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Design of 'Japonica Array'

A SNP array optimized for the Japanese population

September 2, 2015
Tohoku University
Scientists have successfully developed the Japonica Array which is the first ever SNP array optimized for Japanese population.The aim of development of Japonica Array is not only to facilitate the prospective genomic cohort study conducted by ToMMo but also to make a contribution to the genomic medicine studies.

A research group, led by Professor Masao Nagasaki and Senior Assistant Professor Yosuke Kawai at Tohoku University Tohoku Medical Megabank Organization, has successfully designed the first ever SNP*1 array that has been optimized for the Japanese population.

SNP, which stands for Single Nucleotide Polymorphism, is a DNA sequence variation that occurs commonly within a population.

This new array, called the "Japonica Array," covers the whole-genome region from which the SNPs possessed by Japanese people can be obtained with a high degree of accuracy.

The design of the Japonica Array was accomplished by developing and implementing a unique SNP selection algorithm and analyzing, on a supercomputer, all of the genome information from the 1,070 individuals who participated in the cohort studies*2 of the Tohoku Medical Megabank Project.

By using genotype imputation*3 technology, information on a maximum of 20 million SNPs are presumed from only 659,253 SNPs on the Japonica Array.

The Japonica Array has an imputation accuracy that is at least 10% better than other existing SNP arrays that contain an equivalent number of SNPs, and offers a level of performance that is equivalent to or higher than existing SNP arrays that contain three or more times the number of SNPs.

This research has produced a basic analysis tool for the large-scale identification and study of the genes related to the physical constitution and diseases that are peculiar to the Japanese. It has so far yielded important results that can accelerate the research of personalized healthcare and medicine.

The results of this research were released in the online version of the Journal of Human Genetics on June 25, 2015.

Tohoku University Tohoku Medical Megabank Organization (known as ToMMo) has been working in cooperation with Iwate Medical University on the Tohoku Medical Megabank Project. It is part of the universities' contribution towards reconstruction, following the Great East Japan Earthquake in 2011.

Since 2013, the two universities have been conducting cohort studies, which include some150,000 community residents in Miyagi and Iwate prefectures.

*1 Single nucleotide polymorphism (SNP): A variation of a single base of the genome sequence among individuals. Usually, a variation that exists at a constant frequency or higher is called a SNP.

*2 Cohort study: A study in which a specific group of people is tracked for a given period of time to reveal the relationship between diseases and environmental factors such as lifestyle habits, genetics and other factors.

*3 (Genotype) imputation: An information science technique for estimating the genotype of several millions of unmeasured SNPs with a SNP array by combining it with a reference panel.

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Materials provided by Tohoku University. Note: Content may be edited for style and length.

Journal Reference:

  1. Yosuke Kawai, Takahiro Mimori, Kaname Kojima, Naoki Nariai, Inaho Danjoh, Rumiko Saito, Jun Yasuda, Masayuki Yamamoto, Masao Nagasaki. Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals. Journal of Human Genetics, 2015; DOI: 10.1038/jhg.2015.68

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Tohoku University. "Design of 'Japonica Array'." ScienceDaily. ScienceDaily, 2 September 2015. <>.
Tohoku University. (2015, September 2). Design of 'Japonica Array'. ScienceDaily. Retrieved March 3, 2024 from
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