Written in our genes: predicting health with genomics

By Yogesh Hirdaramani and Sean Nolan

Dr Swaine Chen, Senior Research Scientist, Genome Institute of Singapore reads the tea leaves for genome sequencing’s impact on public health.

In 2013, Angelina Jolie shared with the world that she decided to have a double mastectomy surgery in a New York Times op-ed. The reason? She learnt that a variation in her genes made her highly susceptible to breast cancer.

Researchers use genome sequencing to understand the entire genetic makeup of an organism. This method can predict the future of one’s health and empower us to make preemptive decisions. On a larger scale, it can be used to improve public health across entire nations.

Dr Swaine Chen, Senior Research Scientist, Genome Institute of Singapore shares what genome sequencing heralds for the future of public health.

Investigating how illnesses affect different groups

First, genome sequencing can identify how illnesses affect different groups and enable researchers to develop treatments.  For example, it uncovered that raw fish sold in porridge stalls caused a spate of bacterial infections in Singapore, shares Dr Chen.

The outbreak may have remained a mystery as the bacteria in question is linked to an infection commonly found in babies. Genomics revealed that the strain in Southeast Asia can cause viral infections, which was previously unheard of, explains Dr Chen.

This discovery led researchers from Tan Tock Seng Hospital and the Genome Institute of Singapore to notice that the bacteria had been prevalent in Southeast Asia for the past 20 years, shared Channel News Asia.

As the West tends to dominate genome research, it is critical to conduct research in other populations to discover how illnesses may affect them differently, explains Dr Chen. For instance, a subtype of lung cancer occurs more frequently in non-smoking East Asians than in other ethnic groups, he continues.

Furthermore, genomics can predict how evolving viruses may start to affect people differently. After all, researchers could better predict the impact of Covid infections by sequencing the genomes of different Covid variants, he shares.
“How do we know which sequences we want to look for? How do we know what mutations impact blood pressure or cancer risk or higher infection rates? It’s genomics enabling all that research,” he notes.

Improving healthcare for overall groups

Second, genome sequencing can improve healthcare for overall groups, such as a specific ethnicity or nationality, by identifying genetic trends and enabling doctors to intervene early.

When doctors have the genome data of entire groups, they can provide prevention measures for individuals at risk. For example, a doctor may notice that a patient’s genes suggest they have a higher than average risk of diabetes, he shares. Then, the doctor could recommend lifestyle changes.

To collect this data, the Genome Institute of Singapore conducted a study of ten thousand Singaporean genomes. They have developed profiles of different ethnic groups in Singapore with five thousand genomes sequenced by 2019.

“If we can reduce risk by five to ten per cent, that’s going to have a huge impact on healthcare costs and on the overall health of the population,” Dr Chen notes.

He expects that genome research will become more commonplace in our lives, much like the Internet did in the late 20th century.

“It will become easier to do this. With some training, most people can start doing things like citizen science labs and that’s where you’re going to see exciting stuff,” he shares.

For instance, researchers in the US worked with citizen scientists to catch and sequence ticks to limit the spread of tick-borne diseases, according to Frontiers in Genetics.

Tightening food security

Third, genome sequencing can improve food security by detecting and preventing disease outbreaks caused by food.

For example, the Food and Agriculture Organisation of the UN works with developing countries including India, the Philippines, and Tanzania to share experience from genome sequencing projects on how to identify the causes of outbreaks in farms and prevent future outbreaks.

The Singapore’s National Centre for Food Science has also established in-house genome sequencing capacity for bacteria to support foodborne outbreak investigations in 2020.

“With advancements in genomics technology, we might even be able to pre-empt outbreaks in farms,” shares Dr Chen.
 “We might even be able to pre-empt outbreaks in farms.”

Tech tools to speed up research

With the current speed of tech development, researchers can conduct genome sequencing and develop treatments at a much faster rate.

The speed of genomics tech development has gone faster than computing tech development over the past 15 years, Dr Chen shares. “It’s totally amazing.”

For one, there has been a huge acceleration in genetic tech. A prime example is gene editing tech that is paving the way for cancer treatment development. For genome scientists, such tech can quickly identify which DNA mutations lead to illnesses like cancer, he explains.

AI can also help classify DNA pieces from bacteria quickly. For example, AI can identify which DNA pieces let bacteria transfer antibiotic resistance to other bacteria. Being able to identify these pieces is crucial in the fight against antibiotic resistance, he explains.

Doing genome research on the cloud can also save time for researchers. AI tools on the cloud can also automate routine aspects of genome research, he explains. For instance, AI can trim huge amounts of genome data to relevant sequences for researchers to examine.

The cloud is much more efficient at handling the large amounts of data involved in genomic research, he continues. Singapore has built a custom cloud infrastructure to support its large scale study of Singaporean genomes, shared A*STAR.

AI can also help automate the more mundane tasks in the laboratory, such as submitting medical certificates. These little things also help to free up more time for researchers to focus on their work, Dr Chen notes.

After Angelina Jolie’s op-ed, more women began to go for similar genetic testing. Likewise, Covid has raised governments’ and the public’s awareness of how useful genome sequencing can be in predicting the future of public health and leapfrogging future health risks.