World of Genomics: Japan

Original article by Ellie Fung, August 2021. Updated by Kira Newbon in July 2023.

In the latest World of Genomics entry, we shine a spotlight on the land of the rising sun – Japan.

Japan has long been home to a flourishing scientific community that has made numerous transformative contributions to the field of genetics. These include the development of early high-throughput DNA sequencers, the genome-wide association analysis methodology and integrated genomic databanks. Recently, the government has been actively championing the integration of genomic medicine into the national healthcare system. Japan also plans to continue to advance genomic research and strengthen collaboration with international research communities.

The population of Japan

Japan is an island nation situated in the western Pacific Ocean, separated from the Eurasian continent by the Sea of Japan. The East Asian country has a rich, albeit tumultuous, history stretching back 35,000 years when the Jomōn hunter-gatherers first migrated from mainland Asia. The Yayoi arrived later in 500BC and interbred with the Jomōn. The modern Japanese people are believed to be descendants of the two early inhabitants. Japan eventually became unified under a monarchy that persists to this day, though the emperor’s power was constantly challenged by various military groups over the centuries. Due to the country’s long history of self-imposed isolation, immigration has been rare. This changed following the second world war when Japan saw a steady increase in foreign residents. In recent years, the ageing population and shrinking labour force have led to a dramatic rise in the number of foreign workers and immigrants. 

Geographic and demographic information

Summary statistics:

• Land area: 364,485 km² 
• Gross domestic product (GDP): 
• Total: $4.23 trillion (2022) 
• Per capita: $36032.39 (2022) 

Population statistics: 

• Population size: As of July 2023, the population of Japan was estimated to be 123,264,281  
• Birth rate: 7.013 per 1,000 people (2023) 
• Death rate: 11.523 per 1,000 people (2023) 
• Infant mortality rate: 1.564 per 1,000 live births (2023) 
• Average life expectancy: 84 (2021) 
  • Male: 81 (2021) 
  • Female: 87.8 (2021) 
• Ethnicity: Japan considers itself a mono-ethnic country, with the 2018 census reporting that the Japanese made up 97.8% of the total population. The largest non-Japanese ethnic groups are Chinese (0.73%), Korean (0.40%), Vietnamese (0.28%), Filipino (0.23%), Brazilian (0.17%) and Nepalese (0.07%). 

Healthcare system

Japan achieved the world’s highest life expectancy in the 1980s, partly due to the success of its unique healthcare system. The statutory health insurance system (SHIS) provides universal health coverage for 98.3% of the Japanese population. Meanwhile, the separate Public Social Assistance Program provides for the remaining impoverished 1.7%. Under SHIS, every Japanese citizen is required to enroll in either an employment-based or residence-based medical insurance plan. The latter includes separate plans for unemployed individuals and the elderly aged 75 and older. Funding primarily comes from tax revenue, though patients pay for 10-30% of the bill for medical treatment depending on age and income.

National and local governments regulate almost all aspects of SHIS to ensure each system provides a high standard of medical care. SHIS also promotes improvements in the living environment and better nutrition. Faced with the challenge of an ageing population, the system is currently undergoing reforms to maintain its success in the future.

Health priorities

Malignant cancers have been the leading cause of death in Japan since 1981, with the death rate rising every year. It is now expected that one in two people will get cancer during their lifetime. In 2019, cancer was responsible for 27.3% of all deaths in Japan. This was followed by lifestyle diseases (15% of all deaths) and senility (8.8% of all deaths). In recent decades, Japan has also been troubled with growing concerns of suicide, particularly in young people. Although suicide rates have decreased in the last decade, suicide was the leading cause of death for those aged between 15 and 39 in 2019.

Currently, the biggest public health challenges are changing lifestyles and a rapidly ageing population. Obesity incidence is rapidly rising, with male obesity increasing from 1.6 to 4.8% between 1997 and 2016. Smoking and alcohol consumption are also high in men.

To address these issues, the government implemented Health Japan 21 in 2000, a national health promotion plan that places an emphasis on primary prevention. Another major goal of the strategy is to reduce health disparities between socioeconomic groups. By 2011, 35 of 59 targets were met or improved, including improvements in sodium intake, exercise and awareness of metabolic diseases. Only 14 fields remained the same, including suicide rate and heavy drinking, while 9 worsened, such as number of daily steps and diabetic complications. Japan is currently within the second phase of Health Japan 21, running from 2013 to 2022.

In addition, the National Programme on Rare and Intractable Diseases focuses on promoting research and providing support for those with rare diseases. More than half of the 331 diseases included are Mendelian disorders, which are a type of genetic disorder resulting from a mutation in a single gene.

Genomic medicine capabilities

Japan has been heavily involved in human and medical genetics research since the field’s infancy. Through the decades, the country has thus accumulated a wealth of knowledge on the genetic basis of disease. Notably, Japan was one of the six countries involved in the Human Genome Project, contributing significantly to the completion of sequencing chromosomes 11 and 21. Japanese researchers have also placed emphasis on functional genomics, structural biology and bioinformatics.

Since 2015, Japan has been proactively promoting the realisation of genomic medicine on a national level in line with advances in genomic technology.

In 2018, the Centre for Cancer Genomics and Advanced Therapeutics was established to promote the delivery of cancer genomic medicine to patients. In June 2019, the Japanese regulatory agency approved 2 types of tumour genomic profiling tests in 167 hospitals provided under SHIS. These are FoundationOne CDx Cancer Genomic Profile and OncoGuide NCC Oncopanel System. By April 2020, 206 hospitals have been approved to conduct gene panel tests for cancer care. Moving forward, the data collected by hospitals providing cancer genomic medicine can also be used to improve patient care.

However, genetic testing and counselling remain limited in Japan. SHIS only covers genetic testing and genetic counselling for 79 genetic diseases. Meanwhile, prenatal genetic testing and preimplantation diagnoses are not reimbursed by SHIS.

Cancer genomic medicine (CGM) uses tumour genome profiling to optimise treatment for patients suffering from a range of cancer types. As of 2022, 233 institutes have been established that are qualified to offer CGM.

Additionally, the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) has made clinical and genomic data from 36,340 patients openly available to CGM hospitals, academic institutions and industries.

This data sharing platform will be instrumental in the coming years, facilitating a greater understanding of the distribution of genetic alterations across cancer types in Asia and enabling more precise patient treatment.

Furthermore, an additional cloud system is under way called CALculation & Investigation ClOud (C-CAT CALICO) which will store raw sequence data in the effort to examine novel genetic alterations. This development aims to expand C-CAT’s benefits on a global scale.

Notable projects

• Kyoto Encyclopedia of Genes and Genomes (KEGG): KEGG is the world’s first database to integrate genomic, chemical and systematic functional data generated by genome sequencing and other high-throughput experimental technologies.
• BioBank Japan (BBJ): Launched in 2003, the BBJ is one of the world’s largest disease biobanks, containing DNA, serum and clinical information from more than 270,000 Japanese patients. It aims to provide evidence for the clinical implementation of personalised medicine.
• Initiative on Rare and Undiagnosed Diseases (IRUD): Established in 2015, IRUD promotes the use of whole-genome or whole-exome sequencing to diagnose individuals who have previously not been successfully diagnosed. They also share data with other countries.
• Medical Genomics Japan Variant Database (MGeND): MGeND integrates clinical and genomic data of Japanese patients to promote the implementation of genomic medicine. It includes pathological genome variants for a range of diseases and HLA allele frequencies.
• Genome Medical Alliance Japan (GEM Japan): A Global Alliance for Genomics and Health driver project, GEM Japan aims to facilitate sharing of genomic and phenotypic data obtained from Japanese health and disease research projects with domestic and global communities. 

Notable organisations and companies

• Japan Agency for Medical Research and Development (AMED): AMED is the headquarter for national medical research programs, providing public research grants for multiple medical fields. Through The Project for Genome and Health Related Data, AMED promotes the use of genomic data infrastructures and supports multiple research and development projects in genomic medicine.
• RIKEN Centre for Integrative Medical Sciences (IMS): Using multi-omics and AI technologies, IMS aims to elucidate human disease pathogenesis and develop new therapeutics. The four Divisions collaborate to promote state-of-the-art research, spanning genomic medicine, human immunology, disease systems biology and cancer immunology.
• National Institute of Genetics (NIG): Founded in 1949, NIG leverages cutting-edge genetic technologies to conduct bioscience research. It also provides genetic resources and services to global and domestic scientific communities.
• Centre for Cancer Genomics and Advanced Therapeutics (C-CAT): The National Cancer Centre was founded C-CAT in June 2018 to collect, store and manage genomic and clinical information on cancer patients. C-CAT also supports research, development and clinical implementation of cancer genomic medicine with this data.
• Tohoku Medical Megabank Organisation (ToMMo): Established by Tohoku University, ToMMo aims to foster a genome-based medical system to reconstruct the communities affected by the 2011 Great East Japan Earthquake. In January 2021, ToMMo released the first Japanese reference genome.
• Takara Bio: Takara Bio is a biotechnology company based in Japan. It offers a range of research reagents and scientific instruments to support research in the field of life sciences. Their Clontech brand offers products for functional genomic analysis, next-generation sequencing and cDNA library construction.
• Sysmex Corporation: Founded and currently headquartered in Japan, Sysmex Corporation is involved in developing, manufacturing and selling diagnostic technologies. They developed the OncoGuide NCC Oncopanel System cancer genome profiling panel that is now covered under SHIS.

Notable individuals

Several Japanese-born scientists have made a significant impact on the field of genetics. Below are just a few of them:

• Kametaro Toyama (1876-1918): Toyama was a Japanese geneticist known for his research on the interbreeding of silkworms. In 1906, his work revealed that Mendelian inheritance applies to not only plants, but also to animals.
• Akiyoshi Wada (1929-): Wada is a Japanese biophysicist. In 1981, he led a national project to develop the world’s first automated DNA sequencing device. Later on, the device was a crucial step for completing the Human Genome Project.
• Hideki Kambara: Kambara is a Japanese scientist known for developing various genetic technologies. Most notably, he developed the high-throughput, multi-capillary DNA sequencers that were instrumental for the early completion of the Human Genome Project.
• Norio Niikawa (1942-): Niikawa is a Japanese physician and medical geneticist. In 1981, he discovered Kabuki syndrome, a rare autosomal dominant disorder.
• Nobuyo Maeda (early 1950s-): Maeda is a Japanese geneticist and medical researcher. Her work focuses on the genetics and molecular pathology of complex diseases such as atherosclerosis, hypertension and diabetes. Additionally, she generated the first mouse model for atherosclerosis.
• Yusuke Nakamura (1952-): Nakamura is a renowned Japanese geneticist and cancer researcher best known for developing the methodology for genome-wide association studies in 2001. Since its conception, the method has revealed the genetic architecture of numerous human diseases, thereby revolutionising medical genetics. He is also a leader in cancer genetics and personalised medicine, focusing on translating research into clinical cancer care.
• Naomichi Matsumoto (1961-): Matsumoto is a Japanese physician and medical geneticist. He has identified causative genes for several human diseases, such as West syndrome, porencephaly and Coffin-Siris syndrome.
• Shinya Yamanaka (1962-): Yamanaka is a researcher and Nobel Prize winner who is known for his discovery that mature cells could be converted to stem cells.

Next steps

Japan’s rich genetics knowledge base and technological capacity put the country in an ideal spot to realise the potential of genomic medicine. Yet, the clinical implementation of genomic medicine has lagged, especially compared to Europe and the US. This is largely due to inadequate social infrastructure. Firstly, there is a need for regulations and transparency on the use of genetic information. Secondly, there is an overwhelming shortage of trained genetic counsellors, despite growing demand.

In addition, there is a poor public perception and understanding of genetics in Japan. Rare hereditary or genetic diseases remain taboo and are sometimes considered to be the affected individual’s own fault. Moreover, cultural discrimination is still rife in the largely homogenous Japanese society.

The Japan Society of Human Genetics (JSHG) has been making various efforts to address these issues and promote the deployment of genomic medicine. They aim to establish guidelines for the proper use of genetic information, nurture genetics professionals and promote public genetic literacy. Alongside other medical genetics associations, their efforts have included advocating for the incorporation of human genetics and cultural diversity in school curricula and raising awareness of genetic diseases in the public and media.

In lieu of the growing threat of cancer and other rare diseases, Japan is expected to continue to promote research and clinical implementation of genomic medicine. In June 2019, the Japanese health ministry announced that the country would commence whole-genome sequencing analyses on up to 93,000 people, modelled upon Genomics England’s 100,000 Genomes Project.

More recently, Japan is playing a pivotal role in creating open-source genetic databases, both domestically and internationally.

Japan continues to be an undeniable leader in innovation, having brought the world countless transformative technologies. We are excited to see what more the country has to offer to the field of genomics in the near future!

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References

• Aizawa, Y., Watanabe, A. & Kato, K. (2021) Institutional and Social Issues Surrounding Genetic Counselors in Japan: Current Challenges and Implications for the Global Community. Frontiers in Genetics. 12, 552.
• Ezoe, S., Noda, H., Akahane, N., Sato, O., Hama, T., Miyata, T., Terahara, T., Fujishita, M., Sakamoto, H., Abe, S. K., Gilmour, S. & Shobayashi, T. (2017) Trends in Policy on the Prevention and Control of Non-Communicable Diseases in Japan. Health Systems and Reforms. 3 (4), 268-277.
• Fukushima, Y. & Takada, F. (2020) Clinical Genetics in Japan: Efforts of Human Genetics Societies and Related Organizations. JMA Journal. 3 (1), 1-8.
• Mano, H. (2020) Cancer genomic medicine in Japan. Proceedings of the Japan Academy. Series B, Physical and Biological Sciences. 96 (7), 316-321.
• OECD (2019) OECD Reviews of Public Health: Japan A Healthier Tomorrow. OECD Publishing, Paris. https://doi.org/10.1787/9789264311602-en.
• Sakaki, Y. (2019) A Japanese history of the Human Genome Project. Proceedings of the Japan Academy.Series B, Physical and Biological Sciences. 95 (8), 441-458.
• Suzuki, H., Watanabe, T., Uehara, T. & Kosaki, K. (2019) Medical genetics and genomic medicine in Japan. American Journal of Medical Genetics.Part C, Seminars in Medical Genetics. 181 (2), 166-169.
• Takashi Kohno, Kato, M., Shinji Kohsaka, Sudo, T., Tamai, I., Shiraishi, Y., Okuma, Y., Ogasawara, D., Suzuki, T., Yoshida, T. and Mano, H. (2022). C-CAT: the National Datacenter for Cancer Genomic Medicine in Japan. Cancer Discovery, 12(11), pp.2509–2515. doi:https://doi.org/10.1158/2159-8290.cd-22-0417.