Table 1: New Sequencing Technology for Clinical/Diagnostics or Field Applications
Yu-Hui Rogers, Ph.D., Vice President, Core Technology Development and Services, J. Craig Venter Institute
• How to match the right platform and assay with the right target?
• How to establish standards and validation protocols?
Table 2: Alleviating Bottlenecks Created by NGS Sample Preparation
Steven Kain, Ph.D., Director, Product Marketing, NuGEN Technologies, Inc.
• What are the bottlenecks limiting your ability to process more samples by NGS?
• How important is it to standardize protocols?
• Is automation the answer?
Table 3: Successful Cancer Research Approaches Using Next-Generation Sequencing
Tom Schwei, Vice President and General Manager, DNASTAR, Inc.
• Whole genomes vs. exomes vs. targeted genes
• Use of known cancer causing genes and mutations and key database sources for analysis
• Approaches to comparing multiple samples (healthy vs. cancerous tissue, responsive vs. non-responsive samples, etc.)
• Successful approaches and tools to support success
Table 4: How Much Sequencing Should You Do?
Jeffrey Rosenfeld, Ph.D., Senior Scientific Programmer ,University of Medicine and Dentistry of New Jersey
• Is low-coverage and imputation sufficient?
• Should 30-40x be termed high-depth or is there a reason to do higher coverage
• What is the value of pooled sequencing?
Table 5: Geo Distributed NGS Research Collaboration Infrastructure
Jose L. Alvarez, World Wide Director Life Sciences, DataDirect Networks, Inc.
• How can a public or private network be leveraged to virtualize distributed research effort?
• What are the challenges with existing NGS data transfer methods?
• How can we implement a secure, easy to manage and affordable NGS data transfer infrastructure?
Table 6: NGS Technology Management in the Biomedical Environment
Brent Richter, Ph.D., Director, Enterprise Research IS, Partners Healthcare
• What are the current challenges?
• When and where should NGS investments be made?
- Is sequencing a commodity?
- Does it make sense for organizations with regular, but smaller demand to outsource?
- Where is the inflection point?
• What is the current clinical utility on such investments?
Table 7: The “Healthy” Reference Genome
Elizabeth A. Worthey, Ph.D., Assistant Professor, The Human and Molecular Genetics Center, Pediatrics, Bioinformatics, Medical College of Wisconsin
• How do we (or do we) deal with the fact that we know the reference genome is not the “Healthy Genome”?
• Should we try to “fix” this to create the “Omni” human reference genome?
Table 8: Successful Sequencing
Shunsheng (Cliff) Han, Ph.D., Team Leader, Research and Development, Bioscience Division, Los Alamos National Laboratory
• What are the special applications for each platform?
• What are the critical planning steps for sequencing projects?
• How to make the process produce uniform results?
• Which platform is best for my institute?
• How to find needles through the hay (metagenomic analysis)?
Table 9: Beyond Cost Per Base: Are We Getting Our Money's Worth with NGS?
Ghia Euskirchen, Ph.D., Director, DNA Sequencing Program, Center for Genomics and Personalized Medicine, Stanford University School of Medicine
• What are the hidden costs and considerations in going from reagents to data?
• How do emerging, nth generation technologies perform in a shared resource setting?
• When is 'good' good enough? Have some protocols or aspects of NGS stabilized, and if so which ones?
Table 10: Rapid Bacterial Phylotyping and Genome Sequencing
Armand E. K. Dichosa, Ph.D., Research Associate, Genome Science/JGI, Los Alamos National Laboratory
• Can rapid screening and genome amplification be done simultaneously?
• What are the current methods and limitations used to accomplish this?
• Can we improve upon them?
Table 11: Approaches to Analysis of RNA-Seq Data
Jennifer Beane, Ph.D., Assistant Professor, Section of Computational Biomedicine, Department of Medicine, Boston University Medical Center
• What are effective quality control metrics and batch correction strategies?
• What are successful strategies for data filtering and differential expression analysis?
• What approaches are researchers finding successful for detection of novel transcripts and/or alternative splicing?
Table 12: Sequencing of the Human Microbiome
Laura Wegener Parfrey, Ph.D., Research Scientist, Chemistry and Biochemistry, University of Colorado
• What are the key challenges (e.g. metadata quality, differences in sequencing platform) of combining and comparing studies?
• Are new tools (visualizations, analyses, etc) necessary to make sense of the wealth of data?
• What are the current critical limitations?
Table 13: Transcriptome Profiling Using Microarrays and NGS
Nalini Raghavachari, Ph.D., Core Director, Genetics and Development Biology Center, NHLBI, The National Institutes of Health
• Which platform to choose for gene expression analysis
• Should the RNA samples be reduced for ribosomal RNA?
• What is the ideal input amount without compromising the sensitivity on low expressors?
• Study Design and batch processing- How to correct for variability between batches in NGS?
Table 14: Development of a Clinically Actionable Gene Sequencing Panel
Eric Duncavage, M.D., Assistant Professor, Pathology, Anatomic and Molecular Pathology; Laboratory and Genomic Medicine, Washington University
• Working with FFPE-derived DNA
• Identifying mutations beyond single nucleotide variation
• Sequence sensitivity issues in cancer diagnostics
Table 15: Capturing Genomes of Uncultured Bacteria
Jeffrey S. McLean, Ph.D., Staff Scientist, Microbial and Environmental Genetics, J. Craig Venter Institute
• What assembly methods are available?
• How are contaminants dealt with?
• How are genomes made available to the public?
• What are the future applications?