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

Shu Tadaka; Fumiki Katsuoka; Masao Ueki; Kaname Kojima; Satoshi Makino; Sakae Saito; Akihito Otsuki; Chinatsu Gocho; Mika Sakurai-Yageta; Inaho Danjoh; Ikuko N Motoike; Yumi Yamaguchi-Kabata; Matsuyuki Shirota; Seizo Koshiba; Masao Nagasaki; Naoko Minegishi; Atsushi Hozawa; Shinichi Kuriyama; Atsushi Shimizu; Jun Yasuda; Nobuo Fuse; Tohoku Medical Megabank Project Study Group; Gen Tamiya; Masayuki Yamamoto; Kengo Kinoshita

doi:10.1038/s41439-019-0059-5

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

Hum Genome Var. 2019 Jun 18:6:28. doi: 10.1038/s41439-019-0059-5. eCollection 2019.

Authors

Shu Tadaka^#^{1

2}, Fumiki Katsuoka^#^{1

2}, Masao Ueki^{1

3}, Kaname Kojima^{1

2

4}, Satoshi Makino^{1

2}, Sakae Saito^{1

2}, Akihito Otsuki^{1

2}, Chinatsu Gocho¹, Mika Sakurai-Yageta^{1

2}, Inaho Danjoh^{1

2}, Ikuko N Motoike^{1

2

4}, Yumi Yamaguchi-Kabata^{1

2}, Matsuyuki Shirota^{1

2

4}, Seizo Koshiba^{1

2}, Masao Nagasaki^{1

2

4}, Naoko Minegishi^{1

2

5}, Atsushi Hozawa^{1

2}, Shinichi Kuriyama^{1

2

6}, Atsushi Shimizu⁷, Jun Yasuda^{1

8}, Nobuo Fuse^{1

2}; Tohoku Medical Megabank Project Study Group; Gen Tamiya^{1

3}, Masayuki Yamamoto^{1

2

5}, Kengo Kinoshita^{1

4

5

9}

Affiliations

¹ 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
² 2Graduate School of Medicine, Tohoku University, Sendai, Japan.
³ 3Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.
⁴ 4Graduate School of Information Sciences, Tohoku University, Sendai, Japan.
⁵ 5Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan.
⁶ 6International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.
⁷ 7Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Morioka, Japan.
⁸ Miyagi Cancer Center, Miyagi Hospital Organization, Natori, Japan.
⁹ 9Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.

^# Contributed equally.

Abstract

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.

Keywords: Rare variants; Structural variation.