Request for Applications
Application of Genomic Tools to the Detection and Surveillance of Listeria monocytogenes

List of registrations submitted

Overview/Background

Genome Canada, in partnership with the Canadian Food Inspection Agency (CFIA) and Alberta Innovates – BioSolutions (AI-Bio), is seeking proposals focused on the application of the latest genomics technologies to the detection and surveillance of Listeria monocytogenes (Listeria).

To define the parameters of the program, a one-day workshop was held on February 28, 2012 bringing together leaders from the fields of pathogen detection and characterization, genomics technologies, and the food processing industry. The recommendations from that meeting have been incorporated into this RFA.

Objectives

The objective of the Application of Genomic Tools to the Detection and Surveillance of Listeria monocytogenes Request for Applications (RFA) is to support research that will demonstrate how genomics-based research/technologies can contribute to a more evidence-based approach to detection and surveillance of Listeria.

The current RFA is being run under the auspices of Genome Canada'a Emerging Issues Program that supports projects that are reactive and responsive to emerging issues of high importance, both nationally and internationally. An emerging issue has been defined as an unanticipated issue, which has newly arisen or suddenly increased in importance, and requires urgent/immediate attention and timely resolution (e.g. SARS, C. difficile).

It is expected that one consortium will be funded to carry out this research. It is anticipated that the consortium will consist of teams of scientists from academia paired with scientists from the CFIA and possibly other Government departments and agencies working in partnership with the Genome Canada-funded Science and Technology Innovation Centres (STICs) or other Canadian sequencing centres.

Parameters of the Competition

  • Genome Canada will invest a maximum of $250,000.
  • The Canadian Food Inspection Agency (CFIA) will provide co-funding by investing $250,000 ($100,000 in cash and $150,000 in-kind) to allow the participation of its scientists in the research proposal.
  • AI-Bio will invest $100,000 to this program; this funding is NOT limited to researchers in Alberta.
  • Additional co-funding may be sought from other sources so that a total investment of more than $600,000 is possible.
  • The successful project will be awarded funding for a term of up to eighteen months.

Guidelines for Funding

Genome Canada's Guidelines for Funding Research Projects must be adhered to throughout the competition and post-award management processes.

Exceptions to the Guidelines

Exceptions to the Guidelines specific to this RFA include:

  • Integrated GE3LS: An integrated GE3LS component is not required.
  • Project Manager: A dedicated Project Manager is not required but is an eligible expense and the engagement of an individual performing this role even part-time could be considered.
  • Science Advisory Board: A Science Advisory Board (SAB) is not required.
  • Interim Review: There will be no Interim Review for the funded project(s).

Eligible Research Areas

The research must be focussed on the sequencing of a number of Listeria strains, identification, characterization and annotation of Listeria sequences to enable strain identification, monitoring and differentiation (of those indistinguishable by current molecular typing techniques), evaluation of virulence, and/or development of other suitable molecular markers to support the prediction of virulence potential in new or emerging strains. The results of the research should support both regulatory agencies and the food industry in the areas of monitoring, trace-back and epidemiological investigations in the event of an outbreak.

To be eligible for this competition a proposal must:

  • include genomics approaches as essential components in terms of importance to the overall outcomes of the project;
  • be multi-centred and include teams of researchers from academia paired with scientists in the CFIA (and possibly other Government departments and agencies); and
  • work in partnership with the Genome Canada-funded STICs or other Canadian sequencing centres to develop applications for this collaborative program.

Socio-Economic Benefits and End-User Engagement

Applications must describe, with supporting evidence, the deliverable(s) that will be realized by the end of the project. Deliverables must have utility and/or practical applicability in as short a time as possible and lead to social and/or economic benefits for Canada. These benefits could include, for example, changes in the guidelines for the surveillance and detection of Listeria as well as reducing costs for regulators and industry to respond to adverse food safety events.

Proposals must clearly demonstrate end-user engagement in the development and execution of the research plan in order to help ensure receptor uptake and utility or practical applicability of the research. "End-users" in the context of this RFA can be defined as those who are able to use the information generated through the research to make informed decisions on issues such as policies, programs and product development (e.g., regulatory agencies, food-processing companies).

Competition Time Lines

Requests for support must be submitted to Genome Canada through a Genome Centre. Please contact your regional Genome Centre early on for further information on their process and to help facilitate the development of the consortium/consortia.

Date Activity
September 4, 2012 Registration due date – Genome Centres
September 7, 2012 Registration due date – Genome Canada
October 2, 2012 Deadline for Full Applications – Genome Centres
October 22, 2012 Deadline for Full Applications – Genome Canada
Mid-December 2012 Decisions by Genome Canada, CFIA and AI-Bio

Application Process

Applicants are required to apply for funding through their regional Genome Centre.

Registration

A brief Registration form will be used to provide early guidance on elements such as who is applying, what they are planning to do, expected deliverables, approximate budgets and suggested reviewers. This will allow for screening for eligibility by the Genome Centres and facilitate the early selection of reviewers for the peer review process. A list of Registrations (i.e., name of project leader(s), lead institution, title of project, research areas and keywords) will be posted on the Genome Canada website to facilitate the identification of areas of potential synergy between applications from across the country so that applicants could consider engaging with other researchers on a common project.

Full Application

Full Applications must address the evaluation criteria established for the competition, i.e., research, socio-economic benefits, management and financial. A final check for eligibility in this regard will be carried out. A multidisciplinary committee of experts will be established to review applications.

Genome Canada may adjust its evaluation processes where warranted by the number or complexity of proposals received or other relevant factors. Any changes will be rapidly communicated through Genome Canada's website and through the Genome Centres.

Co-Funding

Genome Canada requires that at least 50% of the requested funding for eligible costs be obtained through co-funding from other sources. The CFIA and AI-Bio will provide the required co-funding for this competiton; however, additional co-funding may be sought from other sources. All co-funding must be for new or incremental research activities that are an integral part of the Genome Canada approved project. See the Guidelines for Funding Research Projects for more details.

Contacts

Kim Corbett Genome Canada (613) 751-4460 ext. 234 kcorbett@genomecanada.ca
Cyril Lutze-Wallace CFIA (613) 773-5290 cyril.lutze-wallace@inspection.gc.ca
Cornelia Kreplin AI-Bio (780) 638-3678 cornelia.kreplin@albertainnovates.ca
Shelley King Genome Atlantic (902) 421-5646 sking@genomeatlantic.ca
Catalina Lopez-Correa Genome Québec (514) 398-0668 ext. 203 clopez@genomequebec.com
Klaus Fiebig Ontario Genomics (416) 673-6583 kfiebig@OntarioGenomics.ca
Reno Pontarollo Genome Prairie (306) 668-3576
(204) 975-7740
rpontarollo@genomeprairie.ca
Gijs Van Rooijen Genome Alberta (403) 503-5220 ext. 30 vanrooijen@genomealberta.ca
Gabe Kalmar Genome British Columbia (604) 637-4374 gkalmar@genomebc.ca

Review Criteria

Proposals submitted to Genome Canada are evaluated through a rigorous independent peer review process to assess their research merit and potential for socio-economic benefits for Canada as well as to ensure that sound management and financial practices are implemented. Excellence and innovation at the very highest of international standards must be demonstrated for funding to be awarded.

Eligibility Criteria

Each proposal will be reviewed for eligibility using the following criteria:

Does the proposal:

  • respond to the objectives of the Genome Canada Request for Applications;
  • include genomics approaches as essential components in terms of importance to the overall outcomes of the project;
  • include teams of researchers from a number of academic centres paired with scientists in the CFIA;
  • work in partnership with the Genome Canada-funded STICs or other Canadian sequencing centres.

If considered eligible, the proposal will be reviewed using the criteria described below.

Review Criteria

The review criteria fall into three categories:

  1. Research Proposal;
  2. Socio-Economic Benefits for Canada; and
  3. Management and Finance

Note that the descriptive phrases which follow the criteria below are not all-inclusive.

Research Proposal

  • Research Context and Originality
    • To what extent does the proposed research lead, extend and/or complement national and international work in the area?
    • To what extent does the proposed research reflect creative, original thinking?
    • To what extent is the research relevant to the end-users identified?
  • Research Plans
    • How appropriate are the methods and approaches (including handling of data and resources) in terms of the research objectives?
    • How feasible is the research, given the projected resources and time-lines?
  • Research Expertise
    • How appropriate is the expertise of the research team in terms of realizing the research goals?
    • How well will different types of expertise be integrated?
  • Research Support
    • How suitable are the available facilities, equipment and services (including services to be provided by Genome Canada Science and Technology Innovation Centres (STICs) and other technology service providers)?

Socio-Economic Benefits for Canada

  • Deliverables
    • To what extent have the applicants identified appropriate deliverables?
    • What is the probability that the deliverables will be achieved by the end of the funding period?
  • Expected Benefits
    • How significant are the anticipated benefits described in the proposal in terms of their potential to contribute to a more evidence-based approach to the detection and surveillance of Listeria?
    • Will the benefits be realized within a short timeframe after the end of the project?
  • Strategy for Realizing Benefits
    • How persuasive is the strategy set out by the applicants for realizing benefits from their research?
  • Expertise for Realizing Benefits
    • To what extent are likely end-users involved in the project and the strategy to realize benefits?

Management and Finance

  • Management Plans and Expertise
    • How good is the plan for project management, accountabilities of personnel, and processes for decision-making on research direction and strategy for realizing benefits?
    • How realistic is the project schedule given the likely need to “ramp-up” activities at the front end?
    • How appropriate are the plans for making the research results accessible to the research community?
    • How good are the proposed arrangements with a STIC or other technology service providers to ensure appropriate and timely collaboration?
    • To what extent do the project leaders have experience in managing large-scale projects involving research and the application of results?
  • Budget and Expenditure Controls
    • How reasonable is the proposed budget in terms of the anticipated level of effort and deliverables?
    • To what extent does the proposal provide assurance that expenditures from a funded project would be closely and critically monitored?
  • Financing from Co-Funders
    • To what extent is the proposed co-funding plan well-documented, eligible and feasible?
    • Does the proposed co-funding directly support the objectives of the project?
    • How strong is the likelihood that the project will be able to secure at least 75% of the co-funding for eligible costs at time of the release of funds?