Short Courses

Copy Number Variation

Monday, March 15, 2010

9:00 am – 12:00 pm

(SC1) A PRACTICAL GUIDE TO FINDING REGIONS OF CHROMOSOMAL COPY NUMBER GAIN OR LOSS

The increased popularity and simplification of large scale gene expression experiments have enabled many scientists to incorporate comparative genomics into their routine experimentation. With the increased availability of SNP arrays, large scale assays to measure differences in abundance of genomic DNA are now available. However, the analysis methods are not as mature as methods to identify differentially expressed genes. This course will compare and contrast different methods used to find regions of copy number change and provide a practical guide to finding and validating these genomic regions. Topics to be covered include:

• How are copy number and expression assays similar as well as different
• A detailed description of at least one method of identifying breakpoints and regions of common copy number
• A guide to some key filtering tools to limit and narrow a lengthy list of genomic segments with aberrant copy number
• Visualizing copy number data at a variety of levels

Instructors:
Thomas J. Downey, President, Partek, Inc.
Min Li, Ph.D., Field Application Specialist, Partek, Inc.

Sequencing Data Storage

Monday, March 15, 2010

9:00 am – 12:00 pm

(SC2) DATA MANAGEMENT AND STORAGE: THE NEXT HURDLE FOR NGS
The explosion in demand for next-generation sequencing platforms brings with it a monumental challenge for any research group, organization or facility in setting up the pipeline and infrastructure to handle and manage the torrent of data about to be unleashed. These challenges are only intensifying as labs audition and integrate new platforms, expand capacity, and try to balance a growing array of projects, users and applications. This introductory short course, co-organized by The BioTeam and CHI, is intended to provide in-depth, interactive guidance on the essential do’s and don’ts in coping with the prodigious volumes of data produced in next-generation sequencing. This workshop will focus on the application of new technologies to enable Pfizer’s DNA research.

Additional topics include:

• Building the IT infrastructure, software and LIMS to handle sequencing data
• Strategies for data storage, quality control and analysis
• Needs, design, and maintenance for massive storage and back-up
• Methods for archiving and managing the life cycle of data
• Cost control
• Cloud computing
• Using WIKI technology
• Storage and data management technologies

Course participants are encouraged to share their challenges and bring specific data storage requirements. Ample time will be given for interactive discussion. This collegial atmosphere will encourage productivity from your NGS investment. This course is designed for researchers who have made a NGS platform purchase(s) or are considering one in the near future.

Instructors:
Chris Dagdigian, Founding Partner & Director of Technology, BioTeam, Inc.
Giles Day, Senior Director, BBC Informatics, Pfizer Global R&D
Adam Kraut, Scientific Consultant, BioTeam, Inc.

Quantitative PCR

Sponsored by
Tuesday, March 16, 2010

5:30 - 8:30 pm

(SC3) GETTING THE MOST OUT OF YOUR REAL-TIME PCR EXPERIMENTS

Topics to be addressed in this course include:

• Review of critical assay design parameters
• Optimization of assay performance from experiment set-up to data analysis
• Troubleshooting common problems that impact assay efficiency, reproducibility and sensitivity
• Introduction to MIQE - recommended guidelines for publication of qPCR experiments
• High Resolution Melt Analysis: Power, Potential and Limitations

Who Should Attend & Why: All levels of PCR users are encouraged to participate and will learn good laboratory practices to help you optimize your real-time PCR assays and effectively troubleshoot your results. This will be an interactive workshop - attendees are encouraged to bring questions, data files and problem examples with them. A light dinner will be served at the course.

Instructors:
Francisco Bizouarn, International Field Application Specialist, Gene Expression Division, Bio-Rad Laboratories
Carl Fisher, Ph.D., Product Manager, Gene Expression Division, Bio-Rad Laboratories