Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare

Jun Yasuda; Kengo Kinoshita; Fumiki Katsuoka; Inaho Danjoh; Mika Sakurai-Yageta; Ikuko N. Motoike; Yoko Kuroki; Sakae Saito; Kaname Kojima; Matsuyuki Shirota; Daisuke Saigusa; Akihito Otsuki; Junko Kawashima; Yumi Yamaguchi-Kabata; Shu Tadaka; Yuichi Aoki; Takahiro Mimori; Kazuki Kumada; Jin Inoue; Satoshi Makino; Miho Kuriki; Nobuo Fuse; Seizo Koshiba; Osamu Tanabe; Masao Nagasaki; Gen Tamiya; Ritsuko Shimizu; Takako Takai-Igarashi; Soichi Ogishima; Atsushi Hozawa; Shinichi Kuriyama; Junichi Sugawara; Akito Tsuboi; Hideyasu Kiyomoto; Tadashi Ishii; Hiroaki Tomita; Naoko Minegishi; Yoichi Suzuki; Kichiya Suzuki; Hiroshi Kawame; Hiroshi Tanaka; Yasuyuki Taki; Nobuo Yaegashi; Shigeo Kure; Fuji Nagami; Kenjiro Kosaki; Yoichi Sutoh; Tsuyoshi Hachiya; Atsushi Shimizu; Makoto Sasaki; Masayuki Yamamoto

doi:10.1093/jb/mvy096

Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare

Jun Yasuda, Kengo Kinoshita, Fumiki Katsuoka, Inaho Danjoh, Mika Sakurai-Yageta, Ikuko N. Motoike, Yoko Kuroki, Sakae Saito, Kaname Kojima, Matsuyuki Shirota, Daisuke Saigusa, Akihito Otsuki, Junko Kawashima, Yumi Yamaguchi-Kabata, Shu Tadaka, Yuichi Aoki, Takahiro Mimori, Kazuki Kumada, Jin Inoue, Satoshi MakinoMiho Kuriki, Nobuo Fuse, Seizo Koshiba, Osamu Tanabe, Masao Nagasaki, Gen Tamiya, Ritsuko Shimizu, Takako Takai-Igarashi, Soichi Ogishima, Atsushi Hozawa, Shinichi Kuriyama, Junichi Sugawara, Akito Tsuboi, Hideyasu Kiyomoto, Tadashi Ishii, Hiroaki Tomita, Naoko Minegishi, Yoichi Suzuki, Kichiya Suzuki, Hiroshi Kawame, Hiroshi Tanaka, Yasuyuki Taki, Nobuo Yaegashi, Shigeo Kure, Fuji Nagami, Kenjiro Kosaki, Yoichi Sutoh, Tsuyoshi Hachiya, Atsushi Shimizu, Makoto Sasaki, Masayuki Yamamoto

Research output: Contribution to journal › Article › peer-review

30 Citations (Scopus)

Abstract

Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.

Original language	English
Pages (from-to)	139-158
Number of pages	20
Journal	Journal of biochemistry
Volume	165
Issue number	2
DOIs	https://doi.org/10.1093/jb/mvy096
Publication status	Published - 2019 Feb 1
Externally published	Yes

Keywords

Genome reference panel
Japonica array
Personalized healthcare
Tohoku medical megabank project
Whole genome sequencing

ASJC Scopus subject areas

Biochemistry
Molecular Biology

Access to Document

10.1093/jb/mvy096

Cite this

Yasuda, J., Kinoshita, K., Katsuoka, F., Danjoh, I., Sakurai-Yageta, M., Motoike, I. N., Kuroki, Y., Saito, S., Kojima, K., Shirota, M., Saigusa, D., Otsuki, A., Kawashima, J., Yamaguchi-Kabata, Y., Tadaka, S., Aoki, Y., Mimori, T., Kumada, K., Inoue, J., ... Yamamoto, M. (2019). Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare. Journal of biochemistry, 165(2), 139-158. https://doi.org/10.1093/jb/mvy096

Yasuda, J, Kinoshita, K, Katsuoka, F, Danjoh, I, Sakurai-Yageta, M, Motoike, IN, Kuroki, Y, Saito, S, Kojima, K, Shirota, M, Saigusa, D, Otsuki, A, Kawashima, J, Yamaguchi-Kabata, Y, Tadaka, S, Aoki, Y, Mimori, T, Kumada, K, Inoue, J, Makino, S, Kuriki, M, Fuse, N, Koshiba, S, Tanabe, O, Nagasaki, M, Tamiya, G, Shimizu, R, Takai-Igarashi, T, Ogishima, S, Hozawa, A, Kuriyama, S, Sugawara, J, Tsuboi, A, Kiyomoto, H, Ishii, T, Tomita, H, Minegishi, N, Suzuki, Y, Suzuki, K, Kawame, H, Tanaka, H, Taki, Y, Yaegashi, N, Kure, S, Nagami, F, Kosaki, K, Sutoh, Y, Hachiya, T, Shimizu, A, Sasaki, M & Yamamoto, M 2019, 'Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare', Journal of biochemistry, vol. 165, no. 2, pp. 139-158. https://doi.org/10.1093/jb/mvy096

@article{0f1f38db31374599ba44943780eb0938,

title = "Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare",

abstract = "Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.",

keywords = "Genome reference panel, Japonica array, Personalized healthcare, Tohoku medical megabank project, Whole genome sequencing",

author = "Jun Yasuda and Kengo Kinoshita and Fumiki Katsuoka and Inaho Danjoh and Mika Sakurai-Yageta and Motoike, {Ikuko N.} and Yoko Kuroki and Sakae Saito and Kaname Kojima and Matsuyuki Shirota and Daisuke Saigusa and Akihito Otsuki and Junko Kawashima and Yumi Yamaguchi-Kabata and Shu Tadaka and Yuichi Aoki and Takahiro Mimori and Kazuki Kumada and Jin Inoue and Satoshi Makino and Miho Kuriki and Nobuo Fuse and Seizo Koshiba and Osamu Tanabe and Masao Nagasaki and Gen Tamiya and Ritsuko Shimizu and Takako Takai-Igarashi and Soichi Ogishima and Atsushi Hozawa and Shinichi Kuriyama and Junichi Sugawara and Akito Tsuboi and Hideyasu Kiyomoto and Tadashi Ishii and Hiroaki Tomita and Naoko Minegishi and Yoichi Suzuki and Kichiya Suzuki and Hiroshi Kawame and Hiroshi Tanaka and Yasuyuki Taki and Nobuo Yaegashi and Shigeo Kure and Fuji Nagami and Kenjiro Kosaki and Yoichi Sutoh and Tsuyoshi Hachiya and Atsushi Shimizu and Makoto Sasaki and Masayuki Yamamoto",

note = "Funding Information: grant numbers JP18km0105001 and JP18km0105002); AMED Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation (GRIFIN) project (grant numbers JP18km0405203 and JP18km0405203); and by the Center of Innovation Program from the Japan Science and Technology Agency (JST). All computational resources were provided by the ToMMo supercomputer system (http://sc.megabank.tohoku.ac.jp/ en), which is supported by the Facilitation of R&D Platform for AMED Genome Medicine Support conducted by AMED (grant number JP18km0405001). Funding Information: This work was supported in part by the Tohoku Medical Megabank Project through the Ministry of Education, Culture, Sports, Science and Technology, Japan; by the Reconstruction Agency, Japan; by the Japan Agency for Medical Research and Development (AMED; grant numbers JP18km0105001 and JP18km0105002); AMED Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation (GRIFIN) project (grant numbers JP18km0405203 and JP18km0405203); and by the Center of Innovation Program from the Japan Science and Technology Agency (JST). All computational resources were provided by the ToMMo supercomputer system (http://sc.megabank.tohoku.ac.jp/ en), which is supported by the Facilitation of RandD Platform for AMED Genome Medicine Support conducted by AMED (grant number JP18km0405001) Funding Information: This work was supported in part by the Tohoku Medical Megabank Project through the Ministry of Education, Culture, Sports, Science and Technology, Japan; by the Reconstruction Agency, Japan; by the Japan Agency for Medical Research and Development (AMED; Publisher Copyright: {\textcopyright} The Author(s) 2018. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.",

year = "2019",

month = feb,

day = "1",

doi = "10.1093/jb/mvy096",

language = "English",

volume = "165",

pages = "139--158",

journal = "Journal of Biochemistry",

issn = "0021-924X",

publisher = "Oxford University Press",

number = "2",

}

TY - JOUR

T1 - Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare

AU - Yasuda, Jun

AU - Kinoshita, Kengo

AU - Katsuoka, Fumiki

AU - Danjoh, Inaho

AU - Sakurai-Yageta, Mika

AU - Motoike, Ikuko N.

AU - Kuroki, Yoko

AU - Saito, Sakae

AU - Kojima, Kaname

AU - Shirota, Matsuyuki

AU - Saigusa, Daisuke

AU - Otsuki, Akihito

AU - Kawashima, Junko

AU - Yamaguchi-Kabata, Yumi

AU - Tadaka, Shu

AU - Aoki, Yuichi

AU - Mimori, Takahiro

AU - Kumada, Kazuki

AU - Inoue, Jin

AU - Makino, Satoshi

AU - Kuriki, Miho

AU - Fuse, Nobuo

AU - Koshiba, Seizo

AU - Tanabe, Osamu

AU - Nagasaki, Masao

AU - Tamiya, Gen

AU - Shimizu, Ritsuko

AU - Takai-Igarashi, Takako

AU - Ogishima, Soichi

AU - Hozawa, Atsushi

AU - Kuriyama, Shinichi

AU - Sugawara, Junichi

AU - Tsuboi, Akito

AU - Kiyomoto, Hideyasu

AU - Ishii, Tadashi

AU - Tomita, Hiroaki

AU - Minegishi, Naoko

AU - Suzuki, Yoichi

AU - Suzuki, Kichiya

AU - Kawame, Hiroshi

AU - Tanaka, Hiroshi

AU - Taki, Yasuyuki

AU - Yaegashi, Nobuo

AU - Kure, Shigeo

AU - Nagami, Fuji

AU - Kosaki, Kenjiro

AU - Sutoh, Yoichi

AU - Hachiya, Tsuyoshi

AU - Shimizu, Atsushi

AU - Sasaki, Makoto

AU - Yamamoto, Masayuki

N1 - Funding Information: grant numbers JP18km0105001 and JP18km0105002); AMED Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation (GRIFIN) project (grant numbers JP18km0405203 and JP18km0405203); and by the Center of Innovation Program from the Japan Science and Technology Agency (JST). All computational resources were provided by the ToMMo supercomputer system (http://sc.megabank.tohoku.ac.jp/ en), which is supported by the Facilitation of R&D Platform for AMED Genome Medicine Support conducted by AMED (grant number JP18km0405001). Funding Information: This work was supported in part by the Tohoku Medical Megabank Project through the Ministry of Education, Culture, Sports, Science and Technology, Japan; by the Reconstruction Agency, Japan; by the Japan Agency for Medical Research and Development (AMED; grant numbers JP18km0105001 and JP18km0105002); AMED Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation (GRIFIN) project (grant numbers JP18km0405203 and JP18km0405203); and by the Center of Innovation Program from the Japan Science and Technology Agency (JST). All computational resources were provided by the ToMMo supercomputer system (http://sc.megabank.tohoku.ac.jp/ en), which is supported by the Facilitation of RandD Platform for AMED Genome Medicine Support conducted by AMED (grant number JP18km0405001) Funding Information: This work was supported in part by the Tohoku Medical Megabank Project through the Ministry of Education, Culture, Sports, Science and Technology, Japan; by the Reconstruction Agency, Japan; by the Japan Agency for Medical Research and Development (AMED; Publisher Copyright: © The Author(s) 2018. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

PY - 2019/2/1

Y1 - 2019/2/1

N2 - Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.

AB - Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.

KW - Genome reference panel

KW - Japonica array

KW - Personalized healthcare

KW - Tohoku medical megabank project

KW - Whole genome sequencing

UR - http://www.scopus.com/inward/record.url?scp=85060173847&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85060173847&partnerID=8YFLogxK

U2 - 10.1093/jb/mvy096

DO - 10.1093/jb/mvy096

M3 - Article

C2 - 30452759

AN - SCOPUS:85060173847

SN - 0021-924X

VL - 165

SP - 139

EP - 158

JO - Journal of Biochemistry

JF - Journal of Biochemistry

IS - 2

ER -

Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this