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Call for proposals: SciLifeLab National projects 2015


This call has now been closed.

The final decision on awarded projects has been announced.

 


SciLifeLab welcomes applications for the Swedish Genomes and Biodiversity programs

Background

SciLifeLab is a center for large-scale biosciences with a focus on health and environmental research. The center combines advanced technical knowhow and state of the art equipment with a broad knowledge in translational medicine and molecular bioscience. The National Genomics Infrastructure (NGI) hosted at SciLifeLab offers large-scale DNA sequence data generation and analysis.

SciLifeLab has launched two national programs based on massively parallel DNA sequencing at NGI: The Swedish Genomes and Biodiversity Programs, to be in operation during 2014-2015.

SciLifeLab national projects aim to give significant sequencing support to Swedish scientists to carry out competitive international research.

The programs were launched as multiple calls. A first call has been completed and we now welcome applications for a second call. Please note that the deadline has been extended to May 15th, 2015. An additional call might follow later depending on the outcome of the second call.

National program 1: The Swedish Genomes Program (Whole genome sequencing (WGS) to identify genetic causes of diseases)

Projects can include studies of familiar cases of disease as well as case-control studies. We are expecting projects that contain between 50-3,000 samples (we expect to fund a mix of smaller and larger projects). Only standard 30x Illumina WGS sequencing is included in the call. For tumor samples, multiples of 30x per sample can be included. Case control studies are encouraged to make use of the SciLifeLab Swedish Genetic Variant Database selected to genetically represent the Swedish population (see below for more details). Projects involving multiple universities across Sweden are particularly encouraged.

National program 2: The Biodiversity Program

Projects can target Biodiversity of viruses, bacteria, archaea and eukaryotes, and combinations thereof.

Terms and conditions for the grant

The grants in both programs 1 and 2 will be awarded as a 50% deduction of sequencing reagent costs for projects carried out at NGI. For proposals from Junior Researchers, the complete costs will be covered by the grant. For Junior researchers the doctoral degree must be awarded 2008-01-01 or later (deductions apply for parental leave, illness, residency and specialist training for clinically active professional groups, positions of trust in trade union organizations and student organizations in accordance with criteria applied by the Swedish Research Council).

Standard bioinformatics NGI support is provided, including assembly, mapping of reads, variant calling and basic functional annotation. In addition, SciLifeLab will support the project and ensure efficient handling of the data by providing assistance in coordinating and harmonizing studies from a technical and bioinformatics perspective.

Subsequently, awarded projects are welcome to apply for further bioinformatics support from the national bioinformatics infrastructure at SciLifeLab.

The call is open for scientists with a doctoral degree at a Swedish university or higher education institution.

Instructions for Applying

Application deadline: May 15th, 2015.

Apply electronically here. Please note that you need to complete your application on one occasion (you can not save your application within the application system and continue with it at another time). All files that you upload need to be in pdf-format.

You are responsible for ensuring that the application is complete. Incomplete applications will not be processed. Attach only material that we explicitly request. SciLifeLab will not accept additional information after the closing date for applications, except for information we ourselves explicitly request.

The total reagent cost for human genome sequencing is approximately $1,150/genome given a 30 fold coverage of the human genome. For cost estimates in the Biodiversity Program we refer to the NGI webportal.

A recording of a webinar on biodiversity sequencing possibilities at the National Genomics Infrastructure together with presentations in PDF format is available here.

Information for applicants in program 1: The SciLifeLab Swedish Genetic Variant Database

As a reference tool for the genetics research community and clinical genetics laboratories, a high quality genetic variant database for the Swedish population is being established. The database will include WGS of around 1000 individuals selected to reflect the genetic structure and geographical distribution of the Swedish population. In order to make the genetic variant information easily available a user-friendly and secure database is being constructed. Sequence data will be generated using Illumina short read technology (X-ten) to 30x per individual. Complementary sequencing using long-read technology will later be performed for regions of high medical importance. The 1000 30x Illumina genomes are expected to be sequenced and ready for use during 2015.

Content of the Application

All documents should be in A4 format, using a 25 mm margin and a Times New Roman 12 font. All documents, except when explicitly stated should be in English.

  • Summary (Max 1500 characters).
  • Popular scientific description in Swedish (Max 1500 characters).
  • Research program (See further below) including a project title (Max 6 pages).
  • CV for main applicant (Max 2 pages).
  • List of the 10 most relevant publications in the last five years for the main applicant.
  • Cost estimates for sequencing and account for available co-funding for sequencing reagent costs and bioinformatics support available to the applying group. *
  • A statement from the Head of Department that co-funding is available if applicable.

* For groups that do not have access to bioinformatics resources either within the group or on a collaborative basis there is a possibility to apply for bioinformatics support from Bioinformatics Long-term Support (WABI). Funding for a national project will in this case be subject to the condition that appropriate WABI support is granted.

Research program

The research program must include:

  • Background
  • Purpose and aims
  • Project plan
  • Significance
  • Ethical considerations including relevant ethical approval (Dnr)
  • Additional experimental and/or bioinformatics support needed, if applicable *
  • State the current bioinformatics skills of the data analysis scientist(s) assigned to support this study and their planned involvement in the project

The method section of the project plan must be detailed enough to allow evaluation of the technical feasibility. It must also be clearly stated that sufficient genetic material is available from the study subjects such that a range of sequencing technologies can be used in order to produce high quality genome assemblies.

Evaluation

The applications will be subject to peer review by an evaluation panel with international representation.

Successful applications should fulfil the following main criteria:

  • Scientific quality
  • Involvement of the applicant group particularly in the data analysis phase
  • Feasibility
  • Motivation for the application of whole genome sequencing and power estimates to support the number of genomes proposed

Decisions

The final decision on which projects that will be funded is expected to be taken by the SciLifeLab National Board in early December 2015.

For more information, contact: nationalprojects@scilifelab.uu.se.