GATC Biotech of Germany said this week that it plans to install an Applied Biosystems SOLiD sequencer this fall, making it one of the first commercial sequencing providers — the company says it’s the first — to offer all three next-generation platforms to its customers.
The company expects the new instrument, which it will receive under ABI’s early-access program, to provide 120 gigabases of additional sequencing capacity per year, based on one instrument run every three to four days. In total, this will bring GATC’s capacity to 250 gigabases per year.
The machine is scheduled to arrive at GATC’s Konstanz facility in late October, and the company plans to start offering sequencing services on the SOLiD to its customers by the end of the year, according to GATC chief technology officer Thomas Pohl.
Earlier this year, GATC installed a Roche/454 GS 20, which it recently upgraded to a GS FLX, as well as Illumina’s Genome Analyzer. The company also has an undisclosed number of ABI 3730xl capillary electrophoresis sequencers.
GATC’s decision to add ABI’s SOLiD, the latest entry in the rapidly evolving next-gen sequencing market, to its services offering was based both on soaring demand for high-throughput sequencing services as well as a desire to offer customers a variety of technologies.
“A lot of customers want to have these kinds of runs,” said Pohl, including smaller users such as university-based research groups that might not generate enough demand to justify acquiring their own next-gen sequencer. The company will also offer fractions of a run to such small users.
In addition, being part of ABI’s early-access program will be an advantage for GATC’s customers, Pohl said, giving them early access to new kits for particular sequencing applications. However, the company will not be the only commercial sequence provider to receive the system under the early-access program, according to an ABI spokesperson, who did not disclose any other recipients. Agencourt Bioscience told In Sequence last month that it expects to receive a SOLiD system “shortly.”
GATC has high expectations for the new platform but does not believe it will replace Illumina’s Genome Analyzer anytime soon.
“We have been working for over 10 years now with ABI, and we think they can produce really good machines and good chemistries for their machines,” Pohl said.
But ABI is unlikely to quickly dominate the market in a similar way it did when its capillary electrophoresis sequencers competed with Amersham’s MegaBace technology, he thinks. “Amersham was not an experienced company for sequencers or lab equipment,” said Pohl. Illumina, on the other hand, “can sell and produce machines and kits. It’s a different situation. I think there will be a niche for each of these systems on the market.”
Although the SOLiD and the Genome Analyzer are comparable their stated sequencing cost and output (see In Sequence 5/29/2007), the two platforms use different chemistries. Pohl said there could be a number of differences between the two — for example, in data quality, speed, actual output, and software quality — but noted that he will only find out about each system’s pros and cons once the instruments, which will be housed in different rooms, are up and running at GATC. “I think we can learn a lot by running all three [next-generation] systems next to each other.”
“I think we can learn a lot by running all three [next-generation] systems next to each other.”
So far this year, GATC has invested more than €2 million ($2.74 million) in new sequencing instrumentation, including a Roche/454 FLX, an Illumina Genome Analyzer, ABI’s SOLiD, and an undisclosed number of additional ABI 3730 capillary sequencers.
Pohl expects that the company will use its 454 FLX system mostly for de novo sequencing of bacteria, in combination with Sanger sequencing, as well as for transcriptome sequencing “if you need longer reads.”
Both the Genome Analyzer and SOLiD platforms will be best suited for resequencing of bacteria and eukaryotes, small RNA analysis, tag-based gene expression studies, and chromatin immunoprecipitation analyses, he believes.
What he likes about the Illumina and ABI systems, compared to the 454 platform, is that “everything is quite open,” including access to the primer and adaptor sequences, making it easier for researchers to develop their own sample prep protocols for the new machines.
As a service provider, GATC sees another advantage in the fact that ABI is not offering service work on its SOLiD sequencer. Unlike Illumina and Roche/454, which both offer sequencing services, ABI will thus not become a competitor, facilitating the flow of information on the new system in both directions. “Why should I give tips to someone who is competing with me?” Pohl asked.
The company also plans to develop new applications with customers “where kits are not yet available,” Pohl said, but he declined to elaborate because these customers first want to publish their methods.