Message from past director of the center

Miyano Satoru

Promoting genomic medicine

This is the mission of the Human Genome Center. For that purpose, researchers specializing in genome sequence analysis, bioinformatics, and ELSI (Ethical, Legal, and Social Issues) have gathered at the HGC. The HGC also has SHIROKANE, the largest life science specialized super computer in our country, which has successively produced the most cutting edge research results in the world. For example, in 2016, we analyzed the entire genome sequence and thereby clarified one of the ways in which cancer evades the immune system. By analyzing the data of over 10,000 patients, we are trying to attain some level of understanding of cancer patients for whom immune checkpoint inhibitors are effective. (Kataoka K, Shiraishi Y et al.. Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers. Nature. 534(7607):402-406, 2016)

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The arrival of an age when anyone can use their own genome information, and the implementation of genomic cancer treatments

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As of 2017, the cost of obtaining the data needed to sequence one's own genome is $1,000. Soon it will drop below $100. In this context, we are already completely sequencing the genome information of cancer patients and translating and interpreting that information back to the patients in a clinical context– that is, we are implementing "clinical sequencing." This is not something the HGC can do alone, but is one of Japan's leading edge projects being conducted by a combined team of the Institute of Medical Science at the University of Tokyo, the Advanced Clinical Research Center, and the Health Intelligence Center, all with the cooperation of cancer patients. Of course, SHIROKANE plays a central role in this project.

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Super computers and artificial intelligence are indispensable systems for genomic medicine

Each one of your cells contains a blueprint written in the language of DNA, a string of 3 billion letters spelled ATCG. You read those blueprints and formed your body of tens of trillions of cells from a single fertilized egg. The total length of the DNA reproduced when cells divide is at least 12 times the length of the journey "Hayabusa" took to and from the asteroid Itokawa. Cancer is an illness in which this DNA becomes mutated for various reasons and cannot repair itself, causing the system to go berserk. Using a book as a metaphor, mutations might be things like miswritten letters, missing letters, or ripped pages. Some pages might also be out of order. This changes the story of life, and a diverse mass of cells evolves inside the body, acquiring means of surpassing the immune system and resisting anticancer drugs.

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The doctors on the Tokyo University Institute of Medical Science Sequence Research Team are using super computers and the artificial intelligence system Watson to fight cancer.

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In the past, the International Human Genome Project took 13 years to sequence the DNA of the 3 billion letters that make up the human genome. Today, I can obtain the data needed to sequence all my DNA within a few days. However, this data is as if 30 copies were made of documents with 3 billion letters printed on them, then those copies were put through a shredder and came out as a mountain of paper scraps cut to the length of around 100 letters each. In the future, we will be using SHIROKANE to guess the original DNA like solving a jigsaw puzzle, and to find out what sorts of mutations are happening where.

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Understanding each patient's cancer begins with solving this DNA jigsaw puzzle. A software program called Genomon is doing this. As a result, we have found anywhere from several hundred to several million possibly cancer causing DNA mutations in single cancer patients.

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This is where Watson comes in. Our Watson has learned massive amounts of data such as the summaries of over 26 million medical and life science papers, the information on cancer mutations we have found so far (there are 4 million or more), the biomolecular networks life science has clarified until now, drug patent information, and clinical study information. It is able to read a natural language, English. This is similar to how the "Tachikoma" in the anime Ghost in the Shell read "Flowers for Algernon" (around 21 minutes, 30 seconds). Robots can read it, but no human being has ever looked through all of this data. When we upload mutation information into our Watson, it presents the originating gene and drug candidates along with grounds in about 10 minutes. The doctors click the links to the displayed grounds and review them based on their specialized knowledge, then think about which gene is the culprit, which drugs can be used and which cannot, and whether or not this information can be used in the patient's treatment plan. The doctors take responsibility for diagnoses, and do not simply swallow whatever information Watson displays.

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When a medical specialist goes through this process without Watson, it takes at least 2 weeks even with around 100 mutation candidates. Watson's help has made it possible to do this in around 1 day, including the review. However, there are many cases when nothing is found, and the fact is that we we have a serious deficit of the data, knowledge, and drugs that are the foundation of understanding a patient's condition. With the help of artificial intelligence, at least we may be able to say that we have beat the speed of cancer's progress.

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I think that Watson should really be called "knowledge augmentation" rather than "artificial intelligence." I think that Watson will change cancer treatments in the near future by augmenting the knowledge of doctors.

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We have entered an age in  hich we can expect great things of the world that will open up before us when we knock on the door of individualized genomic medicine.