Biological storage and archival system will help genome centre meet challenges and increase efficiency as they race to complete the sequence of the human and mouse genomes
RTS Life Science International has delivered to the Whitehead Institute a state-of-the-art biological storage and archival system called Automated Store.
This Automated Store will help the Whitehead Genome Centre meet storage and archival challenges and increase efficiency as they race to complete the sequence of the human and mouse genomes, slated for completion in 2003 and 2005, respectively.
The Whitehead Institute's Centre for Genome Research (WICGR) is an international leader in the Human Genome Project - the effort to identify all of the DNA bases that make up the instructions for a human being.
The Centre is the largest public sequencing center in the world, having contributed one-third of the content to the human genome sequence.
The WICGR serves as a flagship for the Human Genome Project, the international consortium of 20 laboratories, including Washington University in St Louis, USA, and The Sanger Centre in Cambridge, England.
Andrew Sheridan, the automation coordinator for the project, explained: "Given the scale and complexity of the genome project, storing and organising our work presents a major challenge.
All our data and samples are currently stored using random barcodes and accessing these samples in a non-automated fashion creates a major bottleneck in our workflows.
Coupling an automated archiving system with our in-house picking system will enable us to increase our workload and do that work more reliably." RTS's system will change the way these scientists organise their work.
By linking the automated sample store to the Whitehead's in-house picking system, the scientists will not only be able to track these samples in an automated fashion, but increase their work rate as well.
The Whitehead's team map a significant portion of the genome in 200,000 base pair chunks called BACs.
After the first pass consisting of groups of 4000 pairs has been completed, the data for that region is assembled and the gaps are identified. Sometimes these gaps have been covered by earlier analyses. Working on piecing the sequences together, to create a complete picture, is the job of the finishing team.
The new system will be used to store glycerols.
These are the live cells containing the human, mouse, or other DNA on which genome sequencing is carried out.
A stretch of unknown DNA is introduced into an E Coli bacterial cell via a vector, like a plasmid, and the information derived from that cell is then read out.
Out of 4000 base pairs within a stretch, only 600 pairs at the end of the stretch can be read, elucidating 1200 bases in total.
Later, a small fraction of this unread information will be used, sometimes within a month or possibly up to a few years later, to fill in gaps that are inevitably found when piecing together the millions of reads which comprise a genome.
A single sample may therefore be accessed several times, depending on the complexity of the region to be covered.
These circumstances result in a very complex sample archiving problem.
RTS's automated store will house the Whitehead Institute's glycerols in shallow well microtitre plates (SWMPs).
These are kept on storage trays, each of which can hold 12 SWMPs.
The store will hold 1680 trays, giving a total system capacity of 20,160.
The system boasts two robots, a store robot and a picking robot.
Over 24 hours, the system will be able to deliver and receive back over 450 SWMPs.
A barcode reader will be able to verify the identity of each SWMP whether it is being received or delivered by the store.
A special pneumatically operated gripper has been designed by RTS to hold the SWMPs.
It is fitted with sensors to detect when the fingers are fully open and fully closed.
The entire system is controlled by advanced d-Sprint scheduling software linked to a database server which both directs all the physical operations within the store and keeps a comprehensive inventory of all the stored SWMPs.
Currently the team has more samples within its standard freezers than the new RTS system will accommodate.
However, Andrew Sheridan explained: "By carrying out a minimal tiling path rearray we should be able to compress our samples, taking out those we already know and picking just the ones of interest from each plate.
This process will help us to focus on what still needs to be completed.
Among RTS's strengths is a demonstrable experience of working within -20C environments".
