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Managing Your NGS Pipeline Effectively and Productively

June 20, 2011

1:30 - 4:30 pm

 

The breadth of responsibilities and time management for genomics laboratory managers can be overwhelming. This short course addresses the daunting yet possible task of managing an NGS lab at peak productivity. Learn from lab managers as they share their strategies for success and how they direct their laboratory on a daily basis.

Who Should Attend: 
This course is specifically designed for genomics laboratory personnel (Core Directors, Lab Managers, Heads, Team Leads, or Senior Technicians) who own an NGS platform or are considering purchasing one in the near future. It also caters to downstream data managers supporting genomics laboratories research.

Lab Managers:
Toumy Guettouche, Ph.D., Director, Oncogenomics Core Facility (OCF),  the Sylvester Cancer Center, University of Miami School of Medicine
Michael W. Smith, Ph.D., Vice President, Director, Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at Frederick
Jimmy Woodward, Operations Manager, Genome Center, National Center for Genome Resources
Ryan Johnson, Senior Process Development Associate, Technology Development, Broad Institute


 

PRESENTATIONS:

Automating Your Second Generation Sequencing Pipeline:  What to Consider for Library Preparation and Sequence Capture
Toumy Guettouche, Ph.D., Director of Oncogenomics Core Facility (OCF) at the Sylvester Cancer Center, University of Miami School of Medicine

  • Overview of automation hardware and space requirements.
  • Advantages of different methods for library preparation in terms of performance and automation.
  • How to convert library preparation and sequence capture protocols from manual to automated.
  • How to implement quality control steps including Bioanalyzer/GX and qPCR.
  • How to deal with constantly changing protocols.

 

Gouttouche ToumyToumy Guettouche, Ph.D., is the Director of Oncogenomics Core Facility (OCF) at the Sylvester Cancer Center, University of Miami School of Medicine. Dr. Guettouche is also the Director for New Technology Assessment and Implementation, Hussman Institute for Human Genomics-Center for Genome Technology, and an Assistant Professor at Hussman Institute for Human Genomics, Dr. John T. MacDonald Foundation Department of Human Genetics. Before joining the University of Miami he worked for Bayer Diagnostics and Digene in diagnostic assay development. Dr. Guettouche holds a Ph.D. in Biochemistry and Molecular Biology from the University of Miami.

A Two Year Odyssey of Setting Up and Running Sequencers in a Core Laboratory for the NCI
Michael W. Smith, Ph.D., Vice President, Director, Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at Frederick
In March 2009, the Center for Cancer Research Sequencing Facility opened from the ground up with three genome analyzers.  A fourth was added in 2009, two in 2010.  Progress, lessons learned, challenges and opportunities for the future will be discussed in regards to serving numerous NCI investigators and bringing these sequencers into routine operation. 

Smith MichaelDr. Smith directs the Genetics and Genomics Group of SAIC-Frederick’s Advanced Technology Program. He provides scientific expertise and vision along with management oversight to the Laboratory of Molecular Technology and the Sequencing Facility. Dr. Smith earned a Ph.D. in genetics from the Johns Hopkins University and completed postdoctoral training in molecular genetics and evolution at the University of California, San Diego. Subsequently, he was the assistant director of the Human Genome Center at the Salk Institute for Biological Sciences and, most recently, a principal investigator in the Laboratory of Genomic Diversity (LGD) at NCI-Frederick studying HIV-1/AIDS, host genetics, and the genetics of other human diseases. Dr. Smith brought and implemented the high-throughput strategies of the genome project to the LGD, and was a key player in utilizing these approaches to successfully address the host genetics of HIV-1 infection and progression along with pioneering the development of the novel gene identification technique of admixture mapping.  Dr. Smith has published over one hundred peer-reviewed publications.

Highly Parallel Project Management in an NGS Core Lab
Core sequencing labs often need to manage dozens of concurrent sequencing and analysis projects.  The multiplicity of sequencing applications and analysis strategies paired with the variable scale of projects requires creative project management.  This presentation will cover methods and technologies which can assist the NGS lab manager.

Jimmy Woodward Jimmy Woodward is the operations manager of the genome center at the National Center for Genome Resources.  He oversees the operations of several high-throughput sequencing platforms as well as a genotyping array core.  He advises scientists on NGS experimental design and coordinates lab and informatics operations.  Before joining NCGR, he worked in the lab of Dr. Doug Cook at the University of California, Davis, department of plant pathology.  He holds an A.S. in Biotechnology from American River College.

 

One Pipeline, Many Protocols:  Reducing Redundancy in NGS Sample Preparation
Ryan Johnson, Senior Process Development Associate, Technology Development, Broad Institute
Current next generation sequencing technologies employ a vast array of different sample preparation methods.  Maintaining multiple versions of similar protocols can consume excessive resources of machinery and personnel often on redundant tasks.  Here we present techniques of modularization and automation that can accommodate a variety of different protocols into a single pipeline with shared quality controls thus simplifying workflow and increasing process robustness.

Ryan Johnson Ryan Johnson directs the cDNA Production Pipeline for the Illumina Platform at the Broad Institute.  He has participated in the development and scale of multiple sample preparation protocols for the Illumina platform.  Before coming to the Broad Institute, he worked in the Department of Neurochemistry of Harvard Medical School  at the New England Primate Research Center.  He has a BS in Biology from Tennessee State University and a BMus from Vanderbilt University. 

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