August 22, 2013
It Takes A Lot Of Computing Power To Decode The Hamster Genome
April Flowers for redOrbit.com - Your Universe Online
The genome of the Chinese hamster - which supplies the cell cultures used by the pharmaceutical industry to produce biopharmaceutical products such as antibodies used in medicine - has been sequenced by an international team of genome researchers led by Professor Dr. Alfred Pühler from Bielefeld University’s Center for Biotechnology (CeBiTec).
The CeBiTec team collaborated with the University of Natural Resources and Life Sciences in Vienna, the Austrian Centre of Industrial Biotechnology (ACIB), and two pharmaceutical companies: Novartis and Pfizer. The findings are published in Nature Geoscience.
This research is of great interest to scientists and industry as well, said Professor Dr. Thomas Noll, Scientific Director of CeBiTec. “In future, the decoded hamster genome will greatly advance the use of cell lines to produce pharmaceuticals,” says Noll, who runs the Cell Culture Technology research group at the Faculty of Technology.
The genome of the Chinese hamster has eleven pairs of chromosomes. There were challenges to decoding such a large genome, including the generation of large datasets that then have to be processed with bioinformatics. The research team used a completely novel method to facilitate the data analysis. The new method sorts the single chromosomes of the genome. Dr. Karina Brinkrolf at CiBeTec led the sequencing efforts, which generated more than 1.4 billion short DNA sequences.
“The major challenge in this project was subsequently piecing these short DNA sequences together to form single total sequences of chromosomes,” explains Pühler. Work such as this can only be done with very large computers. “We had to complete the new CeBiTec computer cluster and apply new software before we could determine the genome sequence,” says the bioinformatics expert Dr. Alexander Goesmann. “By decoding the hamster genome sequence bioinformatics at Bielefeld University has broken new ground.” The Chinese hamster genome has 2.3 billion bases, making it comparable to that of the human genome.
Professor Pühler said the team’s findings are a milestone for CiBeTec. “The decoding of the hamster genome successfully concludes a major CeBiTec project. The hamster sequence is available in the public domain and can be used for research throughout the world.” The CiBeTec team will continue collaborating with the University of Natural Resources and Life Sciences and ACIB. “This places Bielefeld University in a good position to carry on contributing to this highly competitive field of research,” said Pühler.