Thursday, September 18, 2008

Road Trip: 454 Users Conference

Quiz: What can sequence small genomes in a single run? What can more than double or triple the EST database for any organism?
Answer: The Roche (454) Genome Sequencer FLX™ System.

Last week I had the pleasure of attending the Roche 454 users conference where the new release (Titanium) of the 454 sequencer was highlighted . This upgrade produces more, longer reads so that more than 600 million bases can be generated in each run. When compared to previous versions, the FLX Titanium produces about five times more data. The conference was well attended and outstanding with informative presentations on science, technology, and practical experiences.

In the morning of the first full day, Bill Farmerie, from the University of Florida, presented on how he got into DNA sequencing as a service and how he sees Next Gen sequencing changing the core lab environment. Back in 1998 he set out to establish a genomics service and talked to many groups about what to do. They told him two important things:
  1. "Don't sweat the sequencing part - this is what we are trained for."
  2. "Worry about information management - this we are not trained for."
From here, he discussed how Next Gen got started in his lab and related his experiences over the past three years and made these points:
  • The first two messages are still true. Sequencing gets solved, the problem is informatics.
  • DNA sequencing is expanding, more data are being produced faster at lower costs.
  • This is democratizing genomics - many groups now have access to high throughput technology that provides "genome center" capabilities.
  • The next bioinformatics challenge is enabling the research community, the groups with the sequencing projects, to make use of their data and information. This is not like Sanger, core labs need to deliver results with data.
  • The way to approach new problems and increase scale is to relieve bioinformatics staff of the burden of doing routine things so they can focus on developing novel applications.
  • To accomplish the above point, buy what you can and build what you have to.
Other speakers made similar points. The informatics challenge begins in the lab, but quickly becomes a major problem for the end researcher.

Bill has been following his points successfully for many years now. We starting working with him on his first genomics service and continue to support his lab with Next Gen. Our relationship with Bill and his group has been a great experience.

Other highlights from the meeting included:

A talk on continuous process improvements in DNA sequencing at the Broad Institute. Danielle Perrin presented work on how the Broad tackles process optimization issues during production to increase throughput, decrease errors, or save costs. In my perspective, this presentation really stresses the importance of coupling laboratory management with data analysis.

Multiple talks on microbial genomics. A strength of the 454 platform is how it generates long reads making this a platform of choice for sequencing smaller genomes and performing metagenomic surveys. We were also introduced to the RAST (Rapid Annotation using Subsystem Technology) server, an ideal tool for working with your completed genome or metagenome data set.

Many examples of how having millions of reads makes new gene expression and variation analysis discoveries possible when compared to other platforms like microarrays. In these talks speakers were occasionally asked which is better, long 454 reads or short reads from Illumina or SOLiD? The speakers typically said you need both, they complement each other.

The Wolly Mammoth. Steven Schuster from Penn State presented his and colleagues' work on sequencing mammoth DNA and its relatedness over 1000's of years. Next Gen is giving us a new "omics," Museomics.

And, of course, our poster demonstrating how FinchLab provides an end to end workflow solution for 454 DNA sequencing. In the poster (you have to click the image to get the BIG picture), we highlighted some new features coming out at the end of the month. These include the ability to collect custom data during lab processing, coupling Excel to FinchLab forms, and work on 454 data analysis. Now you will be able to enter the bead counts, agarose images, or whatever else you need to track lab details to make those continuous process improvements. Excel coupling makes data entry though FinchLab forms even easier. The 454 data analysis complements our work with Sanger, SOLiD, and Illumina data to make the FinchLab platform complete for any genomics lab.

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