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Genomics Aotearoa: leading the way

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Genomics Aotearoa: leading the way

Society, health care, the economy and the environment all stand to benefit from the new Otago-led Genomics Aotearoa collaboration.

Scientific knowledge is growing at such a pace that it is sometimes difficult to keep track of who is doing what and how new discoveries can best be used to benefit society.

Technological advances in genomics — the study of genes and their functions — are revolutionising research across a wide spectrum of subjects with increasing national and international importance.

So when the Ministry of Business, Innovation and Employment (MBIE) called for proposals to guide new developments based on genomic research, Professor Peter Dearden (Biochemistry) and colleagues saw a way for Otago and New Zealand to lead the world.

“Many of us involved in the subject had been considering research strategy for some years,” says Dearden. “We seized the opportunity to try to focus many of the strands that were lying around to try to ensure that New Zealand scientists could stay up to date and produce world leading research.”

The researchers’ proposal succeeded, attracting $35 million of government funding over seven years, with Dearden becoming the founding director of Genomics Aotearoa.

The collaborative project is an alliance of the universities of Otago, Auckland and Massey, Crown Research Institutes AgResearch, ESR, Landcare Research, and Plant and Food, and 32 associate organisations that include researchers and end users of genomics and bioinformatics, which works to help understand genomic data. (See bioinformatics focus sidebar.)

The aim is to develop new genomic and bioinformatic information that will translate into a wide range of social and economic benefits from health to the environment, including a strong Māori component.

Genomics has become a core discipline, underpinning all kinds of science vital to New Zealand. It’s a fast moving and fast growing research and commercial field, with a high turnover in technologies and approaches, so Genomics Aotearoa has emerged at a good time, says Dearden.

“Genomics has had such a step change in the way it has been done, we wanted not just to keep up to date but lead the way."

“We’ve come so far since 2002, when sequencing the first human genome took hundreds of scientists 12 years and cost several billion dollars. Now new technology means sequencing human genomes costs about US$ 1000 and can take less than a week and you can do many sequences at the same time. With these advances the economics of investigating variations in genomics in various species change dramatically.

“Genomics Aotearoa will be a collaborative research system that significantly up-skills us in the application of genomics and bioinformatics through acquiring new techniques from overseas, developing new and novel methods and maintaining best practice.

“We are poised to provide infrastructure that will lead to improvements in the health of our people and the state of our environment, while adding value to New Zealand Inc.”

The collaboration will advance New Zealand’s capabilities by developing genomic tools and technologies, building international connections and increasing national collaborations between genomics researchers and end users across life sciences relevant to social well-being, the economy and the environment.

Deaden doesn’t draw a distinction between blue sky research and applied science.

“I don't believe there is a fundamental difference between basic knowledge and its application. Even the most basic genomic research is destined to be put out into useful areas ranging across both fundamental and applied sciences. We have so many partners and associates working on and applying research results we generate.

“Genomics is useful in so many ways that we are confident that our work will see beneficial outcomes.”

General benefits include increasing the adoption and impact of genomics technology for scientists, relevant end users and their sectors. Sectors standing to gain include health, society, the environment and the economy.

On the health front, North America and Europe have learnt much about such things as breast cancer because of the amount of human genome sequencing they have done, says Dearden. But their findings don’t always apply to us, as we have our own population, and we haven’t found out about it yet. (See health focus sidebar.)

“Analysing variations in the New Zealand population is going to be a critical piece of foundation work and will have ongoing benefits almost indefinitely, helping health providers with diagnosis and prognosis of disease and genetic conditions.”

This includes respecting cultural differences while working effectively with Māori — which could pay handsomely in many ways, says Dearden. (See Māori focus sidebar.)

“We have to work in a way that works for Māori, working with them and developing trust, working together and developing relationships so they can work independently. We want to engage them so they can do the work themselves. It's a huge challenge but it's a great challenge and there’s lots of goodwill on both sides so we are hoping to lead the world in a study of our own unique indigenous people.”

New Zealand also has unique flora and fauna, and the environment could be a big winner with genomic support for pest-free New Zealand.

“There's been a lot of discussion about the technology involved in gene editing and gene drives for pest control. A lot of research has already been done in these areas but there is still much to do with the basics, such as finding genetic variations in pests. For example, the ship rat, which is a major problem in New Zealand, has still not been sequenced.

“Providing that kind of background information would provide huge opportunities for developing the technologies for pest control. And that’s just one project. Our goals include helping look after our environment, conserving rare species and caring for such things as soil and water.”

Economic benefits should follow research into improving breeding of existing and emerging primary production species.

“Some of our primary production industries are doing really well but still want to breed stock faster and more economically. Other industries still need support, and genomics can be a big boost to them, helping with technology issues and providing information from our data sets. We can also come up with strategies and tools in many areas so industries can use them and do development work themselves.

“Rather than focusing on single areas of research we’re aiming to develop wide-reaching technologies across all areas and help everybody to help themselves. Genomics underpins so many things and sequencing one species is quite likely to benefit many other species.

“We are trying to look at where we have gaps and how we can fill them by using genomics to solve problems for as many people as possible. Genomics Aotearoa is a very serious collaboration, and it’s all about knowledge building.”

For Genomics Aotearoa Board Chairman Dr William Rolleston, CNZM, the study of the genetics of life in New Zealand offers a fundamental definition of its people, plants and animals. “Genomics Aotearoa is simply the most exciting, important and profound project we have ever undertaken as a country.”

Bioinformatics focus

The science of genomics generates so much data that it needs expert wrangling to get the best from it.

Associate Professor Mik Black (Biochemistry) is one of Genomics Aotearoa’s key people, tasked with establishing bioinformatics infrastructure for various teams and projects.

He’ll be helping to co-ordinate the development of methods and software tools for the analysis of biological data derived from research, as well as working on a national genomics data repository and investing in up-and-coming young academics.

“Apart from setting up processes and handling data for Genomics Aotearoa, a very important part of our work is building New Zealand’s research skills and capability for the future."

"Involving younger researchers in Genomics Aotearoa projects will obviously help us generate data, but it will also help them get a good start in developing their own research careers.”

The leading members of the team are passionate about their own work, says Black, but equally passionate about growing research capabilities in New Zealand science.

“The combination of research and infrastructure is one of the best things about large-scale projects like this. As we look to build teams around the country, we’ll be holding training workshops and opening them up, not just to Genomics Aotearoa researchers, but also to other researchers in the New Zealand science community.”

Black’s own research has included developing and applying statistical methods for analysing data from genomics experiments, with a particular emphasis on colorectal and breast cancer.

Once the main bioinformatics programmes have been launched, he plans to focus his expertise on the Genomics Aotearoa Health Theme, which includes projects on human genetic variation, precision oncology and epigenetics.

Health focus

Professor Stephen Robertson (Curekids Chair in Child Health Research, Clinical Genetics Group) is involved in co-ordinating a number of Genomics Aotearoa’s health projects across New Zealand and internationally.

Current projects include:

A collaboration between the University of Otago (Dunedin and Christchurch) and the University of Auckland looking at improving the statistical analysis of genetic and epigenetic data sets.

Epigenetics is how genetic material – our DNA – can be modified and altered due to various environmental effects such as nutrition, exercise and drugs. These effects don’t change the code, but change how the code is read.

“Now we can measure not only DNA, but also alterations to DNA, so these scientists want to develop new tools and new statistical techniques to correlate the effects of environmental exposure,” says Robertson. “They will be looking at large cohorts of people with aneurysms in Dunedin and working with Christchurch-based researchers looking across a wide spectrum of traits in populations enrolled in studies at that centre.”

Beginning a genetic research theme across the lifespan, particularly for Māori and Pacific Island peoples.

“Internationally there have been intensive genetic studies focusing on Western and Asian people, but Māori and Pacific Island peoples have been relatively underserved. We want to apply genetic science to improve health outcomes for Māori and Pacific Island peoples. That will start with conversations about how to do that optimally with respect to their culture, especially around aligning the approach with all-important concepts such as whakapapa, consent and protection of data.”

Trying to get a better clinical understanding of tumours.

“If we can genetically understand a tumour, we can adopt rational approaches to the best treatment to combat the disease for that person.”

Wellington and Otago-based research on viruses and bacteria.

“We are trying to develop culture-independent diagnostic testing so we can sequence DNA directly from body fluids rather than using culture-based methods to identify disease-causing micro-organisms.

“We’re looking at new technology, new skills and new understanding to enable genomics to be delivered more effectively into health care,” says Robertson.

“We want to improve medicine to individualise treatment and make it more accurate and, ultimately, more effective.”

Māori focus

Dr Phil Wilcox (Mathematics and Statistics) co-directs Māori-related components of Genomics Aotearoa.

Wilcox (Ngāti Rakaipaaka, Rongomaiwahine, Ngāti Kahungunu ki Wairoa and Pākeha) also co-leads Vision Matauranga, which shares the aim of unlocking the science and innovation potential of Māori knowledge, resources and people.

He has long championed science and Māori working together to the benefit of both. In 2001 he started the Te Arotūruki initiative, which developed processes for scientists to engage with Māori communities regarding controversial technologies, and has been involved in multiple projects including the Mata Ira: He Tangata Kei Tua project, which developed ethically-informed guidelines for medical genomics.

“Genomics Aotearoa has a lot of Māori-specific work going on,” says Wilcox. “The main themes of health, the environment and the primary sector all have Māori components because Te Ao Māori – the Māori world – has major interests in each of these areas.

“Some of the research and resources being developed focus on Māori-specific outcomes including hauora – Māori health and social well-being – and tiakitanga – the principle of environmental sustainability – from genomics research on indigenous biota.

“For many reasons it’s important to have Māori participating in the research, governing some of the research and benefiting from some of the research. We want to maximise positive outcomes for Māori communities from genomic sciences.”

Genomics Aotearoa director Peter Dearden agrees. “A lot of genomic research is going on overseas and will be solved overseas. But in New Zealand we have the opportunity to work towards the benefit of our unique fauna, unique environment, unique primary production industries and, particularly, our unique people.

“It's really important to us to achieve positive outcomes for Māori so that our work involves and enthuses them, and is of value to them across the board. We want to be seen as an example of how to work with an indigenous population with close links to the environment.”