February Newsletter

AGRF Spotlight on...

1. 

Kelly Hanson, Bioinformatician, is a co-author on the recent BMC Genetics 2011 publication titled "Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa". Kelly was an AGRF staff member throughout the project. Read more . . .

2. 

New Australian tax legislation provides additional incentives for companies investing in Australian research and development!    Read more . . .

Service Showcase

3. 

AGRF acquires four Ion Torrent instruments   Read more . . .

Events

4. 

AGRF Presentation at the AMSI Summer School   Read more . . .

5. 

AGRF Next-Generation Sequencing Bioinformatics Workshop   Read more . . .

Tech Tales

6.

So what happens when AGRF starts a new genomics service?   Read more . . .

State by State

7. 

AGRF and Illumina Genotyping User Group meetings   Read more . . .

8. 

WA Next Generation Sequencing User Group meetings   Read more . . .

9. 

AGRF Trade Displays   Read more . . .

Next-Generation Sequencing Special Interest Group Meetings

10. 

Adelaide

11.

Brisbane

12.

Melbourne

13.

Perth

14.

Sydney

Conferences

15. 

24th Lorne Cancer Conference - February 2012   Read more . . .

16. 

33rd Lorne Genome Conference - February 2012   Read more . .

17. 

Lorne Infection and Immunity Conference - February 2012   Read more . . .

18.

16th Human Genome Meeting - March 2012   Read more . . .

19.

18th Annual ASoC Scientific Meeting - March 2012   Read more . . .

20.

4th Australian Epigenetics Conference - May 2012   Read more . . .

Current Opportunities

21.

No positions currently available   Read more . . .

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AGRF Spotlight on ...

1.  Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa

Background: Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species.

Read the full article here.

2.  Research & Development Tax Incentive

The R&D Tax Incentive is designed to encourage more companies to engage in research and development in Australia, by providing a targeted tax offset.

How it works

• Taxpaying entities need to register their projects with AusIndustry. AusIndustry only registers projects that are truly R&D (eg novel, innovative etc).
• The Australian Tax Office ensures only eligible expenditure for each registered R&D project is considered for the R&D Tax Incentive.

The Incentive

• 45% refundable tax offset (equivalent to a 150% tax deduction) for eligible companies with a turnover of less than $20M per annum. Being refundable means that even if the company has incurred a tax loss for the year, they actually receive the tax offset amount from the ATO
• A non-refundable 40% tax offset (equivalent to a 133% tax deduction) for all other eligible companies

How AGRF can benefit these R&D organisations

• Organisations need to have spent at least $20k on eligible R&D to claim the tax offset. This $20k threshold does not apply, however, if they have contracted the work to a registered Research Service Provider (RSP)
• AGRF is a Registered Research Agency (RRA). Entities who are RRAs are automatically registered as RSPs for the 2011/12 financial year. RSPs are required to renew their registration annually

For further information, please click here to the AusIndustry website.

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Service Showcase

3. AGRF acquires four Ion Torrent instruments

AGRF is pleased to announce the recent purchase of four Ion Torrent PGM instruments, a new sequencing technology that is offered by Life Technologies. Two of the Ion Torrents will be placed in Brisbane, the third in Melbourne and the fourth in Adelaide. These instruments have been funded by Bioplatforms Australia via the Super Science Initiative.

The Ion Torrent will complement AGRF's other Next-Generation sequencing platforms consisting of the Roche GS FLX (utilising 454 technology) and five Illumina HiSeq2000s. The GS FLX and HiSeq instruments sequence DNA utilising light-based detection of the sequencing reaction (optical). The Ion Torrent, however, detects the release of hydrogen ions (protons) released from the same reaction, using millions of small pH-meters etched into the surface of a semiconducting chip. Because the sequencing reaction is detected using semiconducting chips, it overcomes the limitations of optical cameras.

The Ion Torrent currently has read lengths of ~100bp and does not generate as much data as either the GS FLX or the HiSeq. However, as the platform matures, longer reads in more numbers can be expected. The platform will be ideal for researchers investigating microbial and viral genomics, PCR resequencing projects, SNP detection projects as well as providing sample confirmation for larger Next-Gen studies.

With over 5 years of Next-Gen sequencing experience, the Ion Torrents will build on the established Next-Gen services at AGRF. The Ion Torrent service is now available at AGRF.

Confused about Next-Generation sequencing options? AGRF can help you via:

• Dr. Ken McGrath, for Ion Torrent services
• Matt Tinning, for HiSeq2000 and GS FLX services
• Your local Account Manager for all other needs

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Events

4. AGRF Presentation at the AMSI Summer School

AGRF Bioinformatics Manager, Dr Andreas Scherer was the invited speaker at the Australian Mathematical Sciences Institute Summer School, attended by 100 post graduate and honours students in quantitative sciences. During the presentation, Andreas shared career advice on Bioinformatics. Andreas was also part of the panel to field questions from the audience, after the presentations. Students were encouraged to discuss their career aspirations and learn more about AGRF.

For further information, please contact AGRF's Human Resources team at recruitment@agrf.org.au.

5. AGRF Next-Generation Sequencing Bioinformatics Workshop

AGRF recently organised a bioinformatics workshop at the Institute of Molecular Biosciences. The workshop included discussions with commercial suppliers and other users of Next-Gen technology on how to evaluate Next-Gen sequencing results. This workshop also acted as a forum to provide tips on how to use raw data and how to troubleshoot to get the best possible results.

If you would like further information about this workshop please contact us.

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Tech Tales

6. So what happens when AGRF starts a new genomics service?

As many of you will know, generating data from a new piece of equipment involves a great deal more than simply turning it on and feeding it your samples. Likewise, starting a new genomics service involves much more than simply learning how to operate a new technique and instrument. AGRF Perth recently completed this process prior to starting the Pyromark pyrosequencing service which utilises Qiagen's PyroMark Q24 instrument. This article briefly describes what was undertaken to deliver reliable data in a genomics service setting.

Continue reading

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State by State

7. AGRF and Illumina Genotyping User Group meetings

AGRF and Illumina are jointly organising a series of genotyping user group meetings scheduled to be held in Melbourne and Sydney in April. The meetings will include:

• Customer presentations about projects that have utilised the illumina Methylation and Exome chips
• Panel Q&A session
• Opportunity to discuss projects with other users

Please contact Cate McGavin for more information.

8. WA Next-Generation Sequencing User Group meetings

The WA Next-Generation Sequencing User Group was established to bring together WA-based researchers with an interest in high-througput sequencing technologies. The group meet regularly to discuss experimental design and issues associated with storing and visualising the massive amounts of data generated by these ultra-high-throughput technologies.

For more information and to subscribe to the mailing list, please click here

9. AGRF Trade Displays

Come along for information and updates on all our Genomics Services:

• Next-Generation Sequencing
• Sanger Sequencing
• Genotyping
• Gene Expression
• Epigenomics & Structural Genomics
• Bioinformatics
• Nucleic Acid Extraction

New South Wales

Macquarie University

University of Technology, Sydney

To express interest in AGRF visiting your institute, please contact our Marketing Manager, Cate McGavin by Email: cate.mcgavin@agrf.org.au.

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Next-Generation Sequencing Special Interest Group Meetings

Compare and contrast Next-Generation Sequencing platforms that best suit your research needs by joining us with other next-generation users at our special interest group meetings.

To nominate a speaker, whether it's yourself or a colleague, for any of the next-gen SIG meetings, please contact us.

10.  Adelaide Next-Generation Sequencing SIG

Due to unforeseeable circumstances, the next Adelaide Next-Generation Sequencing Special Interest Group Meeting will not be held until May.

To register your attendance for 2012, please email: SArsvp@agrf.org.au by Friday 18th May, 2012.

11.  Brisbane Next-Generation Sequencing SIG

The Brisbane Next-Generation Sequencing Special Interest Group Meeting will be held on:

To register your attendance please email: QLDrsvp@agrf.org.au by Friday 24th February, 2012.

12.  Melbourne Next-Generation Sequencing SIG

The Melbourne Next-Generation Sequencing Special Interest Group Meeting will be held on:

To register your attendance please email: VICrsvp@agrf.org.au by Friday 2nd March, 2012.

13.  Perth Next-Generation Sequencing SIG

The Perth Next-Generation Sequencing Special Interest Group Meeting will be held on

To register your attendance please email: WArsvp@agrf.org.au by Monday 26th March, 2012.

14.  Sydney Next-Generation Sequencing SIG

The Sydney NGS SIG Meeting will be held in conjunction with BioPlatforms Australia, the Ramaciotti Centre for Gene Function Analysis and the Victor Chang Cardiac Research Institute on:

To register your attendance please email: NSWrsvp@agrf.org.au by Tuesday 20th March, 2012.

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Conferences

AGRF will be in attendance at the following conferences:

15. 24th Lorne Cancer Conference - February 2012

The 24th Lorne Cancer Conference Meeting will be held at the Mantra Erskine Beach Resort, Lorne, 9th-11th February 2012. For more information, please click here.

16. 33rd Lorne Genome Conference - February 2012

The 33rd Lorne Genome Conference will be held at the Mantra Erskine Beach Resort, Lorne, 12th -14th February 2012. For more information, please click here.

17. Lorne Infection and Immunity Conference - February 2012

The Lorne Infection and Immunity Conference will be held at the Mantra Erskine Beach Resort, Lorne, 15th - 17th February 2012. For more information, please click here.

18. 16th Human Genome Meeting - March 2012

The 16th Human Genome Meeting will be held at the Sydney Convention Centre, 11th-14th March 2012. For more information, please click here.

19. 18th Annual Australasian Society of Cytogeneticists Scientific Meeting - March 2012

The 18th Annual Australasian Society of Cytogeneticists Scientific Meeting will be held at the Bay Resort, Port Stephens, NSW, 23rd-25th March 2012. For more information, please click here.

20. 4th Australian Epigenetics Conference - May 2012

The 4th Australian Epigenetics Conference will be held at the National Wine Centre of Australia, Adelaide, May 7th -9th March 2012. For more information, please click here.

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Current Opportunities

There are currently no positions available but please click http://careers.agrf.org.au to:

• Send your resume as an expression of interest
• Create a candidate profile and register for job alerts

For further information, please contact AGRF's Human Resources team at recruitment@agrf.org.au.

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