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  1. Article ; Online: Genetic variations in medical research in the past, at present and in the future.

    Kamatani, Yoichiro / Nakamura, Yusuke

    Proceedings of the Japan Academy. Series B, Physical and biological sciences

    2021  Volume 97, Issue 6, Page(s) 324–335

    Abstract: As we look so different, our genomic sequences vary enormously. The differences in our genome, genetic variations, have played very significant roles in medical research and have contributed to improvement of medical managements in the last 2-3 decades. ... ...

    Abstract As we look so different, our genomic sequences vary enormously. The differences in our genome, genetic variations, have played very significant roles in medical research and have contributed to improvement of medical managements in the last 2-3 decades. Genetic variations include germline variations, somatic mutations, and diversities in receptor genes of rearranged immune cells, T cells and B cells. Germline variants are in some cases causative of genetic diseases, are associated with the risk of various diseases, and also affect drug efficacies or adverse events. Some somatic mutations are causative of tumor development. Recent DNA sequencing technologies allow us to perform single-cell analysis or detailed repertoire analysis of B and T cells. It is critically important to investigate temporal changes in immune environment in various anatomical regions in the next one to two decades. In this review article, we would like to introduce the roles of genetic variations in medical fields in the past, at present and in the future.
    MeSH term(s) Biomedical Research ; Genetic Variation/genetics ; Genomics ; Humans ; Neoplasms ; Sequence Analysis, DNA
    Language English
    Publishing date 2021-06-11
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 161781-3
    ISSN 1349-2896 ; 0386-2208
    ISSN (online) 1349-2896
    ISSN 0386-2208
    DOI 10.2183/pjab.97.018
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  2. Article: [Genome Wide Association Study:its theory and methodological review].

    Kamatani, Yoichiro

    Clinical calcium

    2016  Volume 26, Issue 4, Page(s) 525–535

    Abstract: This review article describes the background and practical aspects for the Genome Wide Association Studies(GWAS). I introduce several softwares which are actually used in practice so that the readers could perform GWAS without difficulty. Imputation ... ...

    Abstract This review article describes the background and practical aspects for the Genome Wide Association Studies(GWAS). I introduce several softwares which are actually used in practice so that the readers could perform GWAS without difficulty. Imputation method is also explained. Finally, some comments are provided regarding advanced topics such as missing heritability or intergenic association signals affecting regulatory mechanisms.
    MeSH term(s) Genome-Wide Association Study/methods ; Humans ; Software
    Language Japanese
    Publishing date 2016-04
    Publishing country Japan
    Document type English Abstract ; Journal Article ; Review
    ZDB-ID 2386417-5
    ISSN 0917-5857
    ISSN 0917-5857
    DOI CliCa1604525535
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  3. Article ; Online: Two decades after Human Genome Project: do large-genetic studies lead to path of the genomic medicine of complex diseases?

    Kamatani, Yoichiro / Okada, Yukinori

    Journal of human genetics

    2020  Volume 66, Issue 1, Page(s) 1

    MeSH term(s) Genetic Predisposition to Disease ; Genome, Human/genetics ; Genomics/trends ; Human Genome Project ; Humans ; Medicine
    Language English
    Publishing date 2020-12-11
    Publishing country England
    Document type Editorial
    ZDB-ID 1425192-9
    ISSN 1435-232X ; 1434-5161
    ISSN (online) 1435-232X
    ISSN 1434-5161
    DOI 10.1038/s10038-020-00828-3
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  4. Article ; Online: Efficient prediction of a spatial transcriptomics profile better characterizes breast cancer tissue sections without costly experimentation.

    Monjo, Taku / Koido, Masaru / Nagasawa, Satoi / Suzuki, Yutaka / Kamatani, Yoichiro

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 4133

    Abstract: Spatial transcriptomics is an emerging technology requiring costly reagents and considerable skills, limiting the identification of transcriptional markers related to histology. Here, we show that predicted spatial gene-expression in unmeasured regions ... ...

    Abstract Spatial transcriptomics is an emerging technology requiring costly reagents and considerable skills, limiting the identification of transcriptional markers related to histology. Here, we show that predicted spatial gene-expression in unmeasured regions and tissues can enhance biologists' histological interpretations. We developed the Deep learning model for Spatial gene Clusters and Expression, DeepSpaCE, and confirmed its performance using the spatial-transcriptome profiles and immunohistochemistry images of consecutive human breast cancer tissue sections. For example, the predicted expression patterns of SPARC, an invasion marker, highlighted a small tumor-invasion region difficult to identify using raw spatial transcriptome data alone because of a lack of measurements. We further developed semi-supervised DeepSpaCE using unlabeled histology images and increased the imputation accuracy of consecutive sections, enhancing applicability for a small sample size. Our method enables users to derive hidden histological characters via spatial transcriptome and gene annotations, leading to accelerated biological discoveries without additional experiments.
    MeSH term(s) Breast Neoplasms/pathology ; Female ; Humans ; Transcriptome
    Language English
    Publishing date 2022-03-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-07685-4
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  5. Article ; Online: Genetics of autosomal mosaic chromosomal alteration (mCA).

    Liu, Xiaoxi / Kamatani, Yoichiro / Terao, Chikashi

    Journal of human genetics

    2021  Volume 66, Issue 9, Page(s) 879–885

    Abstract: Mosaic chromosomal alterations (mCAs) are frequently observed in cancer cells and are regarded as one of the common features of cancers. Strikingly, accumulating studies demonstrated that mCAs are also prevalent in elderly individuals without cancer, ... ...

    Abstract Mosaic chromosomal alterations (mCAs) are frequently observed in cancer cells and are regarded as one of the common features of cancers. Strikingly, accumulating studies demonstrated that mCAs are also prevalent in elderly individuals without cancer, implying mCA could be a feature of aging and not necessarily a cancerous state. However, the genetic basis of mCA has been mostly unknown. Recent studies of autosomal mCA based on biobank-scale datasets, including UK Biobank and Biobank Japan, provided a glimpse into the underlying genetic mechanism. In this concise review, we briefly introduced mCA, its link with cancer and aging, and the emerging genetic mechanisms of this phenomenon. We highlighted the following aspects: (1) the interplay between somatic and inherited germline mutations in generating mosaicism; (2) monogenic and polygenic architectures of mCA; and (3) population-specific profiles of mCA. We provided a future perspective emphasizing the need to understand the connection between mCA and other characteristics of aging, in particular, the epigenetic and immunologic features.
    MeSH term(s) Aging/genetics ; Chromosome Aberrations ; Datasets as Topic ; Humans ; Mosaicism ; Mutation
    Language English
    Publishing date 2021-07-28
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1425192-9
    ISSN 1435-232X ; 1434-5161
    ISSN (online) 1435-232X
    ISSN 1434-5161
    DOI 10.1038/s10038-021-00964-4
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  6. Article ; Online: Detection of trait-associated structural variations using short-read sequencing.

    Kosugi, Shunichi / Kamatani, Yoichiro / Harada, Katsutoshi / Tomizuka, Kohei / Momozawa, Yukihide / Morisaki, Takayuki / Terao, Chikashi

    Cell genomics

    2023  Volume 3, Issue 6, Page(s) 100328

    Abstract: Genomic structural variation (SV) affects genetic and phenotypic characteristics in diverse organisms, but the lack of reliable methods to detect SV has hindered genetic analysis. We developed a computational algorithm (MOPline) that includes missing ... ...

    Abstract Genomic structural variation (SV) affects genetic and phenotypic characteristics in diverse organisms, but the lack of reliable methods to detect SV has hindered genetic analysis. We developed a computational algorithm (MOPline) that includes missing call recovery combined with high-confidence SV call selection and genotyping using short-read whole-genome sequencing (WGS) data. Using 3,672 high-coverage WGS datasets, MOPline stably detected ∼16,000 SVs per individual, which is over ∼1.7-3.3-fold higher than previous large-scale projects while exhibiting a comparable level of statistical quality metrics. We imputed SVs from 181,622 Japanese individuals for 42 diseases and 60 quantitative traits. A genome-wide association study with the imputed SVs revealed 41 top-ranked or nearly top-ranked genome-wide significant SVs, including 8 exonic SVs with 5 novel associations and enriched mobile element insertions. This study demonstrates that short-read WGS data can be used to identify rare and common SVs associated with a variety of traits.
    Language English
    Publishing date 2023-05-18
    Publishing country United States
    Document type Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2023.100328
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  7. Article ; Online: Genome-wide Association Studies Categorized by Class of Antihypertensive Drugs Reveal Complex Pathogenesis of Hypertension with Drug Resistance.

    Yamazaki, Keiko / Terao, Chikashi / Takahashi, Atsushi / Kamatani, Yoichiro / Matsuda, Koichi / Asai, Satoshi / Takahashi, Yasuo

    Clinical pharmacology and therapeutics

    2023  Volume 114, Issue 2, Page(s) 393–403

    Abstract: Resistant hypertension is defined as uncontrolled blood pressure (BP) despite the use of three or more antihypertensive drugs of different classes. Although genetic factors may greatly contribute to hypertension with resistance to multiple drug classes, ... ...

    Abstract Resistant hypertension is defined as uncontrolled blood pressure (BP) despite the use of three or more antihypertensive drugs of different classes. Although genetic factors may greatly contribute to hypertension with resistance to multiple drug classes, more than for general hypertension, its pathogenesis remains unknown. To reveal the genetic background of resistant hypertension, we categorized 32,239 patients whose data were obtained from the BioBank Japan Project, by prescription of 7 classes of antihypertensive drugs and performed genome-wide association studies (GWAS). Our GWAS identified four loci with significant association (P < 5 × 10
    MeSH term(s) Humans ; Antihypertensive Agents/therapeutic use ; Antihypertensive Agents/pharmacology ; Genome-Wide Association Study ; Hypertension/drug therapy ; Hypertension/genetics ; Calcium Channel Blockers/therapeutic use ; Blood Pressure ; Drug Resistance
    Chemical Substances Antihypertensive Agents ; Calcium Channel Blockers
    Language English
    Publishing date 2023-05-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 123793-7
    ISSN 1532-6535 ; 0009-9236
    ISSN (online) 1532-6535
    ISSN 0009-9236
    DOI 10.1002/cpt.2934
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  8. Article: Editorial: Current Status and Future Challenges of Biobank Data Analysis.

    Lu, Tzu-Pin / Kamatani, Yoichiro / Belbin, Gillian / Park, Taesung / Hsiao, Chuhsing Kate

    Frontiers in genetics

    2022  Volume 13, Page(s) 882611

    Language English
    Publishing date 2022-04-14
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.882611
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  9. Article ; Online: Genetic risk score of cerebral infarction in atrial fibrillation genome-wide association study.

    Ebana, Yusuke / Liu, Lian / Ihara, Kensuke / Abe, Keiko / Terao, Chikashi / Kamatani, Yoichiro / Sasano, Tetsuo / Furukawa, Tetsushi

    European journal of clinical investigation

    2023  Volume 53, Issue 12, Page(s) e14084

    Abstract: Introduction: Stroke is a leading cause of death and the primary cause of adult-acquired disability. Patients with cardiogenic embolic stroke also have higher mortality and recurrence rates than patients with other stroke subtypes. Atrial fibrillation ( ... ...

    Abstract Introduction: Stroke is a leading cause of death and the primary cause of adult-acquired disability. Patients with cardiogenic embolic stroke also have higher mortality and recurrence rates than patients with other stroke subtypes. Atrial fibrillation (AF) is a major risk factor for cerebral infarction (CI). The large-scale study identified 32 loci in the MEGASTROKE study. However, few studies have attempted to identify novel stroke risk variants in patients with a history of AF. Our overall aim was to identify novel CI risk variants in AF cases and explore whether their associations with the CI risk were affected by the CHADS2 and CHA2DS2-VASc scores.
    Methods: We performed association study with CI using 8181 AF cases in previous genome-wide association study (GWAS) and imputation data without controls. We classified AF cases into those with or without past history of CI, and the genetic associations with the CI risk were examined.
    Results: GWAS identified eight associated loci. The generated genetic risk score (GRS) for the eight loci was significantly associated with CI in patients with AF (1.46 × 10
    Conclusion: We identified eight genetic variants that were potentially associated with the risk of CI of AF cases and the significant GRS, whose associations were independent of the CHADS2 or CHA2DS2-VASc score.
    MeSH term(s) Adult ; Humans ; Atrial Fibrillation/complications ; Atrial Fibrillation/epidemiology ; Atrial Fibrillation/genetics ; Genome-Wide Association Study ; Risk Assessment ; Risk Factors ; Stroke/epidemiology ; Stroke/genetics ; Stroke/complications ; Cerebral Infarction/epidemiology ; Cerebral Infarction/genetics ; Cerebral Infarction/complications ; Predictive Value of Tests
    Language English
    Publishing date 2023-08-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 186196-7
    ISSN 1365-2362 ; 0014-2972 ; 0960-135X
    ISSN (online) 1365-2362
    ISSN 0014-2972 ; 0960-135X
    DOI 10.1111/eci.14084
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  10. Article: Genetically proxied HTRA1 protease activity and circulating levels independently predict risk of ischemic stroke and coronary artery disease.

    Dichgans, Martin / Malik, Rainer / Beaufort, Nathalie / Tanaka, Koki / Georgakis, Marios / He, Yunye / Koido, Masaru / Terao, Chikashi / Anderson, Christopher / Kamatani, Yoichiro

    Research square

    2023  

    Abstract: ... ...

    Abstract HTRA1
    Language English
    Publishing date 2023-11-07
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3523612/v1
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