Understand my genome to understand yours; our take on the budget; and boosting bioinformatics

EMBL Australia

Posted on behalf of Nadia Rosenthal, Scientific Head, EMBL Australia

There’s exciting news for medical research in the first Abbott budget, but mixed news for science as a whole.

I’m looking forward to seeing the details of the new Medical Research Future Fund, and the research destined to come out of it. It’s also great to see the support for science infrastructure – with $150 million for the National Collaborative Research Infrastructure Strategy (NCRIS).

There’s some good news for mid-career researchers too with 100 more Future Fellowships. But unfortunately, some of our collaborators did not fare so well.

Overall, I look forward to exploring the implications of this budget for the future of EMBL Australia.

One thing I am certain about is that genomics will continue to play an important role in medical research.

I recently had my personal genome sequenced using a new technology that makes DNA sequencing more affordable and accessible than ever before. I was relieved to find the only major risk detected was a dominant mutation in a gene associated with mature-onset macular degeneration.

I will have to get my eyes checked more frequently now, and there are surely other disease-associated mutations in my genome that were not detected (only about 10% of genes in the human genome are checked in the current tests), but I can certainly see this kind of sequencing technology becoming standard medical practice within a decade.

The volume of genomic and biomolecular data being collected and used around the world is growing exponentially. Speaking as a geneticist, this is exciting. The more data we have, the more accurately we’ll be able to associate genes with diseases that might be prevented.

So how are we going to make the best use of all this genetic data?

Firstly, we need to be able to store it in a way that allows researchers to use it. One of EMBL Australia’s central mandates is to increase Australian researchers’ access to global biomolecular and genomic resources. That’s why we’re planning to restructure our bioinformatics resource infrastructure (BRAEMBL) to strengthen Australia’s exploitation of global data. We’ll announce more details in the coming months.

But collecting genomic information is relatively futile without the expertise to crunch the data.

That’s where Australia’s bioinformaticians come in. Australia has a growing community of talented and enthusiastic bioinformaticians, and through the Australian Bioinformatics Network, we’re proud to be supporting events and training for bioinformaticians all around Australia to strengthen this community. Below we announce the results of the latest round of Connection Grants.

We’re preparing the ground for the surge of data coming our way.

In this month’s newsletter:

  • Understand my genome to understand yours
  • Boosting Aussie bioinformatics – Connection Grants go to…
  • In other news:
    • Peering into the future of bone repair
    • Register for the Systems Biology Conference
    • Register for EMBL Aus’ PhD symposium
    • Talking techniques at the Synchrotron
  • About EMBL Australia

Understand my genome to understand yours

The latest and most affordable whole-genome sequencing technology is now available to Australians. EMBL Australia’s scientific director, Nadia Rosenthal, was one of the first in the country to find out first-hand what it can do. And also what it can’t do just yet.

The genome sequencing technology developed by Illumina provides clinical-grade sequencing information through a program called Understand Your Genome. Nadia, a geneticist herself, was invited to be part of the first group in Australia to be sequenced.

“It’s a very simple test – some blood was drawn at a genetic counsellor’s office, and several months later he called me with the initial results,” says Nadia.

The group then attended a two-day conference at the Garvan Institute in Sydney, where they were presented with their genomes through an interactive iPad program.

Nadia was pleased to find her own genomic report, as she put it, “fairly boring”.

“The only disease risk found was a dominant mutation in a gene that’s associated with mature onset macular degeneration. So I will go have my eyes checked more frequently now,” she says.

But one of her conference colleagues found a mutation carrying major risk for cardiovascular disease, which has prompted more frequent check-ups and a healthier lifestyle.

Although representing just one more dataset in the global human genome collection, Nadia’s own test has contributed to a growing genomic knowledge bank, the growth of which is critical to improving the clinical insights gained from sequencing.

“Illumina reports on only 1,600 genes and 1,200 known genetic diseases – that’s still a small percentage of the 20,000 genes we carry in our genomes,” says Nadia.

“The only way to redress this limitation is to obtain more human genomes and associate genetic information with clinical information from thousands of healthy people and patients.”

While the test – and the information bank behind it – still has some developing to do, right now it can reveal important insights into health risks and prompt potentially lifesaving preventative measures.

Read the full story on the EMBL website.

Boosting Aussie bioinformatics – Connection Grants go to…

Connection Grants are awarded annually to catalyse new and productive connections for Australian bioinformatics.

“We had fourteen applications this year, all strong. The fact that we could only choose four reflects the limitations of our funds, not the quality of the ideas,” says David Lovell, director of the Australian Bioinformatics Network.

This year, the Australian Bioinformatics Network has awarded four Connection Grants to:

UCSC Genome Browser Roadshow

The UCSC Genome Browser is one of the most widely-used, biologist-friendly genomics tools.

But like many other computer or bioinformatics tools, researchers are only using it for basic functions, says Dr Mark Crowe, training and outreach manager at QFAB.

Following popular training sessions in 2013, this UCSC Genome Browser Roadshow will bring expert user Bob Kuhn back to Australia for sessions that will now include Perth and Adelaide.

“Last year’s training sessions were oversubscribed and we could only cover the eastern seaboard. With this grant, we’ll be able to reach and help boost bioinformatics skills nationwide,” says Mark.

Australian Bioinformatics Conference

While there are many great local bioinformatics meetings regularly held around Australia, there’s currently no national forum for researchers to meet and talk bioinformatics.

The 2014 Australian Bioinformatics Conference, to be held in Melbourne on 11-12 October, is out to change that.

“Just here in Melbourne, there are people working on similar topics who are not yet aware of each other’s work,” says Dr David Goode, postdoctoral fellow in bioinformatics, Peter MacCallum Cancer Centre.

“We want to provide a forum that will work well for researchers working in different areas – industry, academia, agriculture, biomedicine – to help build connection”.

Registrations are now open

Fungal bioinformatics satellite meeting

“Fungal diseases are the main cause of quality and yield losses in Australian crops,” says Dr James Hane, senior research fellow at Curtin University’s Centre for Crop and Disease Management.

“Fungal bioinformatics provides a foundation for the molecular research needed to tackle those losses.”

The Fungal bioinformatics satellite meeting will bring together students, early-career and other researchers for a day focused on their specific work and issues in analysing biomolecular data.

Education session at InCoB 2014: Bringing expertise from GOBLET

The 13th International Conference on Bioinformatics (InCoB2014) will be held in Sydney this year from 31 July to 2 August 2014.

Dr Bruno Gaëta, director of UNSW’s Bioinformatics Program, saw this as a great opportunity to bring educators together from all over the Asia Pacific.

To headline the session, Bruno and his colleagues will be bringing a speaker from GOBLET to provide an international dimension to this forum for educators to exchange ideas, best practice and materials.

There is the full line-up of speakers is available on the conference website and registrations are currently open.

Peering into the future of bone repair

Working out the force of a sabre-toothed tiger bite, building scaffolding for growing stem cells, and developing new strategies to treat osteoporosis – with a systems biology approach, these studies are helping scientists see into the future of bone repair.

Last month’s Victorian Systems Biology Collaborative on Future approaches to bone repair and modelling brought together four leading Australian researchers and an audience for a lively discussion on bone generation, re-modelling, and therapeutic applications.

The presentations and discussion explored how different scientific approaches to bone repair will contribute to the way bone fractures and disease will be treated in the future.

“From my perspective, it was the most successful event to date, and it really captured the essence of what these collaboratives are about – bringing together a diverse group of speakers to approach the same issues from differing angels, and of course, to network too,” said Sarah Boyd, SBI Australia.

The collaborative was facilitated by SBI Australia and Stem Cells Australia.

Read more on the SBI website.

Registration is now open for the 2014 Systems Biology Conference

Are you interested in finding out more about systems biology and how it could apply to your field of research?

Registrations are now open for the International Conference on Systems Biology to be held in Melbourne on 14-18 September 2014.

Hear from international researchers using systems biology to solve problems in biology, computer science, health and wellbeing, engineering, environment, chemistry, and more.

Register before 4 July to save $100. Visit the registration page for more information on pricing. First round registrations will close on 8 August.

New additions to the line-up of speakers are:

Professor Edda Klipp, Humboldt-Universität zu Berlin, Germany, a theoretical biophysicist who is using systems biology to understand cellular organisation, dynamics of cellular processes and stress response.

Dr Huck-Hui Ng, Genome Institute of Singapore, Singapore, whose lab applies a systems biology approach to stem cell research.

Associate Professor Dana Pe’er, Columbia University, USA, who’s using systems biology to investigate personalised treatments for cancer.

We’ll announce the full program in the next newsletter, but get in quick, as early bird registrations close in July.

See the conference website for the line-up of speakers.

Register now for the EMBL Australia PhD Symposium – by students for students

The first EMBL Australia PhD Symposium, Research in life sciences: from in vitro to in vivo, is being held at UNSW from 3-5 December.

Organised by students associated with EMBL from universities, institutes and hospitals around Australia, the Symposium will explore how new technologies and techniques are conceptually and practically modelling disease.

If you’re a student or early postdoc in the life sciences, you can now register to attend.

“It’s a great opportunity for us to come together and present our work under less formal circumstances,” says student organiser, Ziggy Harrison-Tikisci.

“More than anything, it’s an opportunity for like-minded people to get together, discuss common ideas and shape the direction of future research in Australia and abroad.”

Speakers include: Prof Ian Frazer (lead developer of the cervical cancer vaccine and Australian of the Year); Dr Krystal Evans (malaria researcher at WEHI, and prolific Tweeter); Dr Nikola Bowden (melanoma researcher at the Hunter Medical Research Institute); and Dr Jose Polo (stem cell researcher at ARMI and winner of a 2013 Victorian Tall Poppy Science Award).

For more information or to register, head to www.emblphdsymposium.org.au

Or get the latest updates via Facebook and Twitter.

EMBL senior scientist talking techniques at the Australian Synchrotron

Dr Dmitri Svergun, group leader and senior scientist in crystallography at EMBL in Heidelberg will be in Australia this week to meet with Aussie researchers and attend analytical technique workshop events at the Synchrotron.

He’ll be attending a two–day program at the Australian Synchrotron in Clayton, Victoria, which includes a scientific workshop on Photon and Neutron Applications to the Study of Biological and Nanoscale Systems, as well as a ‘school’ for students and early–career researchers.

The Synchrotron events will focus on multi-disciplinary analytical techniques, including synchrotron, neutron and free electron laser-based techniques for the study of biological and nanoscale systems.

The workshop will give students and researchers insights into the advances in research and technique development, and also promote collaboration between the Australian and Italian scientists presenting.

Keep in touch on Twitter and Facebook for more updates.

About EMBL Australia

EMBL – the European Molecular Biology Laboratory – is Europe’s flagship for the life sciences. The Australian government joined EMBL as an Associate Member in 2008.

EMBL Australia is an unincorporated joint venture between members of the Group of Eight universities and the CSIRO, supported by the Australian government.

Read more about EMBL Australia