From tracking the spread of coronavirus to understanding the very nature of what makes us human: genomics impacts daily life in myriad ways.
From tracking the spread of coronavirus through to understanding the very nature of what makes us human: genomics impacts daily life in myriad ways. From the obvious to the abstract, this relatively young branch of science has already impacted how we live and undoubtedly has the power to dramatically improve society.
Genomics is the study of an organism’s DNA sequences, including genes, their function and evolution. This also includes the computational analysis of the big data that is generated as a result. Genomics is not the same as genetics, which focuses more on how traits are passed from one generation to the next.
The field of genomics is still in its infancy, with the first complete human genome published in 2003. But the advent of supercomputers has enabled a rapid acceleration in the time it takes to read, analyse and understand genes. This gives us the potential to influence anything from personalised medicine to protecting critically endangered species. But public understanding of these technologies, including the benefits and risks, is failing to keep pace with that of scientific progress.
With the rapid rate of improvement in genomics technologies, there is an urgent need to take the time to properly articulate just how far we’ve already come.
The outbreak of COVID-19, or coronavirus, in January 2020 is a prime example of how genomics can impact daily life for public good
The outbreak of COVID-19, or coronavirus, in January 2020 is a prime example of how genomics can impact daily life for public good.
Dr Ben Ward, a postdoctoral scientist in the Clavijo Group at EI, says: “the coronavirus epidemic is a great example. Genomics is instrumental in combating this, from understanding the nature of the virus to tracing its potential origins.”
There have already been various hypotheses for where the virus came from and Dr Ward suggests these proposals are usually accompanied by genomic data, through comparing similarities based on mutations and geographical data.
While he was doing his PhD, researchers were “tracking the spread of diseases such as MRSA in Turkey,” he explains. “You could trace exactly where they originated based on the mutation rates.”
Another example of the power of such genomics techniques is in Earlham Institute’s big project in collaboration with the University of Liverpool and the Quadram Institute - tracing the spread of multi-antibiotic resistant salmonella around the globe as part of the 10k salmonella genomes project.
The potential to save lives by being able to target specific antibiotic treatments is huge.
Thanks to genomics, the UK has an incredible capacity to understand salmonella. The fact that we can sequence the genome of any salmonella strain quickly and cheaply gives us an incredible insight into its epidemiology: its evolution and transmission.
The diagnostic power of genomics is helping us in many ways when it comes to human health - from understanding the genetic basis of inherited genetic diseases through to even being able to gene edit somatic cells to protect against certain conditions. Of course, there is a bioethical component to how we develop these technologies going forward, but there is huge potential to make a very positive impact.
The journal Nature has reported on the massive international effort that is transforming how we understand cancer genomics. The study looked at more than 2600 types of cancer across 38 tissues and has revealed the genetic basis of tumours in a greater depth than ever before.
The latest genomics technologies are advancing our abilities to diagnose potentially lethal conditions even in real time. We can sequence DNA for just a few hundred pounds with the Oxford Nanopore MinION, which the Leggett Group at EI has been using along with the Hall Group at the Quadram Institute (QI) to help diagnose sepsis in preterm babies in hours rather than days.
As Dr Richard Leggett, Group Leader at EI, explains: “We are able now to go from faecal sample to pathogen and antibiotic resistance profile in just four to five hours. With high-risk patients, time is absolutely critical. The potential to save lives by being able to target specific antibiotic treatments is huge.”
On the subject of antimicrobial resistance, genomics is revealing how antibiotic resistance exists everywhere in nature and is a real and present threat to human health. Sepsis is now thought to be the world’s second biggest killer after cardiovascular disease. Resistance means it’s likely to be a question of when, not if, it will claim the number one spot.
Dr Matt Bawn, an expert in antibiotic resistance who works at EI and QI, says the future is looking grim. “Unless something drastic happens very soon,” he says, “we’re going to enter an era where antibiotics no longer work for routine things, which means that people will die from normal infections.”
Genomics is helping us not only to diagnose sepsis, and track antibiotic resistance and its spread, but also to help us identify previously undiscovered antimicrobial compounds that could help us keep bacterial diseases at bay.
The power of genomics isn’t limited to medicine. With growing populations, a warming planet and the threat of pests and disease to crops, food security is an area in which genomics can and does play a big role.
It can be a struggle to see how work taking place in the lab, or on a computer (where much of genomics research takes place today), is having an effect on what goes on your table, but big data genomics research is ensuring that food is readily available.
Research at EI is helping to make the insights we glean from genomics applicable in the field. We’re working on all sorts - from sequencing and decoding the wheat genome through to understanding how to improve crops by targeting diversity and resilience to pests and adverse environmental conditions.
In Colombia, EI scientists are helping cocoa growers to tackle soils that are rich in heavy metal pollutants such as cadmium (that’s right, you can thank genomics for ensuring your ongoing chocolate supply). We’re even targeting the grasses used to feed cattle and learning how we might alter the protein content so that cows belch less. Our researchers are also involved in projects that aim to tackle pests such as aphids, and the diseases wrought by fungi, viruses and bacteria that plague our global food supply.
In the long run, our projects looking at biodiversity as a whole are helping us to understand some of the genetic variation that we have perhaps lost through selectively breeding crops, and that helps us breed more resilient varieties for the future.
When Tim Berners Lee set up the world wide web at CERN, did he know quite what it would become?
Dr Ben Ward likens present-day genomics to the internet in its early days. “When Tim Berners Lee set up the world wide web at CERN, did he know quite what it would become?” he asks. “Now, practically everybody uses it to study all sorts of problems.”
If you want to change a headlight bulb on your car, all you have to do is type it into YouTube and watch a three minute tutorial. The same goes for replacing the filter in a coffee machine, or learning how to play a new song on the ukulele.
With genomics, Dr Ward thinks we’re in a very similar situation. We have so much data, and an increasing capacity to analyse it with the advent of bioinformatics, machine learning and supercomputing. As part of the Darwin Tree of Life project, Earlham Institute is contributing to such advancement of knowledge by mining genomes for novel pharmaceuticals. We’re helping to sequence the genomes of 2200 UK animals, plants, protists and fungi in order to help us understand more about evolution.
Protists, for example, cause some of the most potent threats to humanity - malaria being an obvious example. Yet we currently know very little about the sheer diversity of the protists even in a sample of pond water from your average back garden. Genomics will help us to delve into this hidden biodiversity and discover answers to questions we never even knew we would have to ask.
As exciting as all of this is, however, the technological advancement around genomics has been quicker than the public dialogue has had a chance to catch up.
This is just a brief foray into just some of the areas in which genomics has a huge impact on everyday life. That impact is only going to get bigger as genomics technologies continue to develop at an accelerating pace while decreasing in cost and increasing in throughput.
As exciting as all of this is, however, the technological advancement around genomics has been quicker than the public dialogue has had a chance to catch up. As much as the life science community has a role to play in developing these tools, we have a duty also to continue having an open dialogue that acknowledges fears around such technology, as well as the potential risks. There is a continuing debate over who owns genomic data, for example, which only becomes more complicated with the advent of legislation such as GDPR. The ethical considerations around using gene editing to combat a swathe of conditions, particularly in embryos, are far from clear cut.
For the general public, it’s important to note that genomics provides just one angle to hopefully improve lives, but it doesn’t involve gene editing the world around us to solve every problem. In many cases, changes to lifestyle, behaviours and business practices will continue to be most effective in the long run - and hopefully genomics will provide us with the knowledge to help inform those better decisions.
Indeed - with a greater understanding of the role our gut microbes have to play in nutrition, thanks in-part to genomics research, those decisions should eventually become much easier to make.
In a world in which the latest genome sequencing can already be carried out in real time for just a few hundred pounds, with work underway to plug a DNA sequencing machine into any smartphone, it’s exciting to think of what the coming decades might hold for genomics and how it can positively impact society.
