Genome Sequencing – our lab or yours?

We often think it’s cheaper to do experiments in our own laboratory rather than using a core facility.

But does our own lab have the latest and most efficient equipment? Do we think about the time and anguish to be saved by an experienced hand helping in designing the experiment – or in preparing samples for the best outcome? We spoke to Lavinia Gordon about how her Bioinformatics work at the AGRF can benefit the Australian research community.

First published: 18/06/2014

Updated at: 18/06/2014 at 3:44 pm

We often think it’s cheaper to conduct experiments in our own laboratory rather than using a core facility.

But does our own lab have the latest and most efficient equipment? Do we think about the time and anguish to be saved by an experienced hand helping in designing the experiment – or in preparing samples for the best outcome? Nobody likes repeating the experiment.

Using a VPTN core facility, with its experienced staff and state-of-the-art equipment can save you bucket loads in costs, and enhance the quality of your research output.

One such facility is the Australian Genome Research Facility (AGRF). It is a nationwide genome sequencing facility which can save you costs, time and provide the best possible research outcome by using their services.

The AGRF keeps up to date with all the advances in next-generation sequencing and is one of the few organisations with the capabilities and expertise to sequence any assemble and analyse any genome from any organism.

Bioinformatics Manager at the AGRF, Lavinia Gordon, said “The AGRF provides genomics services to academic, applied research and commercial markets spanning biomedicine, plant and animal science, microbiology, evolutionary biology and biodiversity.”

Lavinia is the latest addition to AGRF’s 70-strong team nationally, and she works at the intersection of experimental and computational biology, helping interpret and integrate genomics data.We spoke to Lavinia about her work at AGRF and how this can benefit the Australian research community.

“Because we are a national service provider we enable researchers access to state-of-the-art genomics infrastructure, while keeping costs low through economies of scale and NCRIS operational subsidies. And because we are located in five cities, you can come in and talk to us about your research aims to ensure the best possible experimental outcome.

“Labs looking to get into genomics do not always appreciate the expense of purchasing equipment, as well as maintenance, upgrading and the salaries of trained personnel required to run the instrumentation efficiently and trouble shoot when necessary, minimising the risk of operator error. Our personnel are available to advise researchers on the best strategies to achieve their aims. Staff training programs are assessed by the National Association of Testing Authorities (NATA) as part of the AGRF’s quality assurance process. AGRF’s services are accredited by NATA to the International Standard ISO17025:2005, with data quality also assured through constant benchmarking of large numbers of sample and runs.

“Genomics equipment is much more cost effective (in terms of time and reagent use) if operated at full or near full capacity. Due to the volume of work that we receive and by aggregating projects from around the country, the AGRF can realise these economies of scale.

“Modern genomics instrumentation produces vast amounts of data which requires high-end computing capacity for storage and processing. As well as having a dedicated team of bioinformaticians, LIMS developers, and IT professionals, AGRF links to other high performance computing and bioinformatics initiatives on a national basis.

“Our team of genomic experts is available to provide advice on experimental design and the best sequencing approach. At the moment we have a rather interesting case with a commercial client. We were approached by DNA Security Solutions, a highly innovative boutique engineering company from South Australia, to partner with them and assist them in developing a unique synthetic DNA solution.  This solution will be used with their current security system, which uses synthetic DNA to mark and tag criminals as they leave the scene of the crime. This technology is revolutionizing the security industry and targeted for business subjected to armed robbery and break-in, and residential homes wanting to increase security to protect their assets.

“DNA security systems enlisted the help of AGRF, to become their scientific arm of expertise to help develop a stable and unique DNA product that would work with their technology. We were able to work with the client to develop a product that was suited to their unique application. As an added benefit to this project, they received some funding from the South Australian Government who are encouraging innovative partnerships between the manufacturing and scientific communities to develop ground breaking technology which can only be achieved by working together in their individual areas of expertise.

The Australian Genome Research Facility Ltd (AGRF), a not for profit company, is Australia’s largest provider of genomics services and solutions.  The AGRF has laboratories in Brisbane, Sydney, Melbourne, Adelaide and Perth, each providing a gateway to a national network of state-of-the-art facilities, technology and expertise.

For more information on AGRF click here or email info@agrf.org.au

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