SNISS: Swedish National Infrastructure for Large-scale Sequencing
DNA sequencing has become a basic tool in biology and medicine and the technology for sequencing is changing rapidly. The first generation of technologies, i.e. the Maxam-Gilbert and Sanger methods, were developed in the late 1970 and refined to the point that fluorescent Sanger sequencing was used for the first human genome sequence. The development of massively parallel sequencing technologies in 2006 provided an opportunity to increase the sequence throughput by a factor of at least 1,000. The 2nd generation technologies represent a milestone in the life sciences and for the first time allowed rapid whole genome sequencing. These technologies have dramatically decreased the cost of DNA sequencing and enabled studies of the genome of higher organisms at an unprecedented rate.
The Swedish National Infrastructure for Large-Scale DNA sequencing (SNISS) has been established by the Swedish Research Council in January 2010 as a national core facility at Royal Institute of Technology (KTH), Stockholm and Uppsala University. SNISS presently operates 2nd generation instruments (Applied Biosystems’ SOLiD, Roche’s Genome Sequencer FLX and Illumina’s HiSeq2000).
• An open access core facility for Swedish research groups taking advantage of the instrument infrastructure. Research groups can deliver genomic DNA, RNA or cDNA to either of the nodes for sequence analysis. SNISS provides free of charge all the laboratory work and a basic bioinformatics analysis including mapping to the reference genome and assemblies, before delivery of files to users. In the current mode of operation, the research group will cover only the reagents costs unless advanced sample preparation protocols are needed.
• A flexible infrastructure that enables introduction of new technology developments. During 2008 and 2009 SNISS has updated the sequencing instruments with new hardware and software to offer state-of-the-art 2nd generation sequencing platforms. We have also introduced new paired-end, RNA sequencing and automated multiplex procedures, including sequence capture methodologies enabled by arrays and in solution hybridisation.
• A learning environment where PhD students and postdocs can become familiar with the new analysis methods in genomics. This part has been strengthened by funding to the national Bioinformatics Infrastructure for Life Sciences (BILS) initiative.
• Empower Swedish scientists in the field of the next-generation DNA sequencing by organizing scientific meetings, user workshops and courses as training events.
The SNISS board include representatives for KTH, UU, VR and external users. The SNISS KTH node is headed by Professor Joakim Lundeberg (Director of SNISS) and the Uppsala node by Professor Ulf Gyllensten (Co-director of SNISS).
SNISS will be co-located with the Science for Life Laboratory efforts in Stockholm and Uppsala, which will further strengthen the SNISS infrastructure. SNISS will perform projects in a wide variety of research fields and project types, underscoring the wide utility these technologies are having in essentially all fields of biology and medicine.