How Japan Is Using The World’s Most Powerful Supercomputer To Accelerate Personalized Medicine

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Imagine getting medical checkups, drugs and other therapies tailored to your own genetic makeup. The concept of personalized medicine is based on the idea that medical treatment should not be one size fits all. But this requires analysis of enormous amounts of data, something only a supercomputer can do efficiently. In Japan, scientists are harnessing the world's most powerful supercomputer, Fugaku, to discover new customized treatments and drug therapies.

Making the most of big data

Kamada Mayumi is a researcher in Kyoto University's Graduate School of Medicine. She has been building a database of genomic information and anonymized clinical data from Japanese people for use in computer simulations. The aim is to exploit Japan’s stock of high-quality data to realize medical care that is both data-driven and predictive. 

Kyoto University researcher Kamada Mayumi

“Genomic medicine can help us determine the appropriate treatment for disease, as well as preventive measures,” says Kyoto University researcher Kamada Mayumi.

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Kamada and her colleagues in the Department of Biomedical Data Intelligence want to employ the clinical data to study how genes affect diseases and their treatment. While genetics is the study of genes and how traits are inherited, genomics is the study of all of a person's genetic makeup, or their genome. Genomics helps researchers understand why some people become ill from certain behaviors or environmental conditions while others do not. Genomics is an emerging field—the first drafts of the human genome were published only 20 years ago—but genomic factors have an enormous effect on public health. According to the U.S. National Human Genome Research Institute, if accidents are excluded, genomic factors play a role in nine out of 10 leading causes of death in the United States such as heart disease, cancer and diabetes.

“Our genomes influence how we are affected by disease or how effective medication is for us,” says Kamada, who was drawn to genomics after studies in bioinformatics. “Genomic medicine can help us determine the appropriate treatment for disease, as well as preventive measures. This personalized approach could mean patients will not have to suffer from the unpleasant side effects of cancer treatments, for instance.”

Kamada and her colleagues are preparing to speed up their research with the Fugaku supercomputer, developed by Japan’s RIKEN research center and Fujitsu. Ranked No. 1 in the Top500 list of the world’s most powerful supercomputers, Fugaku has yielded insights into the novel coronavirus, for example helping scientists identify potential therapeutic agents and simulating the behavior of airborne virus particles. But these applications, performed before the machine was officially inaugurated, are just one way in which Fugaku is being used for public health.

Molecular dynamics simulations on supercomputers

Molecular dynamics simulations on supercomputers like Fugaku can be used to help discover new drugs.

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Led by Kyoto University professor Okuno Yasushi, the researchers will run simulations on Fugaku that model the interactions between cells and potential drug molecules. Known as molecular dynamics, this complex simulation can help scientists understand how proteins interact with other molecules. In a 2019 study, Kamada and colleagues used the technique to simulate and predict drug sensitivity for patients with a certain form of lung cancer. With its massive computing power, Fugaku can greatly reduce the time required for these complex simulations. It’s an important tool for interpreting such simulation data and identifying potential new medicines.  

“By using molecular dynamics, you can see how the molecule is moving in the body, so your understanding is more precise,” says Kamada, whose activities include participating in the Global Alliance for Genomics & Health, an international nonprofit. “With these simulations, you can see differences in the genome. It’s a process of accumulating information about how genomic differences cause and affect diseases.”

Accelerating discoveries

Matsuoka Satoshi, head of the Fugaku supercomputer project at the RIKEN Center for Computational Science in Kobe, notes that high performance computing platforms can yield important new medical discoveries because they combine three essential elements: high-speed data processing to handle the enormous volumes of data involved, artificial intelligence applications and complex computer simulations.

Matsuoka Satoshi, head of the RIKEN Center for Computational Science

“High performance computing is really the dawn of a new era for medical research,” says Matsuoka Satoshi, head of the RIKEN Center for Computational Science.

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“High performance machines like Fugaku are platforms for supporting all three very tightly in an integrated fashion,” says Matsuoka. “For medicine, this allows us to come up with a much better ground truth, for example about how genomes are supposed to behave, proteins are supposed to work, or in pharmaceutical research how potential drugs will be interacting with viruses.”

Artificial intelligence systems looking at past clinical data as well as simulations on supercomputers will be able to outperform human experts in predicting health outcomes, says Matsuoka. This will improve prognosis, accelerate pharmaceutical development, and replace some in-vitro experiments and clinical trials.

When coronavirus research is included, about half the major research projects at Fugaku are focused on health and medicine, ranging from heart failure studies to brain simulations. One feature that gives Fugaku an edge in these areas is that it was designed to be a general purpose platform, not dedicated to a specific kind of simulation, without sacrificing performance. It has the power to execute 442 quadrillion computations per second, but it can be programmed almost like a smartphone or PC, notes Matsuoka, who is already looking ahead to the design of a successor machine.  

the supercomputer Fugaku

Built by RIKEN and Fujitsu, the supercomputer Fugaku was created to tackle some of the toughest social issues. In 2020, it was ranked fastest in the world.

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After Fugaku officially launches in March 2021, Kamada and other scientists will begin sharing its resources. Matsuoka is hoping that many institutions, not only in the local Kobe Biomedical Cluster, but those throughout Japan and overseas, will be able to make use of Fugaku to generate medical breakthroughs.

“High performance computing is really the dawn of a new era for medical research,” says Matsuoka. “We expect many groups to be using Fugaku to advance science and technology and advance social needs, and it's our duty to keep the machine pristine.”

Note: All Japanese names in this article are given in the traditional Japanese order, with surname first.

To learn more about RIKEN Center for Computational Science, click here.

To learn more about Kyoto University’s Department of Biomedical Data Intelligence, click here.

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