NEW YORK (GenomeWeb News) — Four academic centers in Germany that are part of a network of genome research institutions will spend €4.5 million ($6 million) in government funds to buy next-generation sequencers from Roche, Solexa, and Applied Biosystems, GenomeWeb News has learned.
The purchases, funded by the German federal government, state governments, and the Max Planck Society, are aimed at helping Germany “make a very bold move towards ultra-high-throughput sequencing,” said Stefan Schreiber, speaker of the steering committee of the German National Genome Research Network, NGFN, which coordinates the initiative.
“This is a synchronized purchase, mainly from federal funds and … the NGFN coordinates the application development in the German system,” Schreiber added.
He organized a meeting on next-generation sequencing in Hamburg last week, in which approximately 90 scientists from basic and clinical research institutions across Germany participated. Solexa, Roche, and Applied Biosystems presented their technologies at the conference.
Schreiber said the new initiative wants to help the nation “strengthen its scientific portfolio in genetic epidemiology and systematic functional exploration of complex diseases.”
As part of the deal, he said, the German Cancer Research Center (DKFZ) in Heidelberg and the Leibniz Institute for Age Research/Fritz Lipmann Institute in Jena — formerly known as Institute of Molecular Biotechnology — will acquire 454 Genome Sequencers FLX, which will succeed the 454 GS 20 model next year. Also, the University of Kiel will obtain both a GS FLX and an Applied Biosystems Agencourt system. Meantime, the Max Planck Institute for Molecular Genetics in Berlin has already installed a Solexa instrument this month.
The purchases are part of a larger, €14 million program for genome-wide association studies that the German federal government recently funded, according to Schreiber. Another part of this program is a case-control consortium in which researchers will use Illumina’s and Affymetrix’s genotyping platforms to analyze 22,000 samples in genome-wide association scans. The aim of this initiative is to find genes involved in a number of complex diseases, including atopic eczema, epilepsy, and Crohn’s disease, he said.
Solexa’s instrument “makes a very good impression. I was very skeptical at the beginning but I am quite excited.”
The four German institutes will use next-generation sequencing to follow up on results from these scans. “From these genotyping studies conducted in thousands of samples, we will have many hundreds of leads being associated with complex phenotypes,” said Schreiber, who is a professor and director of the Institute for Clinical Molecular Biology at the Christian-Albrechts-University in Kiel, in Northern Germany.
The follow-up resequencing projects will ideally be on the order of more than 100 genes in each condition, including all exons, in 1,000 or more individual samples, said Schreiber. In addition, the instruments will be used for cancer resequencing, he said.
Schreiber said the instruments will initially be accessible to research groups within the NGFN network, which include a number of universities, Max Planck institutes, Leibniz institutes, other academic research centers, and several biotechnology companies. Later on, they will also serve other publicly funded researchers in Germany. In the future, German companies that are part of the network will likely establish additional service resources, he said.
At the Max Planck Institute for Molecular Genetics in Berlin, which welcomed a Solexa Genome Analyzer this month, researchers are installing and optimizing protocols but will soon embark on scientific projects, according to Richard Reinhardt, department head of the institute’s automation and service unit.
The instrument, which was funded by the Max Planck Society as opposed to directly from a government agency, “makes a very good impression,” he told GenomeWeb News this week. “I was very skeptical at the beginning but I am quite excited.”
The instrument generates approximately 600 megabases of data per run at the moment, Reinhardt said, but an upgrade next year is supposed to increase this to one gigabase per run. The current read length, he said, is about 30 bases, but he believes Solexa will enable the instrument to reach 40 bases by mid-2007 and 50 later on, with a goal to reach 3 gigabases per run. He said his institute will make the machine available for NGFN-funded projects.
Solexa, which is in the process of being acquired by Illumina, would not comment on whether this is the first system it has placed in Europe. The company has systems installed at the Broad Institute, Washington University School of Medicine, and the British Columbia Cancer Agency in Vancouver.
For Roche, the new placements will significantly strengthen its foothold in Germany. The company has already installed GS20s at the Max Planck Institute in Leipzig, the Leibniz Institute for Age Research/FLI in Jena, and Eurofins- Medigenomix-MWG Biotech in Martinsried, according to a spokesman for Roche Diagnostics. Four new contracts are to be completed soon, he added.
ABI plans to install its Agencourt system in Kiel in June or July, according to Kevin Corcoran, vice president and general manager of genetic analysis at ABI. “Most likely, it will be the first [Agencourt sequencer placed] in Europe,” he told GenomeWeb News yesterday. As part of its early-access program, researchers in Kiel will have access to a US-based system before that, he added.
Although APG’s instrument will be an early-access version, Solexa is in the midst of its early-access program, and Roche has not yet rolled out the 454 GS FLX, all these systems will be real purchases, not free placements, according to Schreiber.
“They are real contracts for money, which means also there are legal commitments by the companies on the performance of these instruments,” he said. All three companies, he added, ”have a strong mutual interest, together with the researchers, that the first large-scale genetic epidemiologic projects run on the instruments are successful.”
Results from these first studies will determine whether federal funding will continue to flow, and whether institutions like the German Research Council will start to fund similar projects, according to Schreiber. “This initiative has to meet biological and clinical milestones,” he said. “I think a year from now it will be measured by the progress in understanding the biology of the phenotypes. It’s not going to be measured by technology.”
At that point, the network might also consider sequencing platforms from other vendors. “It could very well be that other players come into this,” said Schreiber. “Obviously, this will be rapidly evolving, [so] you don’t know who the winner is yet.”