GATC invests both in next-generation sequencing technologies from Illumina/Solexa and Roche Diagnostics

As Europe's first sequencing service provider GATC Biotech announced the acquisition of both a Genome Sequencer FLX instrument from Roche as well as a 1G Genetic Analyzer from Illumina/Solexa. These next-generation sequencing systems will be located in GATC's German research facility in Konstanz and will boost the company's current capacity from 15,6 gigabases to more than 130 gigabases a year.

The deals make GATC the sole service provider Europe-wide to offer high speed end-to-end solutions from sample prep, ultra high speed sequencing to bioinformatics using DNASTAR's SeqMan Pro™ for data assembly and Integrated Genomics ERGO™ for annotation.

By combining both next-generation sequencing systems with GATC's current sequencing platform, which is based on the Sanger method, the company will now be able to offer sequencing services using the three leading sequencing technologies.

While the classic Sanger method is still the state-of-the-art technology for single read sequencing it is also used as backbone system for de novo, comparative and re-sequencing genome projects. The FLX sequencer will be optimal for in-depth analysis of whole transcriptomes in a single run due to its long read length of 250 bases and an output of 400.000 reads per run. The 1G Genetic Analyzer is planned to be used for re-sequencing projects because pertinent data can be obtained even more quickly and inexpensively. This will be especially attractive for re-sequencing of production strains, or for ultra deep sequencing of SNPs or mutations. Additionally, the flexible use of separate sequencing primers drastically minimises PCR artefacts.

As the new technologies will produce vast amounts of raw data, bioinformatic data analysis is the crucial key challenge. GATC offers a wide bioinformatics platform consisting of powerful assembly and annotation engines to meet these future needs. For example, microbial genomes can now be sequenced using the Solexa or FLX system and will be assembled using DNASTAR SeqMan Pro™, the only available bioinformatics software able to assemble sequence data from Sanger and next generation sequencing technologies. Whole genome annotations will be done with ERGO™, the genome analysis suite from Integrated Genomics.

The use of the next-generation sequencing systems will drastically reduce delivery times. GATC expects that the production of raw data for genomes with up to 50 megabases in size, e.g. yeast and fungi, will be executed in just a couple of days.

Within our cooperations we gained profound experience and knowledge in the field of new-generation sequencing technologies in combination with bioinformatic expert systems. We then decided to invest in both new generation sequencing systems as their combination allows a much broader and more customised service spectrum.

Says Peter Pohl, CEO of GATC Biotech: "Back in October 2006, GATC was the first sequencing service provider in Europe offering sequencing via 454 technology within very successful cooperations. These research cooperations were initiated to evaluate bioinformatic expert systems in combination with ultra high speed sequencing technologies. In December we were again first to deliver sequence data of a genome produced on a GS20^®* sequencing machine to an industrial corporate group. Within our cooperations we gained profound experience and knowledge in the field of new-generation sequencing technologies and decided to invest in both systems as their combination allows a much broader and more customised service spectrum. In addition, our long-term cooperation with DNASTAR allows us to offer true end-to-end solutions with short delivery times. Theoretically we are now able to sequence a human genome of 3 gigabases in 1x coverage within 10 days and for less than 100.000 US-$. Just a couple of years ago scientists needed years and millions of dollars for such huge projects."

GATC will present bioinformatics results of a genome project generated with Sanger and 454 technology at DNASTAR's booth during the Plant and Animal Genome Conference XV in San Diego in January.

*GS20 is a trademark of Roche Diagnostics