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Next generation sequencing platform, University of Bern

English title Next generation sequencing platform, University of Bern
Applicant Leeb Tosso
Number 133813
Funding scheme R'EQUIP
Research institution Institut für Genetik Vetsuisse-Fakultät Universität Bern
Institution of higher education University of Berne - BE
Main discipline Genetics
Start/End 01.12.2010 - 30.11.2012
Approved amount 341'000.00
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All Disciplines (15)

Discipline
Genetics
Botany
Agricultural and Forestry Sciences
Cellular Biology, Cytology
Physiology : other topics
Biochemistry
Environmental Research
Veterinary Medicine
Animal Breeding
Experimental Microbiology
Embryology, Developmental Biology
Zoology
Ecology
Medical Microbiology
Molecular Biology

Keywords (6)

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

Lay Summary (English)

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

Responsible applicant and co-applicants

Publications

Publication
New MLSB resistance gene erm(43) in Staphylococcus lentus.
Schwendener Sybille, Perreten Vincent (2012), New MLSB resistance gene erm(43) in Staphylococcus lentus., in Antimicrobial agents and chemotherapy, 56(9), 4746-52.
KDM2B Is Implicated in Bovine Lethal Multi-Organic Developmental Dysplasia
Testoni Stefania, Bartolone Elena, Rossi Marco, Patrignani Andrea, Bruggmann Rémy, Lichtner Peter, Tetens Jens, Gentile Arcangelo, Drögemüller Cord (2012), KDM2B Is Implicated in Bovine Lethal Multi-Organic Developmental Dysplasia, in PLoS One, 7(9), e45634-e45634.

Collaboration

Group / person Country
Types of collaboration
Swiss Institute of Bioinformatics (SIB) Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events



Self-organised

Title Date Place
Genomics Day 18.11.2011 Vetsuisse Faculty, University of Bern

Associated projects

Number Title Start Funding scheme
129651 Identification of the causative mutation for arachnomelia in cattle 01.04.2010 Project funding (Div. I-III)
119422 Molecular and biochemical characterization of the cellular functions involved in drug resistance formation in Giardia lamblia 01.11.2007 Project funding (Div. I-III)
124732 Investigation of the induction mechanisms and function of secretory IgA against commensal bacteria using reversible germ-free colonisation 01.04.2009 Project funding (Div. I-III)
125459 The role of the Foxi3 forkhead transcription factor in hair and tooth development 01.05.2009 Sinergia
133157 Nutrition, capsule and virulence in Streptococcus pneumoniae 01.10.2010 Project funding (Div. I-III)
126074 Local adaptation and complex demography in a spatially explicit landscape and their effect on molecular diversity: Application to humans and voles 01.06.2009 Project funding (Div. I-III)
120615 A genome-wide screen for skin target genes of plakoglobin as compared to beta-catenin 01.04.2008 Project funding (Div. I-III)
127614 Quality control of gene expression: recognition and elimination of nonsense mRNA 01.10.2009 Project funding (Div. I-III)
149313 Causative mutations and pleiotropic effects of depigmentation phenotypes 01.10.2013 Project funding (Div. I-III)
133034 Causative mutations and pleiotropic effects of depigmentation phenotypes 01.10.2010 Project funding (Div. I-III)

Abstract

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.
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