WALNUT CREEK, Calif.--After a four-week trial of automated capillary electrophoresis DNA sequencing instruments from Perkin-Elmer and Amersham Pharmacia Biotech, the US Department of Energy's Joint Genome Institute announced last week that it will install 24 of Amersham's MegaBACE sequencers, tripling the capacity of its human genome production sequencing facility here. Elbert Branscomb, the institute's director, told BioInform the choice was based on technical considerations as well as on the ease with which the machinery could be installed and the level of support provided by Amersham. The MegaBACE devices, which the institute will lease, sell for $200,000 apiece.
Branscomb said that the Human Genome Project's new goal to complete a working draft of the sequence by March 2000 "is overwhelmingly predicated on installing a large number of capillary machines in the public sequencing effort and getting them running quickly." He added, "If that doesn't work, those goals will be seriously threatened."
The institute has already installed three, and is awaiting delivery of four more, Perkin-Elmer ABI Prism 3700 devices, priced at $300,000 each. Said Trevor Hawkins, who heads the institute's sequencing effort, "We got copies of both machines, ran them for a while, and, based on a large number of considerations, decided in the main, but not exclusively, to purchase the MegaBACE."
Samples run on both machines were compared for read length, pass rate, and cost factors such as reagent costs. In trials, Hawkins said the MegaBACE produced longer read lengths more quickly than the 3700. "We were able to get those longer read lengths in about a three-hour turnaround, whereas the same run would have taken five hours on the 3700," he claimed. However, the 3700 outperformed the MegaBACE on pass rate, Hawkins said, explaining, "Essentially the window of DNA concentration that you have to hit to get a really good run on the MegaBACE is much smaller than it is on the 3700."
Hawkins said the fact that Amersham, which had not previously sold the MegaBACE to a noncommercial user, could deliver and install the devices quickly was another deciding factor. The first six machines delivered were operational within 48 hours, he said.
"Because of the huge demand for the Perkin-Elmer 3700, people are having difficulty getting these machines in their shops and getting them installed," Hawkins observed. Celera Genomics is installing 250 of the 3700 machines, and MIT and Washington University have ordered a total of nearly 150.
If funding permits, the institute intends to install additional machinery that would increase its sequencing capacity by another factor of two or three. Branscomb said he is not committed to either manufacturer, and added that the institute's operating lease arrangement with Comdisco will give it the flexibility to swap machines on a yearly basis if it chooses. "We don't regard this as a slam-dunk choice. The way these machines are performing is changing rapidly and probably will continue to," he said. "We have to see how they actually function when we put them into production."