National Genomics Infrastructure (NGI)

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1 National Genomics Infrastructure (NGI) Ellenor Devine Project Coordinator

2 Science for Life Laboratory (SciLifeLab) Umeå Uppsala Stockholm A national center for molecular biosciences with focus on health and environmental research. A collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University, and Uppsala University. Distributed center that serves as a national resource for all of Sweden. Research center timeline: Linköping Göteborg Lund

3 SciLifeLab Mission 1. National infrastructure for life science 2. Collaborative research community 3. Societal impact The infrastructure at SciLifeLab includes stateof-the-art technologies for high-throughput molecular biosciences. 3

4 SciLifeLab organization Infrastructures 4

5 National Genomics Infrastructure (NGI) An internationally competative genomic infrastructure to enable Swedish researchers to perform world-class research in genomics. NGI was established Jan 1, As by 2018; 73 FTE Including head of facility, project coordinators, staff for laboratory and bioinformatics operations, systems developers and IT-experts. National resource A jewel in the crown of Swedish Bioscience. International Panel Review 2017 Swedish Research Council. State-of-theart infrastructure A learning environment 5

6 NGI Organization A distributed infrastructure NGI-Uppsala SNP&SEQ Technology platform Ann-Christine Syvänen, UU Professor in Molecular Medicine NGI-Uppsala Uppsala Genome Center Ulf Gyllensten, UU Professor in Medical Molecular Genetics Lars Feuk, UU Senior lecturer (Deputy) NGI Uppsala NGI NGI Stockholm NGI-Stockholm Joakim Lundeberg, KTH Professor in Gene Technology

7 Services Short-read NGS Applications Whole genome sequencing, de novo sequencing, RNA-seq, ChIP-seq, amplicon sequencing etc. Long-read NGS and mapping Applications De novo sequencing, amplicon sequencing, full length transcript sequencing etc. SNP-typing and other analyses Applications SNP typing incl custom panels, DNA-methylation profiling, copy number variation studies etc. Instrumentation Instrumentation Instrumentation HiSeqX, NovaSeq, HiSeq2500, MiSeq (Illumina) Ion Proton and Ion S5Xl (Thermo Fisher) RSII, SEQUEL (Pacific Bioscience), Chromium (10X Genomics), MinION (Nanopore) iscan, MiSeq (Illumina), MassARRAY (Agena Bioscience), Hidex Sense (Hidex Oy), ABI 3730XL DNA Analyzer (Thermo Fisher) Illumina sequencing and genotyping process accredited by SWEDAC, ISO/IEC

8 NGI in numbers (2017) One of the largest infrastructures within SciLifeLab 1068 Number of projects 288 Number of publications by our users Number of samples (sequencing) Sequencing Genotypning Number of samples (genotyping) Projects Samples

9 NGI project handeling process SWEDAC accredited Illumina service at NGI Web-portal Scientific support Sample QC Sequencing Genotyping Data processing Bioinformatics Planning meetings Agreement Additional service depending on project Scientific Publications (+ IPR) Project support: Consultation, help to choose the best library method and genotyping/sequencing method for your project. Free of charge! We also arrange workshops, courses, roadtrips, seminars and site visits.

10 Funding of Infrastructures in Sweden (Examples) 1. The Swedish Research Council 2. The Swedish Governement 3. Strategiska forskningsområden (SFO) Bottom up Top Down Top down Bottom up / Top down Other Responsible for RI funding in Sweden. Decisions based on per review and applications. Infrastructures prioritized through a 2-year cyclical process (the research councils national roadmap). Only prioritized infrastructures can apply. SciLifeLab is funded directly by the Swedish Government. Strategic research areas. Background: In 2008 the Swedish research funders were commissioned by the Swedish Government to identify important research environments within 20 strategic research areas. 43 different facilities and centers were recommended, including SciLifeLab (research area: Molecular Bioscience). Private funders. Ex Knut and Alice Wallenberg Foundation Stiftelsen för strategisk forskning (SSF) EU funding. Ex Horizon2020 INFRAIA Internal funding within SciLifeLab: ex. Research community programs (RCP). 4-8 years 5 years 5 years ( ) Evaluated 2015 and funding continued. Depends on funder 10

11 Funding (2017) SciLifeLab NGI 261 MSEK 154 MSEK 1. National infrastructure funding (Government funding, direct) 2. Strategic research funding (SFO) (Government funding, via host universities) 46.5 MSEK 1043 MSEK 3. Other funding (External funding to SciLifeLab infrastructures, fees from users of infrastructure, grants to individual SciLifeLab-associated researchers etc) Total MSEK 9.4 MSEK Swedish Research Council + User fees, funding from the university. 11

12 External infrastructure funding SciLifeLab (2017) NGI s source of funding similar to the funding of other platforms and facilities within SciLifeLab. Example from NGI : NGI received 70 MSEK from the Wallenberg foundation for investments in new technology. 12

13 Our RI users Why they are important: 1. A large number of users highlights the need for our service and underpins decisions on continued funding. 2. Societal impact: it is through our users we help translate research into a lasting impact on society. International Other 4% 1% Industry Health care 1% 1% Other gov agencies 3% Academia 90% NGI (2017) User access: Swedish researchers (national academia) have priority but our services are open for all users, including international researchers, industry etc. For Swedish researchers the cost of staff is covered by SciLifeLab. Full cost for industry. 13

14 Infrastructure life cycle The SciLifeLab infrastructure life cycle. The plan includes closing down facilities through a 20% cut of funding over 1.5 years. An annual report with key performance metric is provided to SciLifeLab and to the Swedish Research Council. Evaluation by international scientific advisory board with 3-4 years interval. Additionally The Swedish Research council requires all applicants to provide a short decommissioning plan. Since NGI has no large buildings or instruments, it mostly focusing on the personal. 14

15 Challenges National funding schemes today are easy to apply for and no training is needed but: 1. Lack of funding for new instruments and equipment. The Swedish Research Council and the Wallenberg Foundation have discontinued financing of equipment, making it difficult to establish new applications rapidly Genomics develops rapidly, frequent need of equipment up-grades. 2. Lack of long term funding. Difficult to make long term plans since most funding to NGI is only for 2-4 years, difficult to make plans for training and hiring of staff. Funding from SciLifeLab is currently for 1 year. 3. Frequent evaluations Many different types of funding means, almost one evaluation per year (Swedish Research Council, SciLifeLab, IAB) 4. Funding of the whole research chain, from research project grants to e-infrastructure. Bioinformatics analysis and data storage is an important part of genomic research.: 15

16 Impact of our service Examples of researchers who used our services:. Complex archaea that bridge the gap between prokaryotes and eukaryotes. (2015). Spang A, Saw JH,..., Guy L, Ettema TJ. Nature 521 (7551) Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago (2017). Schlebusch CM, Malmström H,..., Lombard M, Jakobsson M. Science - (-) eaao6266. Mosaic Loss of Chromosome Y in Blood Is Associated with Alzheimer Disease. (2016) Dumanski JP, Lambert JC,..., Lind L, Forsberg LA. Am. J. Hum. Genet. 98 (6) The Plant Genome Integrative Explorer Resource: PlantGenIE.org. (2015) Sundell D, Mannapperuma C,..., Hvidsten TR, Street NR New Phytol. 208 (4)

17 Thank you for your attention