3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome

• Published in: Human genome variation Vol. 6; no. 1; p. 28
• Main Authors: Tadaka, Shu, Katsuoka, Fumiki, Ueki, Masao, Kojima, Kaname, Makino, Satoshi, Saito, Sakae, Otsuki, Akihito, Gocho, Chinatsu, Sakurai-Yageta, Mika, Danjoh, Inaho, Motoike, Ikuko N., Yamaguchi-Kabata, Yumi, Shirota, Matsuyuki, Koshiba, Seizo, Nagasaki, Masao, Minegishi, Naoko, Hozawa, Atsushi, Kuriyama, Shinichi, Shimizu, Atsushi, Yasuda, Jun, Fuse, Nobuo, Tamiya, Gen, Yamamoto, Masayuki, Kinoshita, Kengo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.06.2019; Springer Nature B.V
• Subjects: 631/208/726/649/2157; 631/208/726/649/2219; Biomedical and Life Sciences; Biomedicine; Gene Expression; Gene Function; Gene Therapy; Human Genetics; Molecular Medicine; Population; Population genetics; Rare variants; Structural variation
• DOI: 10.1038/s41439-019-0059-5
• ISSN: 2054-345X

The first step towards realizing personalized healthcare is to catalog the genetic variations in a population. Since the dissemination of individual-level genomic information is strictly controlled, it will be useful to construct population-level allele frequency panels with easy-to-use interfaces. In the Tohoku Medical Megabank Project, we sequenced nearly 4000 individuals from a Japanese population and constructed an allele frequency panel of 3552 individuals after removing related samples. The panel is called the 3.5KJPNv2. It was constructed by using a standard pipeline including the 1KGP and gnomAD algorithms to reduce technical biases and to allow comparisons to other populations. Our database is the first large-scale panel providing the frequencies of variants present on the X chromosome and on the mitochondria in the Japanese population. All the data are available on our original database at https://jmorp.megabank.tohoku.ac.jp . Population genetics: large database of Japanese gene variations constructed A new database provides information on the frequency of genetic variations within 3552 Japanese individuals, and facilitates comparisons with other populations. The reference panel, constructed by Kengo Kinoshita of Tohoku University, Sendai, and colleagues in Japan is also the first large-scale database to provide genetic variation frequency information on the X chromosome and mitochondrial DNA in the Japanese population. The methods used to sequence the genetic data are similar to those used in other large databases, allowing comparisons with other populations. The population size and methods used to compile the database overcome limitations in previous Japanese reference panels. This and similar databases that catalog genetic variations within populations can improve efforts towards personalizing healthcare and contribute to the study of human population genetics. The database is publicly available online.