Terms of Reference

Review of the Fluidigm BioMark platform: Evaluation to assess fitness for purpose in microbial monitoring

National Peer Review – National Capital Region

December 2-4, 2014
Nanaimo, British Columbia

Chairpersons: Roger Wysocki and Gilles Olivier

Context

Fisheries and Oceans Canada is collaborating with the Pacific Salmon Foundation and Genome B.C. on a five year, multi-phase project (the Project) that will combine genomics and fish health technologies to determine what microbes are carried by wild and cultured British Columbia salmonids, where the microbes may have originated and how they may impact the health of salmon.

The stated strategic goal of the Project is “to discover the microbes and potential diseases that may undermine the productivity and performance of British Columbia (wild) salmon and to determine what exchanges may happen between wild and cultured salmon in the evolution of these microbes”. The Project will proceed through four sequential Phases (stages).

Phase 1 (2012 - 2013) establishes a large-scale sampling program, running over twelve months, for wild, hatchery and aquaculture salmon. The sampling was conducted in 2012 and early 2013.

Phase 2 (2013 - 2015) will develop, test, and evaluate a novel genomic technology to determine which microbes associated with disease in salmon worldwide are carried by wild and cultured salmon in British Columbia.

Phase 3 (2014 - 2016) will focus on the microbes identified in Phase 2, with an emphasis on microbes that have not been extensively researched in B.C. and that carry the highest potential for disease in wild salmon. Laboratory challenge studies will be carried out to assess under what conditions specific microbes are associated with disease in Pacific salmon.  Additional studies assessing transmission dynamics of specific microbes will also take place.

Phase 4 (2016 - 2017) will include reporting of research and presentations to management agencies on the potential utility of methods developed and the application of outcomes to future monitoring.

Currently the Study is in Phase 2a, the stated major objective of which is to develop, test, and evaluate the sensitivity, specificity and repeatability of assays using a high throughput micro-fluidics platform (Fluidigm BioMark) designed to quantitatively assess the presence and load of microbes, in multiple samples simultaneously.  This technology utilizes a novel pre-amplification step whose effects have yet to be assessed.  Phase 2a, is not intended to develop an approach/tool to diagnose disease in either wild or cultured salmon.   Evaluation of diagnostic sensitivity and specificity will proceed in Phase 2b of this Study.

The decision to move into Phase 2b of this study is dependent on the analytical performance of the high throughput micro-fluidic platform, and an evaluation of performance is underway.  Ensuring that the performance of any tools developed to assess both the presence and the disease implications of potential microbes is important, because of the potential for wide ranging implications on Canada’s aquatic resources.  Therefore, diagnostic tools should be reliable, i.e. the sensitivity and specificity of the microbe assays run on the platform minimize the potential for false positive or/and negative results.

To inform decisions related to the advancement of the Project to Phase 2b, and ultimately whether the Fluidigm BioMark platform and the assays based on this platform are appropriate for use in large-scale research monitoring for microbes in wild Pacific and farmed Atlantic salmon, the DFO Management Steering Committee for the Project has requested that a Canadian Science Advisory Secretariat (CSAS) National Peer Review (NPR) process be conducted to peer review the evaluation of the Fluidigm BioMark platform performance for microbial detection, with particular emphasis on the impacts, if any, of the pre-amplification step.

Objectives

The objective of this CSAS NPR process is to provide advice about the suitability of the assays, based on the Fluidigm BioMark Platform and using pre-amplification, for large scale research monitoring for microbes in wild Pacific and farmed Atlantic salmon.  A working paper will be reviewed and provide the basis for the advice.

Specifically, this review will assess:

1. The analytical sensitivity, specificity, comparability and repeatability of each microbe assay, as determined in the working paper.
2. To what level the assay results are comparable across the Fluidigm BioMark and ABI 7900 platforms (within the Molecular Genetics Laboratory at the Pacific Biological Station).
3. The effect of the pre-amplification step of multiple independent target species on the analytical sensitivity specificity, and repeatability of the assays.  Specifically:
   • Whether the pre-amplification step introduces biases in the relative abundance of targets and,
   • Whether it generates spurious (false) targets.
4. The benefits, limitations, uncertainties and proposed uses of this methodology (including the design and the statistical analyses) for the identified research purposes.

Expected Publications

• Science Advisory Report
• Proceedings
• Research Document

Participation

• DFO Science
• DFO Fisheries and Aquaculture Management
• Canadian Food Inspection Agency
• Academia
• Aquaculture Industry Representatives
• Province of British Columbia
• Non-government Organizations