Our mission is to:

• provide access to state-of-the-art facilities, technologies, resources and expertise for analysing connections between mammalian genes and physiological processes,
  
  
• foster interdisciplinary linkages between the mammalian genome and phenome, and promote invention and uptake of new genome-phenome analysis tools by Australian and International research and industry in health, agriculture, the environment and biotechnology.

Does a user of APF services retain their intellectual property rights?

The APF encourages users to share research outcomes, scientific data and to acknowledge the facility and the scientific support it provides. The APF supports low cost initial enquiries and investigations provided that any IP created is either jointly owned with the APF or that it is made freely available to other research groups. The more commercial and exclusive the arrangement the more full cost recovery will form the basis for charges to the client. Full commercial rights are available once the costs of the original access are fully recovered. This needs to be advised at the outset of any work and a ledger of these costs will be maintained for future reference.

How are services priced in the Australian Phenomics Facility?

The Commonwealth of Australia, under a Deed of Agreeement with the ANU, has provided the capital to build the APF as a non-profit, self-sustaining Major National Research Facility. The cost of the building, its depreciation and maintenance are provided by the Commonwealth MNRF grant and cash or in kind contributions from the participating institutions.

The APF does not currently receive running costs from the Commonwealth. The recurrent costs of operating the facility and providing services to users of the facility are provided for by cost-recovery charges for each service provided.

Each service is priced based on service units of activity, and standard costs for specific services are provided as a quote to prospective users. A fraction of the service charge is paid up front and the balance on completion of the service.

What are the main kinds of services provided, and how can I estimate or measure my use of a service?

The Australian Phenomics Facility provides the following services to assist researchers in deciphering the genome-phenome code.

Library or strain propagation for phenotyping or genotyping.

The APF provides an unparalleled suite of infrastructure and expertise to propagate and track complex pedigrees of mice. This service includes:

• care, curation, and breeding of mice by highly trained staff and management team, in an ideal specific pathogen free environment;
• tracking and on-line access to all data relating to each mouse (breeding and health records, custom observations, sample collection plates, genotype or phenotype results) via the APF's unique Musterer database system;
• electronic requesting and tracking of workflow, breeding requests, service activity, etc via the Musterer database.

Genome Variant Library Construction and Screening.

The APF has unique expertise in the production of large libraries of mice with subtle genome sequence variants, bred in parallel pedigrees to allow identification of phenotypic variants linked to these sequence changes. New custom libraries will be produced for a project on a cost per pedigree basis. Advice on pedigree structure and detailed quotes are available upon request.

As an alternative to creating a customized library for a specific project, existing APF libraries can be screened, provided the screen does not interfere with screens already in place and meets Ethical Review. Where needed, a new screen may need to be reviewed by the APF Scientific Access and Advisory Committee. A 33% contribution towards the cost of generating each pedigree screened is charged for this service, and this contribution is used to fund construction of additional APF pedigrees. The cost of staff time to coordinate access, perform any tests, and the cost of any additional Library Propagation Units are invoiced separately.

Genotyping

DNA samples suitable for PCR genotyping are obtained in 96-well plate format sufficient for >50 allele-specific PCR or SSLP tests, or in individual tubes sufficient for very large number of genotyping tests and southern blotting.

The APF will perform PCR testing for specific genes or SSLP markers, performed in 96-well plate format, analysed by agarose gel electrophoresis, photo-documented and data entered into Musterer database against individual mice. We expect to introduce SNP typing during the next 9 months.

The APF also provides training, space and equipment for visiting scientists and staff to perform their own genotyping, mapping and sequencing.

Phenotyping.

Specific phenotypic tests can be performed as a service by APF staff, such as body weight measurements, intraperitoneal injections, blood collection, urine testing, subject to approval by the ANU Animal Ethics and Experimentation Committee. The facility can also provide clinical chemistry analysis, flow cytometry, and microarray analysis of tissues or sorted cells.

Expert advice on developing or evaluating the results of specialized phenotyping tests is available through the network of APF Participants.

Sequencing.

Genomic DNA or mRNA converted to cDNA from candidate genes in a mapped interval, is amplified by PCR and sequenced to identify sequence changes or splicing alterations compared to the parental strain sequence and cDNA.

This service is measured per amplicon sequenced, and includes the staff time and materials to design and purchase primers, obtain and amplify DNA or cDNA, perform sequencing reactions and capillary electrophoresis, and analyse sequence traces relative to parental sequence.

Sperm Freezing.

Sperm from male mice are prepared, frozen, and stored in liquid nitrogen. For defined strains deposited for distribution in the NHMRC Australian Phenome Bank, this service is provided for free with the costs covered by an Enabling Grant from the Australian NHMRC.

The service is also provided to cryopreserve strains on an exclusive basis, based on the cost per sample prepared and frozen, and includes staff time, materials, and database tracking. Shipping of mice to APF is not included.

Thawing sperm and regeneration of strain by In Vitro Fertilization (IVF) or Intracytoplasmic Sperm Injection (ICSI).

The APF houses IVF laboratories and experienced IVF/ICSI technicians, enabling cryopreserved sperm to be thawed and used to fertilize mouse oocytes by in vitro fertilization (IVF) of by physical injection of sperm heads into oocytes (ICSI) in the case of low fertility strains.

This service is provided per strain requested, and includes the cost of technician and supervisor time, donor supply, and materials to perform one session of IVF/ICSI and up to four oviduct transfers of fertilized oocytes. Shipping not included.

Importing and rederivation of strains by embryo transfer.

The APF maintains a high security, AQIS-approved quarantine facility. To ensure the SPF status of all mice in the APF, new strains can only be introduced by embryo transfer rederivation, using male donor animals housed in the quarantine facility mated with superovulated females.

This service is provided per strain imported, and includes staff time, donor supply, materials, and typical number of cages maintained per week in quarantine, and up to four oviduct transfers.

Supply of mouse strains.

The APF maintains a large collection of mouse strains, The NHMRC Australian Phenome Bank, either as frozen sperm or as live stock, and supplies these upon request for non-commercial or commercial research and development.

For strains deposited in the Phenome Bank by outside depositors, the service fee includes staff time to arrange the shipment plus the cost per mouse supplied. If the strain is only available as frozen sperm, there is an additional charge to regenerate the strain. The APF maintains an MTA from the depositing institution on file for each strain in the Bank, which will be supplied to the requestor and must be completed with the depositing institution before a strain can be distributed.

For unique strains developed by the APF, a materials transfer agreement and fee is applied, representing a requestor contribution towards the development of the strain and ongoing development and self-sufficiency of the strain resource. Shipping is not included.

Use of Musterer database to manage collections at external sites.

The APF has developed a unique software program, Musterer, which manages and tracks the diverse information related to breeding complex collections of mice. In addition to its internal use to track the APF collections, APF clients can establish the system to manage their own external collections at other sites. The APF IT department will host the external database on its server, advise on necessary hardware, and provide routine database maintenance and training in its use.

This service is provided as a yearly fee for service, based upon the labour and materials to maintain the database and a contribution towards its ongoing development.