Overview
The Functional Analysis Service provides wet lab support for CGM investigators seeking to validate or further study the function of putative causal variants identified in human genetics studies. The validation of candidate genes and variants through functional analyses is a critical first step in translation of genetic discovery results. However, not all investigators participating in genetic discovery research are familiar with or have the resources to conduct the necessary experiments. As such, the CGM seeks to supports PIs in the design and execution of basic functional analyses experiments, to generate preliminary data for internal and external grant proposals.
The service provides three experimental models for analysis: cell culture in the laboratory of Dr. Charles Murtaugh, fruit fly (Drosophila melanogaster) in the laboratory of Dr. Clement Chow, and zebrafish (Danio rerio) in the laboratory of Dr. H. Joseph Yost. Both the fruit fly and zebrafish have been shown to serve as relatively rapid test platforms for functional analysis of disease-causing genetic variants in humans.
Example Projects
A wide variety of experimental approaches are feasible, addressing a range of scientific questions – examples of ongoing projects include the following:
- Does a newly-discovered heterozygous missense variant in a transcriptional regulator cause disease by preventing proteasome-mediated degradation?
- Does any of a series of genes implicated in human infertility cause loss of fertility when disrupted in Drosophila?
- Does a trans-heterozygous mutation implicated in kidney disease cause loss of transporter activity by the encoded protein?
- Does expression in zebrafish of a putative gain-of-function variant in a signaling protein produce brain and other defects similar to that of a patient?
- In many cases, all of the work will be done within the labs of the Functional Analysis Service, but in some instances we will identify outside collaborators with unique and required expertise for a particular project, and provide support work (e.g. designing and cloning of expression constructs) to enable such collaborations.
Cost
Experienced laboratory staff in the Chow, Murtaugh and Yost labs provide assistance with functional analysis in Drosophila models, human cell lines, and zebrafish models, respectively. CGM provides salary support for staff working on functional analysis; it is expected that CGM PIs will provide funds for required supplies and other costs associated with the project. The Functional Analysis Service will provide an estimate and breakdown of such costs before beginning a project.
How to Use
This service is available to CGM faculty. If you are not already a CGM faculty member, you may join by completing a brief survey.
As a first step to using this service, please find a request form which includes fields for summarizing prior work and briefly outlining potential plans for functional analysis. We will review submissions on a first-come, first-served basis, and arrange meetings with PIs within 1-2 weeks of submission. Please submit this form to the directors.
Prioritization
The decision to assign personnel to a project will depend on several factors, including the plausibility of the genetic variant as causal for the disease or phenotype of interest, and the feasibility of establishing an informative model. These factors will be part of our discussion with each submitting PI, so that the scope of the project can be modified to make it more feasible if necessary. If cell culture, zebrafish, or Drosophila models do not appear to be appropriate, we can provide advice on how modeling might be achieved in another modeling system such as mouse.
Turnaround Time
Service will be provided on a first-come, first-served basis, and if demand exceeds available effort, later projects will have to be delayed until earlier ones are complete. We do expect to be able to handle multiple projects at once, but current staff have only partial effort devoted to Functional Analysis Service work. Therefore, please do submit requests as soon as possible, so that we can set up meetings and get projects underway.
After the priority assessment, project goals and timelines will be communicated with the investigator, included a project start date based on the current workload of the laboratory staff. The exact project timelines will depend on details of the gene and model organism used, and work load of the specialist. Once the project commences, the FAS directors or their laboratory staff will provide regular updates on project status to the investigator.
