ESR Senior Science Lead for Bioinformatics and Genomics, Dr Joep de Ligt, explores the transformative potential of genomic sequencing for Aotearoa New Zealand, and the challenges that must be confronted as this technology becomes an ever-present part of our lives.
It is not unreasonable to compare the revolution in genome sequencing to that of the internet. Where at first the web was an exclusive place for scientists, it quickly spread beyond the lab to change the fabric of our lives: how we communicate, work, shop and consume media. Sequencing is going through a similar revolution. Twenty years ago, it was the sole domain of research institutions trying to decipher the human genome. Today, thanks to remarkable advances in technology, sequencing processes that once took months can now be done in hours. And at a fraction of the cost.
Unlocking genetic potential
So, what is sequencing and why does it matter? All living organisms have their own genome – a complete set of genetic instructions found in a cell. Whole genome sequencing is the process of determining the entirety of the DNA (or RNA) sequence of an organism’s genome in one go. In early 2003 the human genome was decoded for the first time. It took 13 years and cost almost USD $3 billion. Today, the same exercise takes less than 24 hours and costs just USD $1,000 – soon predicted to come in around $100.
As the technology has advanced, new opportunities for its application have been unlocked. By analysing a person's genetic code, genome sequencing can help identify specific conditions they may be at risk of developing. This information can be used to guide targeted treatments suited to an individual's needs. Studying genetic data is also giving scientists a better understanding of how diseases evolve and how to defeat them.
For example, the Institute of Environmental Science and Research (ESR), a key player in genomics for infectious diseases within Aotearoa, used data sequenced from COVID-19 patients to demonstrate its spread through airborne transmission, which helped increase understanding about the importance of masking as a protection tool. The sequencing data was also used to predict if antibody treatments would be effective for a severe case by generating genomes in real-time.
Genomic technologies have also been used in our hospitals to identify whether serious antibiotic resistant pathogens detected on a particular ward came in with patients or were spreading within the hospital – vital information that has prevented disruptive and expensive decontaminations of wards and helped identify previously unknown transmission events. This type of on-site sequencing by hospital staff was unthinkable even five years ago.
Beyond healthcare, sequencing is empowering fields as wide-ranging as anthropology, forensic science, food safety, agriculture, as well as environmental protection, including conservation efforts of endangered species through to detection of illegally trafficked products. Here in Aotearoa, the genetic makeup of taonga species, such as the Kākāpō (a native nocturnal parrot), are being studied to better understand genetic diversity which can inform breeding efforts. Genomics is also used understand the factors that contribute to their health and wellbeing, like infections, to increase their survival chances.
New opportunities, new questions
In the same way the internet has altered society in unexpected ways, the rapid innovation and implementation of genomic technologies has raised ethical questions that many countries are grappling with – and that Aotearoa must also address.
A pertinent example is equity of access to genomic science, especially for indigenous and underrepresented communities. Historically, the vast amount of medical research has been carried out on people of European decent, predominantly men, creating huge knowledge gaps. For example, evidence is often lacking about the effectiveness of treatments among non-European populations, which increases inequity and leaves many groups, especially those already marginalised, distrustful of health innovation. Anyone thinking about offering genetic testing and research must fully incorporate equity into their work and continuously ask themselves who will or will not benefit.
In Aotearoa there is currently no legislative protection against genetic discrimination, meaning a genetic risk of disease, however small, can be ‘interpreted’ by financial institutions to increase insurance premiums or refuse loans. For this reason the collaborative alliance Against Genomic Discrimination Aotearoa (AGenDA), of which key ESR staff are signatories, is calling for anti-genetic discrimination legislation to protect all New Zealanders.
Data, lots of data
A single human genome contains over 6 billion base pairs of DNA (approximately 3 billion from each of your parents). Accurately analysing these DNA pairs generates more than 80 GB of information – that’s around 80,000 eBooks worth of data. Although barriers to generating the data are falling, challenges remain in storing, analysing, interpreting and feeding back on all this information in useful ways.
Making the most of the genomics revolution will require systems capable of managing large volumes of information, alongside careful and culturally appropriate governance and stewardship of the data. This includes benefit sharing through culturally responsive data storage, with access regulations that enable expert analysis when needed. Ensuring the appropriate tikanga and protecting the privacy of this information is paramount.
In addition, it will be important to embrace accepted digital standards across different sectors to enable ease of integration between systems and platforms. A motu-wide approach to managing genomic information will not only improve the coordination and quality of data, but will mitigate the risks of regional disparities in accessing these innovative technologies. Some of these disparities are currently evident in many smaller hospitals and healthcare settings that lack genetic capabilities, have a limited ability to easily share data between institutions, and are required to send samples overseas for analysis.
A genomics-enabled future
Technological standards are a small but important part of the overall solution. Charting a course for a genomics-enabled future requires scientists, legislators and community voices coming together to ensure we understand and are addressing the opportunities and implications of genomic sequencing. It is a future in which ESR could have an important role to play – including bringing the right parties together, as well as through the rollout of initiatives like a national e-health platform to ensure genomics gets the attention it deserves.
Work has already started on what this genomics platform could look like for Aotearoa. Initiatives like Rakeiora (a pathfinder project looking for the best ways to incorporate new genomic-based medicine into New Zealand’s healthcare system) will inform platform designs and hold the potential to greatly improve the efficiency and effectiveness of genomic analysis in Aotearoa. This includes a strong equity and Te Tiriti empowering focus, so that the potential of genomics is available to every New Zealander.
Science for life
Predicting the future is hard at the best of times. Consider Time Magazine, that in 1966 declared: “Remote shopping, while entirely feasible, will certainly flop. It has no chance of success.” Then there’s technology entrepreneur Robert Metcalf, and his 1995 prediction: “The internet will go spectacularly supernova, and in 1996 it will catastrophically implode.” We all know better now, but these cautionary tales about predicting the future hold important lessons for predictions about genomics.
Even 10 years ago, we could hardly imagine we would be generating genomes within hours. It is almost impossible to forecast what the science of genomics could unlock in another 10 years. But one thing is true – DNA and RNA are building blocks of life, and contain links to our past, future and environment. Understanding our relationship to our genomes and the appropriate analysis of the data hold keys to our wellbeing. That makes it worth investing in, to ensure a better future for all.