Who can submit a gene?
Australian clinicians and diagnostic labs (including research diagnostic groups) discovering genes or variants of unknown significance (VUS/GUS) in patients, who want to connect with functional genomics researchers who can investigate the functions of those genes and/or the functional attributes of the gene variants.
Which genes/variants should be submitted?
The Network welcomes the submission of functional genomics studies in the following categories associated with either a rare disease or inherited cancer.
- Novel gene: A gene not previously associated with disease - a potential pathogenic variant identified in a single patient/family/isolated population - additional functional data is necessary to support disease-causation.
- Candidate gene: A gene that has not previously been associated with disease, but supported by genetic evidence (potential pathogenic variants identified in more than one case of unrelated patients with a similar clinical phenotype) - functional data is being rapidly sought prior to publication.
- Novel phenotype association in a known disease gene: A variant in a known disease gene causing a clinical phenotype that appears to be different to previously reported genotype-phenotype reports - functional data required to determine how the gene contributes to the phenotype.
- Variant of unknown significance: The variant has characteristics of being an independent disease-causing mutation, but insufficient or conflicting evidence exists - functional data needed to confirm variant is causative.
The Network and Objectives
The Network will mobilise the entire Australian biomedical community of clinicians and scientists to communicate, integrate their resources, and work collaboratively to gain insights into the clinical and functional attributes of rare disease genes and cancer genes. Through the database capturing the resources and expertise existing in the Australian research community, connections will be fostered between teams with matching research interest to deliver a better understanding of the genetic and cellular disease mechanisms, develop prevention guidelines and diagnostic tests, and investigate potential therapies. The goal of the Australian Functional Genomics Network is to improve the lives of patients and their families through the coordination of functional genomics research in Australia.
The specific objectives of the Network are to:
- provide functional validation of human genetic variants that cause disease;
- develop insights into an evidence-based rationale for treatment (e.g. identification of candidate drug targets) via knowledge of disease gene function and molecular pathway;
- complement clinical disease gene discoveries by functional genomics investigation that lead to significant and impact research output, such as publications, health policy and practice of clinical management; and
- establish sustainable collaborations between clinical teams and model system research teams to conduct outstanding research that will attract further competitive funding support.
Connection Process
The clinical team that discovers a novel gene or potentially clinically significant variant that requires functional evaluation will submit a Connection application with all the required information. Applications assessed and approved by a Clinical Review Panel will trigger a search of the Network Registry to identify the best-matched model systems research team. While funding for connection projects is not currently available, the Scientific Review Panel will invite the connected teams to submit an ‘Acceptance’ application expressing their interest to undertake functional work using their own resources. On a positive response from the teams, the Panel will recommend the establishment of the connection with an agreement on the condition of the collaboration, which will be considered for acceptance by the combined teams. When Network Catalyst funding is available, the combined teams will be established, and agreement sought around the funding contract, the scope of work and the conditions of the award.
Partner Participation
The Network has no formal requirement for prior partnership. Applications are welcomed from pre-existing or newly formed teams of clinicians and model system investigators who share an interest in pursuing disease gene discovery or validating variants of unknown significance. The Network also welcomes proposals from other organizations such as rare disease foundations who are interested in funding Catalyst Grants in targeted areas. [contact us at: functional.genomics@mcri.edu.au]
Frequently Asked Questions
What constitutes a declined application?
The most usual reason for the Review Panel to decline an application is the lack of adequate genetic data to support causality. Applications will also be declined if it is deemed that the proposing study is on a relatively common variant in the population. If a variant phenotype in a known gene is proposed, an appropriate justification that this is a distinct phenotype is likely to be underpinned by a different pathogenic mechanism (e.g. gain-of-function versus previously known hypomorphic mutations) may be provided.
Under what circumstances might an application be put "on hold"?
A key objective of the Network is to expedite collaborations on model-based studies of rare disease genes. Although applications from clinical teams are encouraged, we recognise that there could be situations where there is insufficient detailed analysis of genetic data. Such applications will be put “on hold” whereupon additional input from molecular geneticist studies can help build the case for further consideration.
What happens when different clinical groups propose the same gene?
The Panel will call the different groups to consider a multi-team collaboration. Applicants may recognize that a collaborative project is more likely to lead to significant research output, given the fierce competition for publishing research findings in journals of high repute.