Konstanz, Germany-based sequencing service provider GATC Biotech claims it is the only company in Europe that offers sequencing on ABI’s 3730, Illumina’s Genetic Analyzer, and Roche’s 454 Genome Sequencer. Last week, the company said it used all three platforms to sequence nine bacterial genomes for customers in April, which gave it insight into the pros and cons of the various methods at its disposal.
GATC installed Illumina’s Genetic Analyzer in March and 454’s Genome Sequencer 20 in February. Contrary to earlier reports, the company is still waiting for an upgrade to the GS FLX, which it expects to arrive this summer.
So far, GATC has seen good customer demand for the new platforms, especially for sequencing bacterial strains. “This will open a new field of new customers who want to sequence their production strains,” Thomas Pohl, the company’s chief technology officer, told In Sequence.
The nine bacterial genomes that the company sequenced in April were for a number of customers from academia and industry. Eight of the genomes — which ranged in size from 3 megabases to 5 megabases — were resequencing projects, for which GATC used Illumina’s sequencer.
“The advantage of the Illumina system is that it’s quite easy to handle,” Pohl said of the new platform, which Illumina fully launched earlier this year.
Sample preparation, in particular, is easier on the Genetic Analyzer than on 454’s platform, he said, and requires less DNA. Also, Illumina’s platform is “a little bit more flexible” he said, allowing GATC scientists to use their own sequencing primers, for example.
On the other hand, each run on the Illumina instrument takes about three days at the moment, he said, considerably longer than a run on the GS 20, which takes about five hours, according to Roche, but produces less data.
For the Genetic Analyzer, “the huge thing is the bioinformatics afterwards,” Pohl said. “Here, you really need a good pipeline.” For that reason, his firm has invested in a 20-core high-performance cluster and a 10 terabyte storage area network. The system, which is expandable, is necessary to perform Blast searches on a large scale, for example, Pohl said. The company has also written its own alignment tools and data analysis software, he added.
GATC researchers are currently generating 36-base-pair reads on the Illumina instrument and have not yet worked with paired-end reads. So far, the instrument yields one gigabase of data in a good run, but “over time, and with experience, I think you can get one gigabase routinely out of it,” Pohl said.
GATC does not store the image data, up to a terabyte per run, indefinitely. “If you analyze [the images] once, there is no need to keep this data,” Pohl said, adding that it would be easier to do another instrument run, since each library prep provides enough material for several runs.
Illumina’s instrument is expected to help GATC’s customers save both time and money with their resequencing projects, Pohl said. In the past, resequencing one five-megabase genome at 8-fold coverage by Sanger sequencing took about three to four months. “Now with the Illumina/Solexa system you can produce the data of eight five-megabase genomes within three to four weeks,” Pohl said.
He would not disclose how much GATC charges for a bacterial resequencing project using the Illumina sequencer, but said that previously, such a project cost on the order of €100,000 ($135,000), and that the new platforms “dramatically reduce this price.”
“Now with the Illumina/Solexa system you can produce the data of eight five-megabase genomes within three to four weeks.”
He added that pricing depends not only on the size of the genomes, but also on the extent of the bioinformatics analysis that is included.
One recent bacterial genome project required de novo sequencing, for which GATC used a blend of about two-thirds 454 sequencing and one-third Sanger reads. It also resequenced that genome on Illumina’s platform, which helped remove the homopolymer errors that 454’s system introduced.
Besides microbial genome sequencing, GATC also plans to use its new platforms for other applications.
While Pohl sees Illumina’s platform best suited for cDNA sequencing, SNP analysis, and resequencing of genomes from higher organisms — including human genomes — he said 454’s instrument would be the method of choice for de novo sequencing, sequencing of unknown transcripts, or for amplicon sequencing “when you don’t need ultradeep sequencing.”
Despite the investments the company has already made, it will consider new technologies as they become available. “It depends what they can do, what the material costs are, what the capacity is, and what the market is,” Pohl said.
He said the company deliberated for a long time about whether to bring the new platforms in house. “It is a risk, but I think it will open a new market,” he said. “And really only a few service providers will go in this direction,” while many smaller ones focus on sequencing on a small scale.
So far, two European competitors have said they are investing in next-generation sequencing: Eurofins-Medigenomix-MWG Biotech said in November that it acquired a 454 GS 20, and Cogenics said last month that it plans to install a GS FLX at its Genome Express facility near Grenoble, France.