Project

Discipline

next generation sequencing; genome; transcriptome; mutation analysis; bioinformatics; infrastructure

Lead
Lay summary
The R'Equip application was prepared by 9 different groups from the University of Bern. It is supported by 47 additional academic groups form the Universities of Bern and Fribourg who all have projects that require the generation of large-scale sequencing data from nucleic acids.Next generation sequencing (NGS) currently has a comparable impact on biomedical research as the invention of PCR some 20 years ago. NGS enables an increase in throughput of >1000 fold compared to conventional Sanger sequencing and is rapidly becoming an essential technology in most molecular disciplines that work with either DNA or RNA. As NGS requires a highly sophisticated and costly laboratory infrastructure, a platform laboratory shall be established at the Institute of Genetics at the University of Bern. Researchers from the Universities of Bern and Fribourg will get access to this platform laboratory to get support for their next generation sequencing experiments.Projected experiments include the de novo sequencing of prokaryotic and eukaryotic genomes, sequencing of microbial communities, variation detection in mammalian genomes, transcriptome analysis (RNA-seq), and the identification of transcription factor binding sites (ChIP-seq).

Direct link to Lay Summary

Last update: 21.02.2013

Self-organised

Number	Title	Start	Funding scheme

Next generation sequencing (NGS) is currently revolutionizing biological and biomedical research, enabling the comprehensive analysis of genomes, transcriptomes and interactomes. The currently available second generation of sequencing technologies increased the throughput by three to four orders of magnitude compared to the latest conventional Sanger sequencing instruments. One key feature of the new technologies is the parallel processing of thousands to billions of sequencing reactions in one tube. Thus the need for complex robotics has been eliminated, which was essential in previous large-scale sequencing projects, where each sequencing reaction was individually processed. These exciting technological developments now allow regular academic groups to do experiments that would have been restricted to the major genome sequencing centers only a few years ago. With current instrumentation, it is nowadays feasible to re-sequence an entire mammalian genome within two weeks for less than US$ 20’000 reagent costs. Similarly, multiple bacterial genomes or even metagenomes from environmental samples can be sequenced within days. NGS has also opened up many new applications for sequencing, such as e.g. global transcript expression profiling (RNA-seq), the identification of transcription factor binding sites (ChIP-seq) and many others more.Biological and biomedical research institutions need to have access to NGS technology, if they want to perform cutting edge experimental research. In Switzerland, the universities of Basel, Geneva, Lausanne, and Zurich have bought NGS instruments during the last 18 months. Researchers at the Universities of Bern and Fribourg currently have to do their NGS experiments with either external academic or commercial partners, which causes delays and additional costs. We therefore apply to establish an NGS platform at the University of Bern, which will be jointly used by the researchers of the Medical, Science, and Vetsuisse Faculties. Although priority will be given to projects of the applicants, the available capacities of the proposed instruments should be sufficient for all other researchers from the Universities of Bern and Fribourg, and maybe even for projects from other Swiss academic institutions. During the planning of the NGS platform we interacted with experts from other Swiss NGS laboratories. This will ensure that complimentary expertise and infrastructure will be built up and redundancies between the Swiss universities are minimized.The technical development of NGS instruments is advancing rapidly and the specifications of the available instruments improve almost every other month. This application was prepared in April 2010 and thus reflects the knowledge at this time. The applicants will closely monitor the technical developments and adapt the choice of instruments according to future developments, if necessary. At the time of writing we propose to buy a Roche GS Junior instrument, which generates ~100’000 sequencing reads of 300-500 bp length during one 10 hour run (40 Mb raw data) and an illumina HiSeq2000 instrument, which generates up to two billion reads of 100 bp length during an 8 day run (200 Gb raw data). Thus we will have complimentary instrumentation for longer and shorter reads and varying throughput requirements. This should be optimally suited to accommodate the needs of the different research groups at the Universities of Bern and Fribourg. Together with the NGS instruments we will install a high-performance Linux computer cluster, which is necessary to process the large volume of data that will be produced with new instruments.