicks, Ph.D., Research Professor, Cancer Genomics, Cold Spring Harbor Laboratory 

4:45 Quantitative Single-Cell Analysis of Patient-Derived Cancer Stem Cells Identifies Unique Chemotherapy Response Signatures

Michael Masterman-SmithMichael Masterman-Smith, Ph.D., President and CEO, Harmony Biosciences, Inc.

Microfluidic chip-based assay technologies permitting molecular characterization of microscopic patient samples may transform cancer diagnosis and treatment. A quantitative immunocytometry approach was used to profile EGFR-PTEN-Akt-mTOR signaling in single cells of human cancer stem cell (CSC) lines in ~1000 cells/sample. Bioinformatic analysis revealed drug response and resistance signatures and showcased the clinical utility of microfluidics platforms and personalized CSC models.

5:15 Diagnosing Intratumor Heterogeneity in Breast Cancer with Single-Cell Genome Sequencing

Yong WangYong Wang, Ph.D., Senior Postdoctoral Fellow, Nicholas E. Navin Laboratory, Genetics, Bioinformatics, MD Anderson Cancer Center

We developed a whole-genome and exome single-cell sequencing approach to study clonal diversity and mutational evolution in breast cancer. Our data shows that copy number profiles are highly stable in the tumor mass, while point mutations evolve gradually, generating extensive clonal diversity. We apply these tools to diagnose genetic heterogeneity in breast tumors and develop new therapeutic targeting strategies.

5:45 Single-Cell Metabolomics and Proteomics: Toward Complementing Single-Cell Genomics for Cancer Research

Peter NemesPeter Nemes, Ph.D., Assistant Professor, Chemistry, George Washington University

Single-cell mass spectrometry is a recent technological development. Here we demonstrate that it can detect, identify and profile hundreds of metabolites and peptides in single isolated cells without a priori knowledge of specimen composition or chemical labels. The combination of single-cell genomics and single-cell mass spectrometry would extend bioanalysis to the level of systems biology, potentially aiding cancer research.

6:15 Close of Day

6:00 Dinner Short Course Registration


Recommended Dinner Short Course*

6:30-8:30 pm Regulatory and Reimbursement Issues with NGS and Multiplex Assays

*Separate registration required



Day 1 | Day 2 | Short Courses | Download Brochure