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RNA-Seq Experimental Design and Bioinformatics

Genetic Privacy: Technology and Ethics

Microbes and Human Health: The What, Where, How and Why 

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Short Course Agenda

Pre-Conference Short Courses
Monday, August 13

8:00 – 8:30 am Pre-Conference Short Course Registration

8:30 -11:30 Recommended Pre-Conference Short Courses*


SC1: Sequencing 101  

8:30 Chairperson's Opening Remarks


8:40 A Brief History of Next-Gen Sequencing

Kevin DaviesKevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Just as the advent of next-gen sequencing in 2005-06 has revolutionized basic genomic research, a new wave of NGS “3rd-generation” technologies seems destined to finally bring about the $1,000 genome and revolutionize clinical diagnostics, particularly in the realm of exome and whole-genome sequencing. Kevin Davies, author of The $1,000 Genome, will dicuss the recent history of NGS, emerging trends in nanopore sequencing and other technologies, and highlights some outstanding challenges facing the NGS community


9:15 A Guide to Today's NGS Platforms and a Peek Into the Future

Shawn BakerShawn C. Baker, Ph.D., Knowledge Bank Curator, BlueSEQ

The field of next-generation sequencing (NGS) has been experiencing explosive growth over the past several years and shows little sign of slowing down. The increasing capabilities and dramatically lowered costs have expanded NGS's reach beyond that of the human genome into nearly every corner of biological research. An overview of the platforms on the market today, including an assessment of their relative strengths and weaknesses, will be presented. The presentation will conclude with a peek into where the technology is going and what will be available in the future.

9:50 Networking Coffee Break

10:10 Considerations for Next-Gen Sequence Assembly and Analysis Software Selection

Tom Schwei, Vice President and General Manager, DNASTAR, Inc.

Next-gen sequencing won’t help you solve your problems if you don’ t have the right software to meet your needs.  This interactive session will focus on the key issues to be considered when selecting software to support your next-gen sequence assembly and analysis projects.  This discussion will help you identify which factors are most important to consider when selecting appropriate software and which factors probably don’t need to be heavily weighted in your selection process.  

10:45 Developing a Sample Prep Pipeline for Next-Generating Sequencing

Danielle Dionne, Senior Process Development Associate, Genomics Platform, The Broad Institute

Choosing and buying a next generation sequencer is only the beginning, you need to be able to create libraries that will meet your specific needs. This talk will cover a range of available kits and technologies as well as strategies for controlling quality. The presentation will include considerations for creating a robust and scalable sample prep pipeline at your institution.

11:20 Short Course Wrap-Up

11:30 pm End of Short Course One


SC1 Speaker Bio's 


Shawn C. Baker, Ph.D., Knowledge Bank Curator, BlueSEQ 

Shawn Baker is a marketing consultant with over 13 years experience in the field of genomics. Having received his Ph.D. at the University of California - Davis, he started his career as a Research Scientist at Illumina when it was a 15-person startup. After spending several years at the bench developing gene expression array products, he transitioned to Product Marketing where he led a team in charge of Illumina’s Expression and Regulation sequencing portfolio. Shawn is currently developing BlueSEQ’s Knowledge Bank, a neutral source of next generation sequencing information.

Tom Schwei, Vice President and General Manager, DNASTAR, Inc.

Tom is currently the Vice President, General Manager and CFO of DNASTAR, Inc., where he has been employed since 2004.  DNASTAR is a developer of desktop software solutions for molecular biologists, specializing in sequence assembly and analysis applications.  The company has been in business for more than 25 years.  Tom has overall day-to-day responsibility for the business operations, sales and marketing. Tom has 30 years of business experience, including 17 years working in senior management positions with biotech companies.  Tom is a Certified Public Accountant and a graduate of the University of Wisconsin, Milwaukee. 


SC2: A Practical Guide to Choosing the Right SNP Detection Tool


8:30 Chairperson’s Opening Remarks

8:40 Comparison Study of NGS SNP Detection Tools

Ming Yi, Ph.D., IT Manager, Functional Genomics/Bioinformatics Support Group, Advanced Biomedical Computing Center, SAIC-Frederick, FNLCR

- Brief background and introduction for the current status of SNP detection field and each of the selected tools to be compared
- Description of our benchmark exome-seq data with pedigree info and SNP array data from matched-samples and why they are useful for comparison of these tools for SNP call     quality
- Comparison and validation results of these tools using the benchmark data
- Conclusion and take-home message
- Q & A session

9:50 Networking Coffee Break

10:10 Detailed Illustration of the Practical Usage of Each SNP Detection Tool

Ming Yi, Ph.D., IT Manager, Functional Genomics/Bioinformatics Support Group, Advanced Biomedical Computing Center, SAIC-Frederick, FNLCR


-Brief introduction of practical aspects of the tools (e.g., download, installation, interface, running environment, basic system requirement etc)
-Practical command lines for command-driven tool(s), parameter options, wrapper script examples for the command-driven tools, interface for commercial tools
-Brief discussion of result files and some diagnosis plots, etc.
-Q & A session

11:20 Short Course Wrap-Up

11:30 End of Short Course Two




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