Tuesday, May 6, 2008

The Next Gen Sequencing Lab

Illumina's Genome Center in a mailroom message really captures the impact of next generation sequencing technology. Each Illumina Genome Analyzer, AB SOLiD instrument, or Roche Genome Sequencer (454) has the per run capacity of a Genome Center's daily output. More importantly this is possible because you can do your DNA prep work on a single lab bench. Of course you'll have to find someplace to put the data.

In the old days (last year) if you wanted to collect data on a genome center scale, you had to not only have a large warehouse with 100's of capillary electrophoresis genetic analyzers, you also had to have multiple large rooms that were devoted to sample preparation. In the largest genome centers, one full room is used to prepare DNA libraries, another is used to purify DNA templates and finally a large space is need to run the sequencing reactions (we're not even talking about media, autoclaves and other support). Multiple robots are required to pick bacterial colonies, transfer liquids between 384-well plates, and aliquot purified DNA, primers, and enzyme/nucleotide cocktails. To support these activities a small army of technicians work to set up the materials, move plates through the process, and load the instruments. This is all tracked by a custom LIMS (Laboratory Information Management System) and team of developers who keep it running and develop tools to process the data.

With Next Gen sequencing all of this is replaced by a mailroom, laboratory bench, and a couple of people.

While you can make do with less space, fewer people, robotics, and custom LIMS systems, you do need to track what is happening at the bench. You are probably also going to want to know which of those many thousands of files go with what samples. Today's Next Gen systems allow you to partition your sequencing materials into slide chambers (also called lanes and sections) to give between eight and 32 separate data sets per run. To track samples and lab workflows, and link data and results together you will need to have a software system that can perform the following basic functions:
  1. Allow you set up different interfaces to collect experimental information
  2. Assign specific workflows to experiments
  3. Track the workflow steps in the laboratory
  4. Prepare samples for data collection runs
  5. Link data from the runs back to the original samples
  6. Process data according to the needs of the experiment
And if you are a core lab you'll likely want to set up experiments as services and create billing statements for the work.

Traditionally, this kind of system was only possible through custom software development, either you did it yourself or you worked with a company to build the features that were needed. Now you can get this support in a software product that is quick to deploy and can be configured to your needs. Over the coming weeks and months I'll show you how this can be done with the Geospiza FinchLab. If you want to know now give us a call.

No comments: