Sequencing service provider GATC Biotech will soon offer next-generation sequencing services in-house after acquiring both 454’s Genome Sequencer FLX and Solexa’s 1G Genetic Analyzer, the company said this week.
GATC, based in Konstanz, Germany, has ordered both instruments and expects them to arrive within the next few months “or earlier,” the company’s CEO Peter Pohl told In Sequence last week.
The two systems are expected to increase the company’s sequencing capacity from 15.6 gigabases to more than 130 gigabases per year. GATC also hopes the new tools will help it boost its revenues by 30 percent within the next two years, according to Pohl.
Pohl said GATC spent around $1.5 million on the new instruments, additional laboratory equipment for sample preparation, and bioinformatics hardware and software.
He said GATC plans to offer a variety of services on the two new systems, including de novo sequencing, re-sequencing, SNP and mutation analysis, and transcriptome analysis. For genome sequencing projects, the company will combine Sanger backbone sequencing with either of the new platforms.
Solexa’s instrument, which can provide large numbers of inexpensive reads, will be especially attractive for resequencing projects such as analyzing microbial production strains for fine chemicals, or for SNP analyses, according to GATC.
Gene-expression analysis is new territory for GATC, which does not offer microarray-based expression services. “This is a really huge market,” said Bernd Matzenbach, GATC’s sales director. Microarray services, he said, are mostly provided by university facilities in Germany.
According to Matzenbach, the transcriptomics market is divided: Some scientists only want to identify transcripts, requiring 25-mer or 30-mer reads that can be delivered by Solexa’s system. Another group of scientists, he said, seeks longer transcript reads, which the company plans to provide on the GS FLX, which offers 250-base reads.
GATC will not only provide raw sequencing data but also data-analysis services. It will assemble microbial genomes using DNAStar’s SeqMan Pro software, which can assemble a combination of data from Sanger sequencing, 454’s instrument, and Solexa’s system. It will also use Integrated Genomics’ ERGO software for annotating genomes.
Customers, which are currently equally split between academic and corporate researchers, can already order 454 sequencing services that GATC provides through a group of undisclosed collaborators in Europe. The service will be performed at GATC’s Konstanz research facility when it installs its own instrument.
Similarly, GATC plans to offer Solexa sequencing “within the next months” initially through Solexa, according to Pohl. This, too, will be shifted to the Konstanz facility when it installs the instrument.
Though GATC has not determined pricing for either service, the upshot for customers will be both lower cost and a quicker turnaround than Sanger sequencing, he said.
“This investment is quite substantial for us, so we really wanted to be sure to invest in the right technology.”
GATC evaluated 454’s technology last year by collaborating with a group of undisclosed research institutes in Europe that provided access to their GS 20 instruments. “For us it was important … to have access to the technology and evaluate it for ourselves,” said Pohl. “This investment is quite substantial for us, so we really wanted to be sure to invest in the right technology.”
Through these collaborations, GATC used 454 and Sanger technologies to sequence the genome of an undisclosed organism for an undisclosed company. GATC delivered the sequence last month, and said the customer plans to publish the results within the next few weeks. At next week’s Plant and Animal Genome conference in San Diego, GATC plans to present data of this project at DNAStar’s booth.
GATC evaluated Solexa’s technology at the company’s UK site. “In that case, we did not do a run, but it looks so robust that we think that’s the right way to go,” Pohl said.
The company is also keeping an eye on other emerging sequencing technologies, such as ABI’s Agencourt system and Helicos BioSciences’ technology, he said. However, “they are not available on the market right now,” and might not be until much later this year, he added.
GATC, which has 48 employees at the moment and expanded its facilities to be able to accommodate the two new instruments, is not the only commercial sequencing provider that has started to add next-generation technologies. The company’s main competitor in Germany, Eurofins-Medigenomix-MWG Biotech, said in November that it acquired a 454 GS 20 and expected to install it in December at MWG Biotech’s Ebersberg, Germany, facility. Also, Macrogen of Korea added 454 sequencing last spring.