Next Generation Dx Summit

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THURSDAY, AUGUST 21


7:30 – 8:25 Problem-Solving Breakout Discussions with Continental Breakfast

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.

Making Single-Cell Analysis Cost Effective for Clinical Use

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

  • Methods for capture: What are the tradeoffs?
  • Combining RNA, DNA and protein analysis
  • What genomic assays are most informative?
  • Can assays be certifiable?

Finding a Needle in a Haystack: Towards Diagnosing Rare Soft Tissue Cancer Stem Cells (CSCs)

Moderator: Michael Masterman-Smith, Ph.D., Entrepreneurial Scientist, UCLA California NanoSystems Institute

  • Rethinking companion diagnostics for cancer to incorporate analysis of CSCs
  • Current direct methodologies of CSC detection/isolation
  • Current proxy methodologies of CSC detection/isolation
  • The hope and promise of single-cell assay tools and technologies

Why Single-Cell Sequencing?

Moderator: Jan Vijg, Ph.D., Professor and Chairman, Genetics, Albert Einstein College of Medicine

  • Sample limitations, e.g., prenatal diagnostics and CTCs
  • To study cell-to-cell variation, e.g., in tumors as well as normal tissues
  • To overcome technological constraints, e.g., detecting somatic mutations
  • Cell-to-cell fluctuations in gene expression can easily impair function, yet can be undetectable by measuring averages
  • How many different cell types are there?
 

TIPS ‘N TRICKS FOR A NEW SEQUENCING FRONTIER

8:25 Chairperson’s Opening Remarks

Jan Vijg, Ph.D., Professor and Chairman, Genetics, Albert Einstein College of Medicine

8:30 1000 Genomes: Methods for CTC Analysis

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

We will discuss methods for cell capture, amplification and informatics for CNV profiling and the focused resequencing of rare circulating cells from various forms of metastatic cancer.

 

9:00 Single-Cell Molecular Profiling of a Brain Tumor

John F. ZhongJohn F. Zhong, Ph.D., Associate Professor, Pathology, University of Southern California School of Medicine

With microfluidic technology, we are able to obtain transcriptomes of single tumor cells from a brain tumor. Comparing mutations detected by next-generation sequencing in a primary tumor and cell lines derived from a primary tumor, we identified genes that play a role in treatment-resistant clones. (July 2014 Interview)  


 

 BD Biosciences9:30 Flow Cytometric Sorting of Dissociated Cells from PDX Model Derived Human Solid Tumors Enables Targeted Downstream Analysis 

RainerBRainer Blaesius, Technology Manager, Genomic Sciences Group, BD Technologies

Current molecular analysis methods for solid tumor biopsies generally use bulk material and ignore intratumor heterogeneity. We have developed methods to dissociate tissue samples and select subpopulations based on FACS® sorting. Our methods have been used for species specific sequencing as well as single cell index sorting to enable a variety of downstream analysis modalities.

 

 


 

Maverix Biomics9:45 Streamlining Single-Cell RNA Sequencing Analysis for Biologists with the Maverix Analytic Platform 

Patricia_ChanPatricia Chan, CTO, Maverix Biomics, Inc.

With the advancement of single-cell sequencing methodologies, the demand for analytic tools to handle complex data has grown rapidly. We will present the Maverix Analytic Platform, a cloud-based environment built for biologists that leverages best-in-class tools and provides an integrated UCSC-genome browser to enable visualization of results in broad context.
 

 

10:00 Coffee Break in the Exhibit Hall with Poster Viewing

10:45 Genome-Wide Mapping of DNA Rearrangements in Single Cells Using DNA Template Strand Sequencing

Mark HillsMark Hills, Ph.D., Research Scientist, Peter M. Lansdorp Laboratory, BC Cancer Research Centre

While genomic sequencing from single cells push the boundaries of current technologies, an unprecedented amount of new information can be gained from these types of analyses. Using Strand-seq, we have generated quantitative data across all chromosomes within a single cell that presents us with a novel means to characterize genomes. This characterization includes identifying structural variation within the human population, together with the fine-mapping of diverse “cancer genomes”, whereby in a single cancer we are able to localize common structural changes as well as rare variants present in a small subset of cells. In addition, the power of Strand-seq to assemble and fine-tune reference genomes will be illustrated.

11:15 Genome-Wide Analysis of Copy Number Variations and Mutation Profiles of Single Tumor Cells Using Massively Parallel Paired-End Sequencing

Parveen KumarParveen Kumar, Research Scientist, Thierry Voet Laboratory, Human Genetics, University of Leuven

We will compare different whole-genome amplification methods to analyze single cells for CNVs. We will also discuss the study of intra-tumor genetic heterogeneity in breast cancer to single-cell resolution, as well as the study of CTCs at single-cell level using low-coverage paired-end sequencing for copy number variation (CNV) analysis and targeted re-sequencing of 453 cancer-related genes for somatic mutation analysis. (July 2014 Interview)  


Featured Presentation 

11:45 Single-Cell Genomics in Aging and Cancer

Jan VijgJan Vijg, Ph.D., Professor and Chairman, Genetics, Albert Einstein College of Medicine

Massively parallel sequencing has enabled the quantification and characterization of high-abundant DNA mutations in the tumor genome. However, low-abundant mutations in the normal and tumor genome thus far remain out of reach. We are using single-cell genomics assays to study the landscape of low-abundant somatic DNA mutations in the genome of normal animal and human tissues from which tumors arise.

12:15 pm Sponsored Presentation (Opportunity Available)

12:45 Luncheon Presentations: (Sponsorship Opportunities Available) or Lunch on Your Own

1:45 Session Break


Translating Into the Clinic

2:00 Chairperson’s Remarks

Edward Abrahams, Ph.D., President, Personalized Medicine Coalition

2:05 First FDA Clearances of Next-Generation Sequencing Technology and Tests 

Živana TežakŽivana Težak, Ph.D., Associate Director, Science and Technology, Personalized Medicine, Office of In Vitro Diagnostic Device Evaluation and Safety (OIVD), Center for Devices and Radiological Health (CDRH), FDA

With the rapid emergence of novel, ultrahigh-throughput technologies, the FDA has met new regulatory challenges while still applying scientific evidence-based oversight of diagnostics. Recently, the FDA authorized for marketing four high-throughput gene sequencing diagnostic devices, marking the first time a next-generation sequencing system has received FDA premarket clearance. The regulatory pathway and performance evaluation for these devices will be discussed.

2:35 Magnetic Microchip Technology for Large-Scale Single-Cell Analysis

Benjamin Yellen, Ph.D., Associate Professor, Mechanical Engineering and Materials Science, Duke University

Here we describe a microchip technology that can organize single cells and cell pairs into large arrays, continuously evaluate the single cell and cell pair behavior for long durations when exposed to different ambient conditions and/or pharmaceutical compounds and retrieve specific cells for downstream gene expression analysis and/or clonal expansion. The comprehensive characterization of individual cell-cell interactions from the live state to the cell lysis is paramount to furthering our understanding of immunology, cancer and neuronal networks, and will lead to the development of new therapies for human disease.

3:05 Cross-Cancer Analysis

Theresa ZhangTheresa Zhang, Ph.D., Vice President, Research Services, Personal Genome Diagnostics





3:35 PANEL DISCUSSION: From Discovery to Diagnostic

Personalized medicine principles now influence business plans across pharma. However, the business model underpinning individualization, which requires integrating drugs and diagnostics, is unclear. Implementing discovery and development programs that capitalize on this integration has been challenging, but not impossible. This panel will explore the path from scientific discovery to the clinic, looking at the key drivers of commercial success.  

EdwardAbrahamsModerator: Edward Abrahams, Ph.D., Personalized Medicine Coalition


 

 

 

 

 

Panelists:

Elaine LyonElaine Lyon, Ph.D., ARUP

 

 

 

 

 

 

Michael Masterman-SmithMichael Masterman-Smith, Ph.D., UCLA California NanoSystems Institute

 

 

 

 

 

 

Živana TežakŽivana Težak, Ph.D., FDA

 

 

 

 

 

 

Benjamin Yellen, Ph.D., Duke University

 

4:05 Close of Conference  

 



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