Nature Search

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.

Masao Nagasaki
Jun Yasuda
Masayuki Yamamoto
ResearchOpen Access21 Aug 2015
Nature Communications

Volume: 6, P: 1-13
Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM

The measles virus hemagglutinin (MVH) promotes viral attachment to host cells via interaction with signaling lymphocyte activation molecule (SLAM). Now the crystal structure of MVH head ___domain in complex with the distal ___domain of SLAM, together with functional work, reveals the details of this interaction and explains the effectiveness of the currently used vaccine.

Takao Hashiguchi
Toyoyuki Ose
Yusuke Yanagi
Research09 Jan 2011
Nature Structural & Molecular Biology

Volume: 18, P: 135-141
dbTMM: an integrated database of large-scale cohort, genome and clinical data for the Tohoku Medical Megabank Project

Soichi Ogishima
Satoshi Nagaie
Masayuki Yamamoto
ResearchOpen Access10 Dec 2021
Human Genome Variation

Volume: 8, P: 1-8
Genetic effects on gestational diabetes mellitus and their interactions with environmental factors among Japanese women

Tomoki Kawahara
Nobutoshi Nawa
Takeo Fujiwara
Research21 Mar 2025
Journal of Human Genetics

Volume: 70, P: 265-273
Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

Cryo-EM and liposome assays reveal that Atg9 functions as a lipid scramblase, transporting phospholipids between inner and outer liposome leaflets. Analyses of mutants in yeast support a role for this activity in autophagy.

Kazuaki Matoba
Tetsuya Kotani
Nobuo N. Noda
Research26 Oct 2020
Nature Structural & Molecular Biology

Volume: 27, P: 1185-1193
Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy

High-speed AFM imaging enables a semiquantitative, realistic description of the dynamic structure of intrinsically disordered proteins.

Noriyuki Kodera
Daisuke Noshiro
Toshio Ando
Research23 Nov 2020
Nature Nanotechnology

Volume: 16, P: 181-189
p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response

Liquid-liquid phase separation of p62/SQSTM1 has been previously described, although the significance in vivo remains unclear. Here the authors show p62 droplets contain ubiquitin, autophagy-related proteins and Keap1 to serve as platform of not only autophagosome formation but also Nrf2 activation.

Shun Kageyama
Sigurdur Runar Gudmundsson
Masaaki Komatsu
ResearchOpen Access04 Jan 2021
Nature Communications

Volume: 12, P: 1-16
Gabexate Mesilate (FOY) as a New Additional Therapy to High Dose Intravenous Gammaglobulin for High Risk Kawasaki Disease

Takao Okafuji
Naoya Sakaguchi
Yoshikatsu Etoh
Research01 Jan 2003
Pediatric Research

Volume: 53, P: 182
Genome-wide association meta-analysis identifies GP2 gene risk variants for pancreatic cancer

Previous genome-wide association studies have identified risk loci for pancreatic cancer but were centered on individuals of European ancestry. Here the authors identify GP2 gene variants associated with pancreatic cancer susceptibility in populations of East Asian ancestry.

Yingsong Lin
Masahiro Nakatochi
Keitaro Matsuo
ResearchOpen Access24 Jun 2020
Nature Communications

Volume: 11, P: 1-12
Simulating metabolic pathways to enhance interpretations of metabolome genome-wide association studies

Shun Kodate
Mitsuharu Sato
Kengo Kinoshita
ResearchOpen Access16 May 2025
Scientific Reports

Volume: 15, P: 1-11
High–Level ATP Production by a Genetically–Engineered Candida Yeast

Yasuyoshi Sakai
Tomohiro Rogi
Yoshiki Tani
Research01 Mar 1994
Bio/Technology

Volume: 12, P: 291-293
A frequent variant in the Japanese population determines quasi-Mendelian inheritance of rare retinal ciliopathy

Genetic variants in RP1 can cause hereditary retinal degeneration (HRD). Here, in a genomic screen of 331 Japanese HRD patients, the authors identify a near-polymorphic RP1 variant that causes Mendelian HRD in trans with an Alu insertion and otherwise is associated with HRD according to a complex model of inheritance.

Konstantinos Nikopoulos
Katarina Cisarova
Carlo Rivolta
ResearchOpen Access28 Jun 2019
Nature Communications

Volume: 10, P: 1-7
SPF-5506-A₄, a New Peptaibol Inhibitor of Amyloid β-Peptide Formation Produced by Trichoderma sp.

Nobuo Hosotani
Kazuo Kumagai
Ikutaro Saji
Research01 Mar 2007
The Journal of Antibiotics

Volume: 60, P: 184-190
Profiling of runs of homozygosity from whole-genome sequence data in Japanese biobank

Aye Ko Ko Minn
Motomichi Matsuzaki
Gen Tamiya
ResearchOpen Access03 Apr 2025
Journal of Human Genetics

Volume: 70, P: 287-296
Returning genetic risk information for hereditary cancers to participants in a population-based cohort study in Japan

Kinuko Ohneda
Yoichi Suzuki
Masayuki Yamamoto
ResearchOpen Access17 Jan 2025
Journal of Human Genetics

Volume: 70, P: 147-157
Zfhx4 regulates endochondral ossification as the transcriptional platform of Osterix in mice

Nakamura et al. used expression studies to identify an enrichment of Zfhx4 in cartilage and revealed through global gene knock-down that it is required for proper endochondral ossification in mice. They further demonstrated a physical and genetic interaction between Zfhx4 and Osterix, which is of interest to the field of transcriptional regulation of mammalian endochondral ossification.

Eriko Nakamura
Kenji Hata
Riko Nishimura
ResearchOpen Access03 Nov 2021
Communications Biology

Volume: 4, P: 1-11
Pathological variants in genes associated with disorders of sex development and central causes of hypogonadism in a whole-genome reference panel of 8380 Japanese individuals

Naomi Shiga
Yumi Yamaguchi-Kabata
Junichi Sugawara
ResearchOpen Access28 Sept 2022
Human Genome Variation

Volume: 9, P: 1-9
Expression of varied GFPs in Saccharomyces cerevisiae: codon optimization yields stronger than expected expression and fluorescence intensity

Misato Kaishima
Jun Ishii
Akihiko Kondo
ResearchOpen Access26 Oct 2016
Scientific Reports

Volume: 6, P: 1-15
Estimation of the carrier frequencies and proportions of potential patients by detecting causative gene variants associated with autosomal recessive bone dysplasia using a whole-genome reference panel of Japanese individuals

Shinichi Nagaoka
Yumi Yamaguchi-Kabata
Junichi Sugawara
ResearchOpen Access15 Jan 2021
Human Genome Variation

Volume: 8, P: 1-17
Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals

Yumi Yamaguchi-Kabata
Jun Yasuda
Masayuki Yamamoto
Research01 Dec 2017
Journal of Human Genetics

Volume: 63, P: 213-230
Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing

Masao Nagasaki
Yoko Kuroki
Masayuki Yamamoto
ResearchOpen Access07 Jun 2019
Human Genome Variation

Volume: 6, P: 1-18
The structural origin of metabolic quantitative diversity

Seizo Koshiba
Ikuko Motoike
Masayuki Yamamoto
ResearchOpen Access16 Aug 2016
Scientific Reports

Volume: 6, P: 1-14
Association of olfactory and cognitive function test scores with hippocampal and amygdalar grey matter volume: a cross-sectional study

Shuichi Sato
Takao Imaeda
Atsushi Hozawa
ResearchOpen Access19 Aug 2024
Scientific Reports

Volume: 14, P: 1-10
The association of birth weight and current BMI on the risk of hypertension: the Tohoku medical megabank community-based cohort study

Hiromi Himuro
Mana Kogure
Junichi Sugawara
ResearchOpen Access08 Aug 2024
Hypertension Research

Volume: 47, P: 3025-3034
Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator

Yamada, Motoike, Kojima et al. undertake a GWAS study on 19,722 participants from two Japanese populations for lung function with adjustment for fractional exhaled nitric oxide levels to account for airway inflammation. The authors identify variants of the RNF5/AGER locus and explore their three-dimensional protein interactions to better investigate the association between these variants and lung function.

Mitsuhiro Yamada
Ikuko N. Motoike
Masayuki Yamamoto
ResearchOpen Access15 Nov 2021
Communications Biology

Volume: 4, P: 1-15
Depressive symptoms as risk factors for the onset of home hypertension: a prospective cohort study

Sayuri Tokioka
Naoki Nakaya
Atsushi Hozawa
ResearchOpen Access10 Jul 2024
Hypertension Research

Volume: 47, P: 2989-3000
Associations of combined genetic and lifestyle risks with hypertension and home hypertension

Masato Takase
Takumi Hirata
Masayuki Yamamoto
ResearchOpen Access24 Jun 2024
Hypertension Research

Volume: 47, P: 2064-2074
Uptake of osteoblast-derived extracellular vesicles promotes the differentiation of osteoclasts in the zebrafish scale

Kobayashi-Sun et al. characterise the healing of fractured bone in the transgenic zebrafish scale by transplantation assays and live imaging, revealing that immature osteoclasts engulf osteoblast-derived extracellular vesicles (EVs) under fracture stress, leading to osteoclast differentiation. This study provides insights into the role of EVs in osteoclastogenesis.

Jingjing Kobayashi-Sun
Shiori Yamamori
Isao Kobayashi
ResearchOpen Access23 Apr 2020
Communications Biology

Volume: 3, P: 1-12
Relationship between traditional risk factors for hypertension and systolic blood pressure in the Tohoku Medical Megabank Community-based Cohort Study

Masato Takase
Naoki Nakaya
Atsushi Hozawa
ResearchOpen Access29 Feb 2024
Hypertension Research

Volume: 47, P: 1533-1545
The association between depressive symptoms and masked hypertension in participants with normotension measured at research center

Depressive symptoms were associated with masked hypertension in individuals with normotension measured at research center.

Sayuri Tokioka
Naoki Nakaya
Atsushi Hozawa
ResearchOpen Access31 Oct 2023
Hypertension Research

Volume: 47, P: 586-597
The risk of withdrawal from hypertension treatment in coastal areas after the Great East Japan Earthquake: the TMM CommCohort Study

Rieko Hatanaka
Naoki Nakaya
Atsushi Hozawa
ResearchOpen Access13 Oct 2023
Hypertension Research

Volume: 46, P: 2718-2728
The return of individual genomic results to research participants: design and pilot study of Tohoku Medical Megabank Project

Hiroshi Kawame
Akimune Fukushima
Masayuki Yamamoto
Research08 Jul 2021
Journal of Human Genetics

Volume: 67, P: 9-17
Identification of critical genetic variants associated with metabolic phenotypes of the Japanese population

By combining whole genome sequencing and metabolomics, Koshiba et al. identify a large number of associations between genetic variants and plasma metabolites. They find that some genetic variants affect the interaction between the host and symbiotic bacteria. This study provides insights into how genetic and environmental factors interact to shape human metabolism.

Seizo Koshiba
Ikuko N. Motoike
Masayuki Yamamoto
ResearchOpen Access11 Nov 2020
Communications Biology

Volume: 3, P: 1-15
3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome

Shu Tadaka
Fumiki Katsuoka
Kengo Kinoshita
ResearchOpen Access18 Jun 2019
Human Genome Variation

Volume: 6, P: 1-9
Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing

Takahiro Mimori
Jun Yasuda
Masayuki Yamamoto
ResearchOpen Access19 Jan 2018
The Pharmacogenomics Journal

Volume: 19, P: 136-146
Identification of a novel uterine leiomyoma GWAS locus in a Japanese population

Kensuke Sakai
Chizu Tanikawa
Koichi Matsuda
ResearchOpen Access27 Jan 2020
Scientific Reports

Volume: 10, P: 1-8
Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies

Tsuyoshi Hachiya
Ryohei Furukawa
Atsushi Shimizu
ResearchOpen Access13 Apr 2017
npj Genomic Medicine

Volume: 2, P: 1-14

Search

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM

dbTMM: an integrated database of large-scale cohort, genome and clinical data for the Tohoku Medical Megabank Project

Genetic effects on gestational diabetes mellitus and their interactions with environmental factors among Japanese women

Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy

p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response

Gabexate Mesilate (FOY) as a New Additional Therapy to High Dose Intravenous Gammaglobulin for High Risk Kawasaki Disease

Genome-wide association meta-analysis identifies GP2 gene risk variants for pancreatic cancer

Simulating metabolic pathways to enhance interpretations of metabolome genome-wide association studies

High–Level ATP Production by a Genetically–Engineered Candida Yeast

A frequent variant in the Japanese population determines quasi-Mendelian inheritance of rare retinal ciliopathy

SPF-5506-A₄, a New Peptaibol Inhibitor of Amyloid β-Peptide Formation Produced by Trichoderma sp.

Profiling of runs of homozygosity from whole-genome sequence data in Japanese biobank

Returning genetic risk information for hereditary cancers to participants in a population-based cohort study in Japan

Zfhx4 regulates endochondral ossification as the transcriptional platform of Osterix in mice

Pathological variants in genes associated with disorders of sex development and central causes of hypogonadism in a whole-genome reference panel of 8380 Japanese individuals

Expression of varied GFPs in Saccharomyces cerevisiae: codon optimization yields stronger than expected expression and fluorescence intensity

Estimation of the carrier frequencies and proportions of potential patients by detecting causative gene variants associated with autosomal recessive bone dysplasia using a whole-genome reference panel of Japanese individuals

Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals

Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing

The structural origin of metabolic quantitative diversity

Association of olfactory and cognitive function test scores with hippocampal and amygdalar grey matter volume: a cross-sectional study

The association of birth weight and current BMI on the risk of hypertension: the Tohoku medical megabank community-based cohort study

Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator

Depressive symptoms as risk factors for the onset of home hypertension: a prospective cohort study

Associations of combined genetic and lifestyle risks with hypertension and home hypertension

Uptake of osteoblast-derived extracellular vesicles promotes the differentiation of osteoclasts in the zebrafish scale

Relationship between traditional risk factors for hypertension and systolic blood pressure in the Tohoku Medical Megabank Community-based Cohort Study

The association between depressive symptoms and masked hypertension in participants with normotension measured at research center

The risk of withdrawal from hypertension treatment in coastal areas after the Great East Japan Earthquake: the TMM CommCohort Study

The return of individual genomic results to research participants: design and pilot study of Tohoku Medical Megabank Project

Identification of critical genetic variants associated with metabolic phenotypes of the Japanese population

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

Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing

Identification of a novel uterine leiomyoma GWAS locus in a Japanese population

Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies

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