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Rare variant discovered through deep whole-genome sequencing of 1,070 Japanese people

Date:
October 14, 2015
Source:
Tohoku University
Summary:
A research group has successfully constructed a Japanese population reference panel, from the genome information of 1,070 individuals. They have 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.
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A research group in Japan has successfully constructed a Japanese population reference panel, from the genome information of 1,070 individuals. They have 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.

A research group at Tohoku Medical Megabank Organization (ToMMo) has successfully constructed a Japanese population reference panel (1KJPN), from the genome information of 1,070 individuals who had participated in the cohort studies*1 of the Tohoku Medical Megabank Project.

ToMMo identified through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) *2at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions.

ToMMo also catalogued structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide.

The data demonstrates the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.

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.


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Journal Reference:

  1. Masao Nagasaki, Jun Yasuda, Fumiki Katsuoka, Naoki Nariai, Kaname Kojima, Yosuke Kawai, Yumi Yamaguchi-Kabata, Junji Yokozawa, Inaho Danjoh, Sakae Saito, Yukuto Sato, Takahiro Mimori, Kaoru Tsuda, Rumiko Saito, Xiaoqing Pan, Satoshi Nishikawa, Shin Ito, Yoko Kuroki, Osamu Tanabe, Nobuo Fuse, Shinichi Kuriyama, Hideyasu Kiyomoto, Atsushi Hozawa, Naoko Minegishi, James Douglas Engel, Kengo Kinoshita, Shigeo Kure, Nobuo Yaegashi, Akito Tsuboi, Fuji Nagami, Hiroshi Kawame, Hiroaki Tomita, Ichiro Tsuji, Jun Nakaya, Junichi Sugawara, Kichiya Suzuki, Masahiro Kikuya, Michiaki Abe, Naoki Nakaya, Noriko Osumi, Riu Yamashita, Soichi Ogishima, Takako Takai, Teiji Tominaga, Yasuyuki Taki, Yoichi Suzuki, Masayuki Yamamoto. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nature Communications, 2015; 6: 8018 DOI: 10.1038/ncomms9018

Cite This Page:

Tohoku University. "Rare variant discovered through deep whole-genome sequencing of 1,070 Japanese people." ScienceDaily. ScienceDaily, 14 October 2015. <www.sciencedaily.com/releases/2015/10/151014163812.htm>.
Tohoku University. (2015, October 14). Rare variant discovered through deep whole-genome sequencing of 1,070 Japanese people. ScienceDaily. Retrieved May 23, 2017 from www.sciencedaily.com/releases/2015/10/151014163812.htm
Tohoku University. "Rare variant discovered through deep whole-genome sequencing of 1,070 Japanese people." ScienceDaily. www.sciencedaily.com/releases/2015/10/151014163812.htm (accessed May 23, 2017).

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