Constructing the First Version of the Japanese Reference Genome

Although genome sequencing has come leaps and bounds over the past 20 years, there did not exist a reference genome specific to the Japanese. That is until now. Researchers at Tohoku University have completed and released the first Japanese reference genome by analyzing the genomes of three Japanese individuals using high coverage, long-read next-generation sequencing technologies.

The Ideogram of JG1

The Japanese now have their own reference genome thanks to researchers at Tohoku University who completed and released the first Japanese reference genome (JG1).

Their study was published in the journal Nature Communications on January 11, 2021.

"JG1 can aid with the clinical sequence analysis of Japanese individuals with rare diseases as it eliminates the genomic differences from the international reference genome," said Jun Takayama, co-author of the study.

Back in 2003, the Human Genome Project, through a gargantuan global effort, cracked the code of life and mapped all the genes of the human genome.

Since then, more accurate versions of the human reference genome have been realized. Aiding this has been the advancement in next-generation sequencing technologies that allow for short read of approximately several hundred bases in a massively parallel way, reducing the costs and time to sequence DNA and RNA.

The international reference genome is based on an individual of African-European descent. This hampers investigating genetic variants or rare disease and cancer driving genes in Japanese owing to natural genomic difference reflective in different populations.

Associate professor Takayama and professor Gen Tamiya from Tohoku University's Tohoku Medical Megabank Organization (ToMMo) and the Advanced Research Center for Innovations in Next-Generation Medicine (INGEM) and colleagues from Tohoku University School of Medicine, School of Information Sciences, RIKEN AIP Center, and Miyagi Cancer Research Institute developed JG1 as the first part of the Japanese Reference Genome Assembly (JRGA) project.

This high-precision reference sequence is applicable to the whole human genome analysis and was constructed by analyzing the genomes of three Japanese individuals using high-coverage, long-read next-generation sequencing technologies.

Researchers can efficiently investigate the causal genetic variants of rare diseases and cancer driver genes with JG1.

"JG1 may be applicable to other populations, especially those from Asia. In addition, with the JG1, the accuracy of the Japanese allele frequency and haplotype reference panels gets improved," added Takayama.


Fuji Nagami
Department of Public Relations and Planning,
Tohoku University Tohoku Medical Megabank Organization
Email: [email protected]

Published: 29 Jan 2021


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Title: Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference
Authors: Jun Takayama, Shu Tadaka, Kenji Yano, Fumiki Katsuoka, Chinatsu Gocho, Takamitsu Funayama, Satoshi Makino, Yasunobu Okamura, Atsuo Kikuchi, Sachiyo Sugimoto, Junko Kawashima, Akihito Otsuki, Mika Sakurai-Yageta, Jun Yasuda, Shigeo Kure, Kengo Kinoshita, Masayuki Yamamoto, and Gen Tamiya
Journal: Nature Communications
DOI: 10.1038/s41467-020-20146-8

Funding information:

The Tohoku Medical Megabank (TMM) Project from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and the Reconstruction Agency

the Japan Agency for Medical Research and Development (AMED; Grant Numbers JP20km0105001 and JP20km0105002) for Tohoku University.

JSPS KAKENHI Grant Numbers JP19H05200 and JP19K06625.

All computational resources were provided by the ToMMo supercomputer system (, which is supported by Facilitation of R&D Platform for AMED Genome Medicine Support conducted by AMED (Grant Number JP20km0405001).