Scientists comment on new genomic research infrastructure

More detail on the new genomics infrastricture can be found here.

John McEwan, Animal Genomics Principal Scientist, AgResearch Invermay:

Will the new infrastructure significantly enhance genomic research in New Zealand?

“Yes it will make a very significant advance in several ways. First it creates a stable structure that allows sensible purchasing decisions around next generation sequencing and genotyping equipment for New Zealand as the technology advances. The quantity of information these technologies generate is many thousands fold more than previously available and still increasing rapidly. The amount of information also means that specialised databases, computers and bioinformaticians need to be available in order to store and process the results and this is also provided as part of the initiative. The scale and scope is outside historical university structures and was previously only available in large “sequencing centres” overseas. The exception was the bioinformatics and linked computing capacity in AgResearch which is part of the new initiative.

“New Zealand is extremely dependent on exports of biological products, as well as having a unique flora and fuana, and a long history of biomedical research. This new infrastructure directly addresses these research needs.”

How would you describe New Zealand’s track record in genomic research to date?

“New Zealand has a very proud track record in genomics research. It is particularly strong in agricultural biotechnology. However, in recent years as the scale and the quantity of DNA sequence and genotypes escalated so few groups had the capacity or financial resources to make the capital equipment investment required. In many cases this led to groups over the last decade increasingly contracting significant quantities of sequencing and genotyping offshore. The development of NZGC now allows this work to be done within New Zealand. However, more importantly it allows New Zealand to also build up its human resources that can both create and process the resulting data. It is in my opinion this capacity that will be critical to New Zealand’s future.”

Do you see your own research being able to benefit from this new arrangement?

“In my own case, I have been associated with a number of international consortia that have over the last decade undertaken very large scale sequencing and genotyping. This included several projects that sequenced and annotated the bovine genome over a period of 5-6 years. This work, totalling in excess of US$60M was done offshore and New Zealand contributed several million dollars towards the work. We were involved in analysis of the resulting information. This greatly aided our research producing DNA markers for production traits. A number of these are now commercially used in New Zealand cattle and sheep. “Perhaps of most importance was the rapid uptake of a technology derived directly from the results of this work called “whole genome selection” that been implemented in the New Zealand dairy industry over the last year. The benefits stemming from this technology alone will dwarf New Zealand’s initial research investment, increasing the rate of genetic gain of this multi-billion dollar industry by 50-70%.

“We are now doing the same in sheep, but for around 5% of the cost in cattle. The difference is New Zealand’s contribution of around half the project was done using a next generation 454 FLX sequencer based at Otago. The sequencing was done in 6 months late last year and the initial assembly used AgResearch bioinformatics infrastructure. Both of these will be associated with the new initiative.

“A key further component was the introduction of the KAREN high speed research network, which allowed transfer between groups of large quanities of data and on which the NZGC will be dependent. Currently, we are now tracking about 12 months behind cattle in the introduction of whole genomic selection.

“That this work was done in less than 10% of the time and 5% of the cost and was also the first mammalian genome assembled outside the North America and Europe shows just how rapidly this field is moving. As costs decline even further, and they have declined about 5 fold in the last year, I predict this process will be repeated for many other species of agricultural and horticultural importance to New Zealand.

“To summarise these technologies are critically important to New Zealand because of our dependence on biological exports. The results of this research are also being rapidly adopted by industry.”

Andrew Shelling, Associate Professor at the Medical Genetics Research Group, University of Auckland:

“New Zealand scientists have often been presented as punching above their weight. In terms of research output per dollar invested in research or national GDP, we seem to be doing well. There is often a sense that New Zealand scientists put a lot of thought into designing experiments, as research funding is short and therefore valued, and often it takes a while for reagents to arrive, so planning is important.

“That attitude will continue to exist, however, for some research areas, access to critical infrastructure is now central to research progress. Genetic research has undergone a dramatic change in the past few years, with changes in equipment and study design. Large scale projects are being recognised as being the only way to address the underlying basis of complex disease, along with high tech equipment, and access to signficant computing power and bioinformatics skills. For New Zealand to compete on the international stage in genetic research, investment in the infrastucture as seen in this new initiative is imperative.

“My own research on cancer and reproductive disorders is looking at the investigation of larger groups of patient samples, and more detailed and systematic analysis. Gene expression microarrays, genotyping SNP chips, and next generation DNA and transcriptome sequencing will be the tools of the next few years, and now we have the opportunity to do that in our own back-yard, rather than sending samples or scientists off-shore to undertake these types of studies.”

To speak to these and other experts on genetics and genomic research, contact the Science Media Centre on 04 499 5476 or