Sweden's Science for Life Laboratory, SciLifeLab, will offer subsidized whole-genome sequencing to scientists through two national research programs that it plans to fund with a total of about $3 million over the coming year.
Earlier this month, SciLifeLab, a collaboration between four Swedish universities that has locations in Stockholm and Uppsala, put out a call for the two programs, the Swedish Genomes Program, which it plans to fund with 15 million Swedish krona ($2.33 million), and the Biodiversity Program, which it will fund with 5 million Swedish krona ($780,000).
Researchers need to apply by May 15 to be considered for the call, which will be followed by a second call at a later stage. SciLifeLab expects to award the first grants before the summer and anticipates supporting "a limited number of projects of high scientific value."
The Swedish Genomes Program will apply whole-genome sequencing "to identify the genetics causes of diseases of high health relevance," according to the call, and will consider projects studying familial diseases as well as case-control studies. Another goal of the program is to establish a whole genome sequencing-based database of genetic variation in the Swedish population.
The Biodiversity Program aims to sequence viruses, bacteria, archaea, eukaryotes, "and combinations thereof."
Both programs are open to researchers at Swedish universities and institutes of higher education. The sequencing will be conducted by the National Genomics Infrastructure, NGI, which is hosted at the SciLifeLab. The grants will cover 50 percent of sequencing reagent costs for the projects, and all costs for the national genetic variant reference database and for proposals from junior researchers.
As part of the Swedish Genomes Program, "we hope to sequence a few thousand individuals in the first round," Joakim Lundeberg, a professor at the KTH Royal Institute of Technology and the director of the NGI at SciLifeLab, told In Sequence.
Projects funded under the program will take advantage of Sweden's extensive health records, he said, and might involve samples from Swedish individuals that have already been characterized in genome-wide association studies or in exome sequencing projects.
"I hope this will open eyes for many projects that have been doing exomes so far to convert their projects into genomes," Lundeberg said.
The biodiversity program will consider a wide variety of projects, he said, ranging from bacterial communities in different environments to plants and animals.
Between its two locations, SciLifeLabs' NGI has 16 Illumina HiSeq instruments that will be used for the sequencing projects.
Last month, SciLifeLab became the first European member of the lllumina Genome Network, through which Illumina offers human whole-genome sequencing services to customers. To become a member of IGN, the lab had to be certified as a service provider by Illumina and have at least 10 HiSeq instruments installed. Being an IGN member helps the lab obtain better reagent prices for human whole-genome sequencing.
In addition, SciLifeLab has the Pacific Biosciences PacBio RS, the Ion Torrent PGM and Proton, and OpGen's optical mapping available, which may also be applied in the projects.
Last year, SciLifeLab researchers and their collaborators published the genome of the Norway spruce, a project that involved a combination of Illumina, SOLiD, PacBio, and 454 sequencing data. "That kind of inspired us to go for a national program in genome sequencing," Lundeberg said.
SciLifeLab will not only provide production sequencing for the funded projects but will also help with project planning and data analysis. "Things get more complicated with whole human genomes, to do the annotations and handle structural variations. I definitely think this enables us to build competence in the field of human genome sequencing," including the secure storage of human genome data, Lundeberg said.
Grantees can also apply for additional funding for bioinformatics support from the National Bioinformatics Infrastructure, which is also housed at SciLifeLab.
SciLifeLab was formed in 2010 with support from the Swedish government and is a collaboration between the Karolinska Institute, KTH Royal Institute of Technology, Stockholm University, and Uppsala University. Last year, it also became a national resource for all of Sweden.