Details of the Researcher

PHOTO

Yumi Yamaguchi
Section
Tohoku Medical Megabank Organization
Job title
Senior Assistant Professor
Degree

  • 博士（理学）（総合研究大学院大学）

  • 修士（理学）（九州大学）

Research History 4

  • 2020/04 - Present
    Tohoku University　Tohoku Medical Megabank Organization　Senior assistant professor

  • 2013/01 - 2020/03
    Tohoku University　Tohoku Medical Megabank Organization

  • 2006/12 - 2012/12
    理化学研究所　ゲノム医科学研究センター　研究員

  • 2001/12 - 2006/11
    産業技術総合研究所　生物情報解析研究センター　研究員

Professional Memberships 5

  • SOCIETY OF EVOLUTIONARY STUDIES, JAPAN

  • THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

  • THE AMERICAN SOCIETY OF HUMAN GENETICS

  • THE JAPAN SOCIETY OF HUMAN GENETICS

  • THE GENETICS SOCIETY OF JAPAN

Research Areas 2

  • Life sciences / Evolutionary biology /

  • Life sciences / Genomics /

Papers 69

  1. 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. International-journal Peer-reviewed

    Naomi Shiga, Yumi Yamaguchi-Kabata, Saori Igeta, Jun Yasuda, Shu Tadaka, Takamichi Minato, Zen Watanabe, Junko Kanno, Gen Tamiya, Nobuo Fuse, Kengo Kinoshita, Shigeo Kure, Akiko Kondo, Masahito Tachibana, Masayuki Yamamoto, Nobuo Yaegashi, Junichi Sugawara

    Human genome variation　9　(1)　34-34　2022/09/28

    DOI： 10.1038/s41439-022-00213-w 　

    More details Close

    Disorders of sex development (DSD) comprises a congenital condition in which chromosomal, gonadal, or anatomical sex development is atypical. In this study, we screened for pathogenic variants in 32 genes associated with DSDs and central causes of hypogonadism (CHG) in a whole-genome reference panel including 8380 Japanese individuals constructed by Tohoku Medical Megabank Organization. Candidate pathogenic (P) or likely pathogenic (LP) variants were extracted from the ClinVar, InterVar, and Human Gene Mutation databases. Ninety-one candidate pathological variants were found in 25 genes; 28 novel candidate variants were identified. Nearly 1 in 40 (either ClinVar or InterVar P or LP) to 157 (both ClinVar and InterVar P or LP) individuals were found to be carriers of recessive DSD and CHG alleles. In these data, genes implicated in gonadal dysfunction did not show loss-of-function variants, with a relatively high tendency of intolerance for haploinsufficiency based on pLI and Episcore, both of which can be used for estimating haploinsufficiency. We report the types and frequencies of causative variants for DSD and CHG in the general Japanese population. This study furthers our understanding of the genetic causes and helps to refine genetic counseling of DSD and CHG.

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

    Kinuko Ohneda, Yoichi Suzuki, Yohei Hamanaka, Shu Tadaka, Muneaki Shimada, Junko Hasegawa-Minato, Masanobu Takahashi, Nobuo Fuse, Fuji Nagami, Hiroshi Kawame, Tomoko Kobayashi, Yumi Yamaguchi-Kabata, Kengo Kinoshita, Tomohiro Nakamura, Soichi Ogishima, Kazuki Kumada, Hisaaki Kudo, Shin-Ichi Kuriyama, Yoko Izumi, Ritsuko Shimizu, Mikako Tochigi, Tokiwa Motonari, Hideki Tokunaga, Atsuo Kikuchi, Atsushi Masamune, Yoko Aoki, Chikashi Ishioka, Takanori Ishida, Masayuki Yamamoto

    Journal of human genetics　70　(3)　147-157　2025/03

    DOI： 10.1038/s10038-024-01314-w 　

    More details Close

    Large-scale population cohort studies that collect genomic information are tasked with returning an assessment of genetic risk for hereditary cancers to participants. While several studies have applied to return identified genetic risks to participants, comprehensive surveys of participants' understanding, feelings, and behaviors toward cancer risk remain to be conducted. Here, we report our experience and surveys of returning genetic risks to 100 carriers of pathogenic variants for hereditary cancers identified through whole genome sequencing of 50 000 individuals from the Tohoku Medical Megabank project, a population cohort study. The participants were carriers of pathogenic variants associated with either hereditary breast and ovarian cancer (n = 79, median age=41) or Lynch syndrome (n = 21, median age=62). Of these, 28% and 38% had a history of cancer, respectively. We provided information on cancer risk, heritability, and clinical actionability to the participants in person. The comprehension assessment revealed that the information was better understood by younger (under 60 years) females than by older males. Scores on the cancer worry scale were positively related to cancer experiences and general psychological distress. Seventy-one participants were followed up at Tohoku University Hospital; six females underwent risk-reducing surgery triggered by study participation and three were newly diagnosed with cancer during surveillance. Among first-degree relatives of hereditary breast and ovarian cancer carriers, participants most commonly shared the information with daughters. This study showed the benefits of returning genetic risks to the general population and will provide insights into returning genetic risks to asymptomatic pathogenic variant carriers in both clinical and research settings.

  3. ゲノムコホート研究参加者5万人を対象としたBRCA1/2遺伝情報の回付と医療への連携

    濱中 洋平, 大根田 絹子, 川目 裕, 布施 昇男, 長神 風二, 鈴木 洋一, 山口 由美, 多田 寛, 原田 成美, 宮下 穣, 江幡 明子, 佐藤 未来, 柳垣 美歌, 山本 雅之, 石田 孝宣

    日本乳癌学会総会プログラム抄録集　31回　89-89　2023/06

    Publisher: (一社)日本乳癌学会

  4. Returning individual genomic results to population-based cohort study participants with BRCA1/2 pathogenic variants. Peer-reviewed

    Kinuko Ohneda, Yohei Hamanaka, Hiroshi Kawame, Nobuo Fuse, Fuji Nagami, Yoichi Suzuki, Yumi Yamaguchi-Kabata, Muneaki Shimada, Atsushi Masamune, Yoko Aoki, Takanori Ishida, Masayuki Yamamoto

    Breast cancer (Tokyo, Japan)　30　(1)　110-120　2022/09/26

    DOI： 10.1007/s12282-022-01404-7 　

    More details Close

    BACKGROUND: Recent advances in human genome research have provided evidence for genotype-phenotype associations, pathogenicity, and clinical actionability of variants and genomic risk prediction of disease. However, the return of individual genomic results to healthy individuals is fraught with ethical and practical complexity. METHODS: Individual genomic results were returned to BRCA1/2 pathogenic variant (PV) carriers of the Tohoku Medical Megabank cohort study participants with an information on hereditary breast and ovarian cancer syndrome (HBOC). One hundred and eighty participants, including 9 BRCA1/2 PV carriers, were asked about their willingness to receive individual genomic results, without revealing the gene name and related disorders, prior to the study. Of the 142 participants who responded, 103 showed willingness to know their genomic information. Each of the six BRCA1/2 PV carriers who consented to participate in the study received information about HBOC in person and underwent validation testing with blood resampling. RESULTS: All participants were in their 60s or 70s; of the four females and two males, two had a history of breast cancer and five had a family history of HBOC-related cancers. All participants appreciated the information, without remarkable negative psychological impact of the return, and intended to undergo clinical risk surveillance. Five participants were accompanied by family members while receiving the results, and three first-degree female relatives wished to undergo genomic testing at the hospital. CONCLUSIONS: Our results suggest that returning actionable genomic information to participants in a population-based genome cohort study is beneficial for preventing or providing early-stage intervention for associated diseases.

  5. 全ゲノム/全エキソーム解析による生殖細胞系列多型の探索 一般住民コホートにおけるBRCA遺伝子バリアントの探索及び結果の回付事業について(Exploration of BRCA1/2 gene variants in a general population cohort and return of genomic results to the participants)

    徳永 英樹, 安田 純, 島田 宗昭, 濱中 洋平, 重田 昌吾, 布施 昇男, 勝岡 史城, 荻島 創一, 山口 由美, 寳澤 篤, 川目 裕, 大根田 絹子, 青木 洋子, 山本 雅之, 八重樫 伸生

    日本癌学会総会記事　81回　S8-1　2022/09

    Publisher: (一社)日本癌学会

    ISSN： 0546-0476

  6. A Pilot Study for Return of Individual Pharmacogenomic Results to Population-Based Cohort Study Participants. Peer-reviewed

    Kinuko Ohneda, Masahiro Hiratsuka, Hiroshi Kawame, Fuji Nagami, Yoichi Suzuki, Kichiya Suzuki, Akira Uruno, Mika Sakurai-Yageta, Yohei Hamanaka, Makiko Taira, Soichi Ogishima, Shinichi Kuriyama, Atsushi Hozawa, Hiroaki Tomita, Naoko Minegishi, Junichi Sugawara, Inaho Danjoh, Tomohiro Nakamura, Tomoko Kobayashi, Yumi Yamaguchi-Kabata, Shu Tadaka, Taku Obara, Eiji Hishimuma, Nariyasu Mano, Masaki Matsuura, Yuji Sato, Masateru Nakasone, Yohei Honkura, Jun Suzuki, Yukio Katori, Yoichi Kakuta, Atsushi Masamune, Yoko Aoki, Masaharu Nakayama, Shigeo Kure, Kengo Kinoshita, Nobuo Fuse, Masayuki Yamamoto

    JMA journal　5　(2)　177-189　2022/04/15

    DOI： 10.31662/jmaj.2021-0156 　

    More details Close

    Introduction: Pharmacogenomic (PGx) testing results provide valuable information on drug selection and appropriate dosing, maximization of efficacy, and minimization of adverse effects. Although the number of large-scale, next-generation-sequencing-based PGx studies has recently increased, little is known about the risks and benefits of returning PGx results to ostensibly healthy individuals in research settings. Methods: Single-nucleotide variants of three actionable PGx genes, namely, MT-RNR1, CYP2C19, and NUDT15, were returned to 161 participants in a population-based Tohoku Medical Megabank project. Informed consent was obtained from the participants after a seminar on the outline of this study. The results were sent by mail alongside sealed information letter intended for clinicians. As an exception, genetic counseling was performed for the MT-RNR1 m.1555A > G variant carriers by a medical geneticist, and consultation with an otolaryngologist was encouraged. Questionnaire surveys (QSs) were conducted five times to evaluate the participants' understanding of the topic, psychological impact, and attitude toward the study. Results: Whereas the majority of participants were unfamiliar with the term PGx, and none had undergone PGx testing before the study, more than 80% of the participants felt that they could acquire basic PGx knowledge sufficient to understand their genomic results and were satisfied with their potential benefit and use in future prescriptions. On the other hand, some felt that the PGx concepts or terminology was difficult to fully understand and suggested that in-person return of the results was desirable. Conclusions: These results collectively suggest possible benefits of returning preemptive PGx information to ostensibly healthy cohort participants in a research setting.

  7. Loss of CAPS2/Cadps2 leads to exocrine pancreatic cell injury and intracellular accumulation of secretory granules in mice. International-journal Peer-reviewed

    Yotaroh Sato, Miho Tsuyusaki, Hiromi Takahashi-Iwanaga, Rena Fujisawa, Atsushi Masamune, Shin Hamada, Ryotaro Matsumoto, Yu Tanaka, Yoichi Kakuta, Yumi Yamaguchi-Kabata, Tamio Furuse, Shigeharu Wakana, Takuya Shimura, Rika Kobayashi, Yo Shinoda, Ryo Goitsuka, So Maezawa, Tetsushi Sadakata, Yoshitake Sano, Teiichi Furuichi

    Frontiers in molecular biosciences　9　1040237-1040237　2022

    DOI： 10.3389/fmolb.2022.1040237 　

    More details Close

    The type 2 Ca2+-dependent activator protein for secretion (CAPS2/CADPS2) regulates dense-core vesicle trafficking and exocytosis and is involved in the regulated release of catecholamines, peptidergic hormones, and neuromodulators. CAPS2 is expressed in the pancreatic exocrine acinar cells that produce and secrete digestive enzymes. However, the functional role of CAPS2 in vesicular trafficking and/or exocytosis of non-regulatory proteins in the exocrine pancreas remains to be determined. Here, we analyzed the morpho-pathological indicators of the pancreatic exocrine pathway in Cadps2-deficient mouse models using histochemistry, biochemistry, and electron microscopy. We used whole exosome sequencing to identify CADPS2 variants in patients with chronic pancreatitis (CP). Caps2/Cadps2-knockout (KO) mice exhibited morphophysiological abnormalities in the exocrine pancreas, including excessive accumulation of secretory granules (zymogen granules) and their amylase content in the cytoplasm, deterioration of the fine intracellular membrane structures (disorganized rough endoplasmic reticulum, dilated Golgi cisternae, and the appearance of empty vesicles and autophagic-like vacuoles), as well as exocrine pancreatic cell injury, including acinar cell atrophy, increased fibrosis, and inflammatory cell infiltration. Pancreas-specific Cadps2 conditional KO mice exhibited pathological abnormalities in the exocrine pancreas similar to the global Cadps2 KO mice, indicating that these phenotypes were caused either directly or indirectly by CAPS2 deficiency in the pancreas. Furthermore, we identified a rare variant in the exon3 coding region of CADPS2 in a non-alcoholic patient with CP and showed that Cadps2-dex3 mice lacking CAPS2 exon3 exhibited symptoms similar to those exhibited by the Cadps2 KO and cKO mice. These results suggest that CAPS2 is critical for the proper functioning of the pancreatic exocrine pathway, and its deficiency is associated with a risk of pancreatic acinar cell pathology.

  8. The return of individual genomic results to research participants: design and pilot study of Tohoku Medical Megabank Project. International-journal Peer-reviewed

    Hiroshi Kawame, Akimune Fukushima, Nobuo Fuse, Fuji Nagami, Yoichi Suzuki, Mika Sakurai-Yageta, Jun Yasuda, Yumi Yamaguchi-Kabata, Kengo Kinoshita, Soichi Ogishima, Takako Takai, Shinichi Kuriyama, Atsushi Hozawa, Naoki Nakaya, Tomohiro Nakamura, Naoko Minegishi, Junichi Sugawara, Kichiya Suzuki, Hiroaki Tomita, Akira Uruno, Tomoko Kobayashi, Yayoi Aizawa, Tomoharu Tokutomi, Kayono Yamamoto, Kinuko Ohneda, Shigeo Kure, Yoko Aoki, Hideki Katagiri, Yasushi Ishigaki, Shojiro Sawada, Makoto Sasaki, Masayuki Yamamoto

    Journal of human genetics　67　(1)　9-17　2021/07/08

    DOI： 10.1038/s10038-021-00952-8 　

    More details Close

    Certain large genome cohort studies attempt to return the individual genomic results to the participants; however, the implementation process and psychosocial impacts remain largely unknown. The Tohoku Medical Megabank Project has conducted large genome cohort studies of general residents. To implement the disclosure of individual genomic results, we extracted the potential challenges and obstacles. Major challenges include the determination of genes/disorders based on the current medical system in Japan, the storage of results, prevention of misunderstanding, and collaboration of medical professionals. To overcome these challenges, we plan to conduct multilayer pilot studies, which deal with different disorders/genes. We finally chose familial hypercholesterolemia (FH) as a target disease for the first pilot study. Of the 665 eligible candidates, 33.5% were interested in the pilot study and provided consent after an educational "genetics workshop" on the basic genetics and medical facts of FH. The genetics professionals disclosed the results to the participants. All positive participants were referred to medical care, and a serial questionnaire revealed no significant psychosocial distress after the disclosure. Return of genomic results to research participants was implemented using a well-prepared protocol. To further elucidate the impact of different disorders, we will perform multilayer pilot studies with different disorders, including actionable pharmacogenomics and hereditary tumor syndromes.

  9. ゲノムコホート研究におけるBRCA1/2遺伝情報返却とその後の医療機関との連携の取組み

    濱中 洋平, 多田 寛, 宮下 穣, 原田 成美, 佐藤 章子, 江幡 明子, 大根田 絹子, 布施 昇男, 川目 裕, 鈴木 洋一, 長神 風二, 鈴木 吉也, 佐藤 政文, 平塚 真弘, 櫻井 美佳, 宇留野 晃, 山口 由美, 平良 摩紀子, 山本 雅之, 石田 孝宣

    日本乳癌学会総会プログラム抄録集　29回　21-21　2021/07

    Publisher: (一社)日本乳癌学会

  10. 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. International-journal Peer-reviewed

    Shinichi Nagaoka, Yumi Yamaguchi-Kabata, Naomi Shiga, Masahito Tachibana, Jun Yasuda, Shu Tadaka, Gen Tamiya, Nobuo Fuse, Kengo Kinoshita, Shigeo Kure, Jun Murotsuki, Masayuki Yamamoto, Nobuo Yaegashi, Junichi Sugawara

    Human genome variation　8　(1)　2-2　2021/01/15

    DOI： 10.1038/s41439-020-00133-7 　

    More details Close

    Bone dysplasias are a group of rare hereditary diseases, with up to 436 disease types. Perinatal diagnosis is clinically important for adequate personalized management and counseling. There are no reports focused on pathogenic variants of bone dysplasias in the general population. In this study, we focused on autosomal recessive bone dysplasias. We identified pathogenic variants using whole-genome reference panel data from 3552 Japanese individuals. For the first time, we were able to estimate the carrier frequencies and the proportions of potential patients. For autosomal recessive bone dysplasias, we detected 198 pathogenic variants of 54 causative genes. We estimated the variant carrier frequencies and the proportions of potential patients with variants associated with four clinically important bone dysplasias: osteogenesis imperfecta (OI), hypophosphatasia (HPP), asphyxiating thoracic dysplasia (ATD), and Ellis-van Creveld syndrome (EvC). The proportions of potential patients with OI, ATD, and EvC based on pathogenic variants classified as "pathogenic" and "likely pathogenic" by InterVar were closer to the reported incidence rates in Japanese subjects. Furthermore, the proportions of potential patients with HPP variants classified as "pathogenic" and "likely pathogenic" in InterVar and "pathogenic" in ClinVar were closer to the reported incidence rates. For bone dysplasia, the findings of this study will provide a better understanding of the variant types and frequencies in the Japanese general population, and should be useful for clinical diagnosis, genetic counseling, and personalized medicine.

  11. Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes from a dataset of 3,552 Japanese whole genomes (3.5KJPNv2). International-journal Peer-reviewed

    Hideki Tokunaga, Keita Iida, Atsushi Hozawa, Soichi Ogishima, Yoh Watanabe, Shogo Shigeta, Muneaki Shimada, Yumi Yamaguchi-Kabata, Shu Tadaka, Fumiki Katsuoka, Shin Ito, Kazuki Kumada, Yohei Hamanaka, Nobuo Fuse, Kengo Kinoshita, Masayuki Yamamoto, Nobuo Yaegashi, Jun Yasuda

    PloS one　16　(1)　e0236907　2021

    DOI： 10.1371/journal.pone.0236907 　

    More details Close

    Identification of the population frequencies of definitely pathogenic germline variants in two major hereditary breast and ovarian cancer syndrome (HBOC) genes, BRCA1/2, is essential to estimate the number of HBOC patients. In addition, the identification of moderately penetrant HBOC gene variants that contribute to increasing the risk of breast and ovarian cancers in a population is critical to establish personalized health care. A prospective cohort subjected to genome analysis can provide both sets of information. Computational scoring and prospective cohort studies may help to identify such likely pathogenic variants in the general population. We annotated the variants in the BRCA1 and BRCA2 genes from a dataset of 3,552 whole-genome sequences obtained from members of a prospective cohorts with genome data in the Tohoku Medical Megabank Project (TMM) with InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAFs) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar were used for filtration criteria. Familial predispositions to cancers among the 35,000 TMM genome cohort participants were analyzed to verify the identified pathogenicity. Seven potentially pathogenic variants were newly identified. The sisters of carriers of these moderately deleterious variants and definite P and LP variants among members of the TMM prospective cohort showed a statistically significant preponderance for cancer onset, from the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potentially pathogenic variants in BRCA genes in the Japanese population. These results should help to follow up the carriers of variants of uncertain significance in the HBOC genes in the longitudinal prospective cohort study.

  12. Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes in a 3,552 Japanese whole-genome sequence dataset (3.5KJPNv2) Peer-reviewed

    Hideki Tokunaga, Keita Iida, Atsushi Hozawa, Soichi Ogishima, Yoh Watanabe, Shogo Shigeta, Muneaki Shimada, Yumi Yamaguchi-Kabata, Shu Tadaka, Fumiki Katsuoka, Shin Ito, Kazuki Kumada, Yohei Hamanaka, Nobuo Fuse, Kengo Kinoshita, Masayuki Yamamoto, Nobuo Yaegashi, Jun Yasuda

    2020/07/17

    Publisher: Cold Spring Harbor Laboratory

    DOI： 10.1101/2020.07.17.208454 　

    More details Close

    <title>Abstract</title>Identification of pathogenic germline variants yet no clinical evidence in <italic>BRCA</italic> genes has become important in patient care of hereditary breast and ovarian cancer syndrome (HBOC). Computational scoring and prospective cohort studies may help to identify such pathogenic variants. We annotated the variants in the <italic>BRCA1</italic> and <italic>BRCA2</italic> genes from a dataset of 3,552 whole-genome sequences obtained from members of the genome cohorts by Tohoku Medical Megabank Project (TMM) with the InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAF) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar are used for filtration criteria. Familial predispositions in cancers among the 35,000 TMM genome cohort participants are analyzed to verify the pathogenicity. Seven potentially pathogenic variants were newly identified. Carriers of these potential pathogenic variants and definite P and LP variants among participants of the TMM prospective cohort show a statistically significant preponderance in cancer onset in sisters in the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potential pathogenic variants in <italic>BRCA</italic> genes for Japanese population. These results will be helpful to follow up the carriers of variants of uncertain significance in the HBOC genes.

  13. 大規模ゲノムコホート調査におけるBRCA1/2遺伝子の病的バリアント保持者への遺伝情報回付に関する課題

    濱中 洋平, 石田 孝宣, 布施 昇男, 川目 裕, 山口 由美, 安田 純, 多田 寛, 宮下 穣, 原田 成美, 佐藤 章子, 青木 洋子, 長神 風二, 八重樫 伸生, 木下 賢吾, 呉 繁夫, 山本 雅之

    日本乳癌学会総会プログラム抄録集　27回　332-332　2019/07

    Publisher: (一社)日本乳癌学会

  14. Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals. International-journal Peer-reviewed

    Yamaguchi-Kabata Y, Yasuda J, Uruno A, Shimokawa K, Koshiba S, Suzuki Y, Fuse N, Kawame H, Tadaka S, Nagasaki M, Kojima K, Katsuoka F, Kumada K, Tanabe O, Tamiya G, Yaegashi N, Kinoshita K, Yamamoto M, Kure S, Tohoku Medical Megabank Project, Study Group

    Human genetics　138　(4)　389-409　2019/03

    DOI： 10.1007/s00439-019-01998-7 　

    ISSN： 0340-6717

    More details Close

    Incidence rates of Mendelian diseases vary among ethnic groups, and frequencies of variant types of causative genes also vary among human populations. In this study, we examined to what extent we can predict population frequencies of recessive disorders from genomic data, and explored better strategies for variant interpretation and classification. We used a whole-genome reference panel from 3552 general Japanese individuals constructed by the Tohoku Medical Megabank Organization (ToMMo). Focusing on 32 genes for 17 congenital metabolic disorders included in newborn screening (NBS) in Japan, we identified reported and predicted pathogenic variants through variant annotation, interpretation, and multiple ways of classifications. The estimated carrier frequencies were compared with those from the Japanese NBS data based on 1,949,987 newborns from a previous study. The estimated carrier frequency based on genomic data with a recent guideline of variant interpretation for the PAH gene, in which defects cause hyperphenylalaninemia (HPA) and phenylketonuria (PKU), provided a closer estimate to that by the observed incidence than the other methods. In contrast, the estimated carrier frequencies for SLC25A13, which causes citrin deficiency, were much higher compared with the incidence rate. The results varied greatly among the 11 NBS diseases with single responsible genes; the possible reasons for departures from the carrier frequencies by reported incidence rates were discussed. Of note, (1) the number of pathogenic variants increases by including additional lines of evidence, (2) common variants with mild effects also contribute to the actual frequency of patients, and (3) penetrance of each variant remains unclear.

  15. Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare. International-journal Peer-reviewed

    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

    Journal of biochemistry　165　(2)　139-158　2019/02/01

    DOI： 10.1093/jb/mvy096 　

    ISSN： 0021-924X

    More details Close

    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.

  16. 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome. Peer-reviewed

    Tadaka S, Katsuoka F, Ueki M, Kojima K, Makino S, Saito S, Otsuki A, Gocho C, Sakurai-Yageta M, Danjoh I, Motoike IN, Yamaguchi-Kabata Y, Shirota M, Koshiba S, Nagasaki M, Minegishi N, Hozawa A, Kuriyama S, Shimizu A, Yasuda J, Fuse N, Tohoku Medical Megabank Project, Study Group, Tamiya G, Yamamoto M, Kinoshita K

    Human genome variation　6　(1)　28　2019

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41439-019-0059-5 　

    eISSN： 2054-345X

  17. Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project. International-journal Peer-reviewed

    Jun Yasuda, Fumiki Katsuoka, Inaho Danjoh, Yosuke Kawai, Kaname Kojima, Masao Nagasaki, Sakae Saito, Yumi Yamaguchi-Kabata, Shu Tadaka, Ikuko N Motoike, Kazuki Kumada, Mika Sakurai-Yageta, Osamu Tanabe, Nobuo Fuse, Gen Tamiya, Koichiro Higasa, Fumihiko Matsuda, Nobufumi Yasuda, Motoki Iwasaki, Makoto Sasaki, Atsushi Shimizu, Kengo Kinoshita, Masayuki Yamamoto

    BMC genomics　19　(1)　551-551　2018/07/24

    DOI： 10.1186/s12864-018-4942-0 　

    More details Close

    BACKGROUND: Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify strongly associated variants in genome-wide association studies. The Tohoku Medical Megabank (TMM) project was established to support the development of precision medicine, together with the whole-genome sequencing of 1070 human genomes from individuals in the Miyagi region (Northeast Japan) and the construction of the 1070 Japanese genome reference panel (1KJPN). Here, we investigated the performance of 1KJPN for genotype imputation of Japanese samples not included in the TMM project and compared it with other population reference panels. RESULTS: We found that the 1KJPN population was more similar to other Japanese populations, Nagahama (south-central Japan) and Aki (Shikoku Island), than to East Asian populations in the 1000 Genomes Project other than JPT, suggesting that the large-scale collection (more than 1000) of Japanese genomes from the Miyagi region covered many of the genetic variations of Japanese in mainland Japan. Moreover, 1KJPN outperformed the phase 3 reference panel of the 1000 Genomes Project (1KGPp3) for Japanese samples, and IKJPN showed similar imputation rates for the TMM and other Japanese samples for SNPs with minor allele frequencies (MAFs) higher than 1%. CONCLUSIONS: 1KJPN covered most of the variants found in the samples from areas of the Japanese mainland outside the Miyagi region, implying 1KJPN is representative of the Japanese population's genomes. 1KJPN and successive reference panels are useful genome reference panels for the mainland Japanese population. Importantly, the addition of whole genome sequences not included in the 1KJPN panel improved imputation efficiencies for SNPs with MAFs under 1% for samples from most regions of the Japanese archipelago.

  18. Integrated analysis of human genetic association study and mouse transcriptome suggests LBH and SHF genes as novel susceptible genes for amyloid-β accumulation in Alzheimer's disease. International-journal Peer-reviewed

    Yumi Yamaguchi-Kabata, Takashi Morihara, Tomoyuki Ohara, Toshiharu Ninomiya, Atsushi Takahashi, Hiroyasu Akatsu, Yoshio Hashizume, Noriyuki Hayashi, Daichi Shigemizu, Keith A Boroevich, Manabu Ikeda, Michiaki Kubo, Masatoshi Takeda, Tatsuhiko Tsunoda

    Human genetics　137　(6-7)　521-533　2018/07

    DOI： 10.1007/s00439-018-1906-z 　

    ISSN： 0340-6717

    More details Close

    Alzheimer's disease (AD) is a common neurological disease that causes dementia in humans. Although the reports of associated pathological genes have been increasing, the molecular mechanism leading to the accumulation of amyloid-β (Aβ) in human brain is still not well understood. To identify novel genes that cause accumulation of Aβ in AD patients, we conducted an integrative analysis by combining a human genetic association study and transcriptome analysis in mouse brain. First, we examined genome-wide gene expression levels in the hippocampus, comparing them to amyloid Aβ level in mice with mixed genetic backgrounds. Next, based on a GWAS statistics obtained by a previous study with human AD subjects, we obtained gene-based statistics from the SNP-based statistics. We combined p values from the two types of analysis across orthologous gene pairs in human and mouse into one p value for each gene to evaluate AD susceptibility. As a result, we found five genes with significant p values in this integrated analysis among the 373 genes analyzed. We also examined the gene expression level of these five genes in the hippocampus of independent human AD cases and control subjects. Two genes, LBH and SHF, showed lower expression levels in AD cases than control subjects. This is consistent with the gene expression levels of both the genes in mouse which were negatively correlated with Aβ accumulation. These results, obtained from the integrative approach, suggest that LBH and SHF are associated with the AD pathogenesis.

  19. Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals. International-journal Peer-reviewed

    Yumi Yamaguchi-Kabata, Jun Yasuda, Osamu Tanabe, Yoichi Suzuki, Hiroshi Kawame, Nobuo Fuse, Masao Nagasaki, Yosuke Kawai, Kaname Kojima, Fumiki Katsuoka, Sakae Saito, Inaho Danjoh, Ikuko N Motoike, Riu Yamashita, Seizo Koshiba, Daisuke Saigusa, Gen Tamiya, Shigeo Kure, Nobuo Yaegashi, Yoshio Kawaguchi, Fuji Nagami, Shinichi Kuriyama, Junichi Sugawara, Naoko Minegishi, Atsushi Hozawa, Soichi Ogishima, Hideyasu Kiyomoto, Takako Takai-Igarashi, Kengo Kinoshita, Masayuki Yamamoto

    Journal of human genetics　63　(2)　213-230　2018/02

    DOI： 10.1038/s10038-017-0347-1 　

    ISSN： 1434-5161

    More details Close

    Clarifying allele frequencies of disease-related genetic variants in a population is important in genomic medicine; however, such data is not yet available for the Japanese population. To estimate frequencies of actionable pathogenic variants in the Japanese population, we examined the reported pathological variants in genes recommended by the American College of Medical Genetics and Genomics (ACMG) in our reference panel of genomic variations, 2KJPN, which was created by whole-genome sequencing of 2049 individuals of the resident cohort of the Tohoku Medical Megabank Project. We searched for pathogenic variants in 2KJPN for 57 autosomal ACMG-recommended genes responsible for 26 diseases and then examined their frequencies. By referring to public databases of pathogenic variations, we identified 143 reported pathogenic variants in 2KJPN for the 57 ACMG recommended genes based on a classification system. At the individual level, 21% of the individuals were found to have at least one reported pathogenic allele. We then conducted a literature survey to review the variants and to check for evidence of pathogenicity. Our results suggest that a substantial number of people have reported pathogenic alleles for the ACMG genes, and reviewing variants is indispensable for constructing the information infrastructure of genomic medicine for the Japanese population.

  20. 「遺伝の仕組み」と「多様性」を学ぶための小児を対象とした遺伝教育ツール開発の取り組み

    小林 朋子, 菅原 美智子, 石原 利乃, 本郷 一夫, 相澤 弥生, 山口 由美, 齋藤 さかえ, 田中 由佳里, 栗木 美穂, 長神 風二, 安田 純, 栗山 進一, 川目 裕, 山本 雅之, 鈴木 洋一

    日本遺伝カウンセリング学会誌　38　(2)　89-89　2017/05

    Publisher: 日本遺伝カウンセリング学会

    ISSN： 1347-9628

  21. Selection pressure on human STR loci and its relevance in repeat expansion disease Peer-reviewed

    Makoto K. Shimada, Ryoko Sanbonmatsu, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Yoshiyuki Suzuki, Ranajit Chakraborty, Takashi Gojobori, Tadashi Imanishi

    MOLECULAR GENETICS AND GENOMICS　291　(5)　1851-1869　2016/10

    DOI： 10.1007/s00438-016-1219-7 　

    ISSN： 1617-4615

    eISSN： 1617-4623

  22. The structural origin of metabolic quantitative diversity Peer-reviewed

    Seizo Koshiba, Ikuko Motoike, Kaname Kojima, Takanori Hasegawa, Matsuyuki Shirota, Tomo Saito, Daisuke Saigusa, Inaho Danjoh, Fumiki Katsuoka, Soichi Ogishima, Yosuke Kawai, Yumi Yamaguchi-Kabata, Miyuki Sakurai, Sachiko Hirano, Junichi Nakata, Hozumi Motohashi, Atsushi Hozawa, Shinichi Kuriyama, Naoko Minegishi, Masao Nagasaki, Takako Takai-Igarashi, Nobuo Fuse, Hideyasu Kiyomoto, Junichi Sugawara, Yoichi Suzuki, Shigeo Kure, Nobuo Yaegashi, Osamu Tanabe, Kengo Kinoshita, Jun Yasuda, Masayuki Yamamoto

    SCIENTIFIC REPORTS　6　31463　2016/08

    DOI： 10.1038/srep31463 　

    ISSN： 2045-2322

  23. Construction of 1070 whole-genome Japanese reference panel and bioinformatics

    Masao Nagasaki, Yosuke Kawai, Kaname Kojima, Takahiro Mimori, Yumi Yamaugchi-Kabata

    Seikagaku　88　(1)　15-24　2016

    Publisher: Japanese Biochemical Society

    DOI： 10.14952/SEIKAGAKU.2016.880015 　

    ISSN： 2189-0544 0037-1017

  24. Corticotropin-Releasing Hormone Receptor 2 Gene Variants in Irritable Bowel Syndrome. International-journal Peer-reviewed

    Hazuki Komuro, Naoko Sato, Ayaka Sasaki, Naoki Suzuki, Michiko Kano, Yukari Tanaka, Yumi Yamaguchi-Kabata, Motoyori Kanazawa, Hitoshi Warita, Masashi Aoki, Shin Fukudo

    PloS one　11　(1)　e0147817　2016

    DOI： 10.1371/journal.pone.0147817 　

    More details Close

    BACKGROUND: Corticotropin-releasing hormone (CRH) plays an important role in the pathophysiology of irritable bowel syndrome (IBS) and regulates the stress response through two CRH receptors (R1 and R2). Previously, we reported that a CRHR1 gene polymorphism (rs110402, rs242924, and rs7209436) and haplotypes were associated with IBS. However, the association between the CRHR2 gene and IBS was not investigated. We tested the hypothesis that genetic polymorphisms and haplotypes of CRHR2 are associated with IBS pathophysiology and negative emotion in IBS patients. METHODS: A total of 142 IBS patients and 142 healthy controls participated in this study. Seven single nucleotide polymorphisms (SNPs) of the CRHR2 gene (rs4722999, rs3779250, rs2240403, rs2267710, rs2190242, rs2284217, and rs2284220) were genotyped. Subjects' psychological states were evaluated using the Perceived-Stress Scale, the State-Trait Anxiety Inventory, and the Self-Rating Depression Scale. RESULTS: We found that rs4722999 and rs3779250, located in intronic region, were associated with IBS in terms of genotype frequency (rs4722999: P = 0.037; rs3779250: P = 0.017) and that the distribution of the major allele was significantly different between patients and controls. There was a significant group effect (controls vs. IBS), and a CRHR2 genotype effect was observed for three psychological scores, but the interaction was not significant. We found a haplotype of four SNPs (rs4722999, rs3779250, rs2240403, and rs2267710) and two SNPs (rs2284217 and rs2284220) in strong linkage disequilibrium (D' > 0.90). We also found that haplotypes of the CRHR2 gene were significantly different between IBS patients and controls and that they were associated with negative emotion. CONCLUSION: Our findings support the hypothesis that genetic polymorphisms and haplotypes of CRHR2 are related to IBS. In addition, we found associations between CRHR2 genotypes and haplotypes and negative emotion in IBS patients and controls. Further studies on IBS and the CRH system are warranted.

  25. Whole-genome Japanese Reference Panel and future directions Peer-reviewed

    Nagasaki Masao, Yasuda Jun, Katsuoka Fumiki, Nariai Naoki, Kojima Kaname, Kawai Yosuke, Yamaguchi-Kabata Yumi, Yokozawa Junji, Danjoh Inaho, Saito Sakae, Sato Yukuto, Mimori Takahiro, Tsuda Kaoru, Saito Rumiko, Pan Xiaoqing, Nishikawa Satoshi, Ito Shin, Kuroki Yoko, Tanabe Osamu, Fuse Nobuo, Kuriyama Shinichi, Kiyomoto Hideyasu, Hozawa Atsushi, Minegishi Naoko, Kinoshita Kengo, Kure Shigeo, Yaegashi Nobuo, Yamamoto Masayuki

    GENES & GENETIC SYSTEMS　90　(6)　377　2015/12

    ISSN： 1341-7568

  26. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals Peer-reviewed

    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, Masayuki Yamamoto

    NATURE COMMUNICATIONS　6　8018　2015/08

    DOI： 10.1038/ncomms9018 　

    ISSN： 2041-1723

  27. iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing. International-journal Peer-reviewed

    Yamaguchi-Kabata Y, Nariai N, Kawai Y, Sato Y, Kojima K, Tateno M, Katsuoka F, Yasuda J, Yamamoto M, Nagasaki M

    Human genome variation　2　15050-15050　2015

    DOI： 10.1038/hgv.2015.50 　

    More details Close

    The integrative Japanese Genome Variation Database (iJGVD; http://ijgvd.megabank.tohoku.ac.jp/) provides genomic variation data detected by whole-genome sequencing (WGS) of Japanese individuals. Specifically, the database contains variants detected by WGS of 1,070 individuals who participated in a genome cohort study of the Tohoku Medical Megabank Project. In the first release, iJGVD includes >4,300,000 autosomal single nucleotide variants (SNVs) whose minor allele frequencies are >5.0%.

  28. Estimating copy numbers of alleles from population-scale high-throughput sequencing data Peer-reviewed

    Takahiro Mimori, Naoki Nariai, Kaname Kojima, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki

    BMC BIOINFORMATICS　16　S4　2015/01

    DOI： 10.1186/1471-2105-16-S1-S4 　

    ISSN： 1471-2105

  29. HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data Peer-reviewed

    Naoki Nariai, Kaname Kojima, Sakae Saito, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Jun Yasuda, Masao Nagasaki

    BMC GENOMICS　16　S7　2015/01

    DOI： 10.1186/1471-2164-16-S2-S7 　

    ISSN： 1471-2164

  30. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads Peer-reviewed

    Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki

    BMC GENOMICS　15　S5　2014/12

    DOI： 10.1186/1471-2164-15-S10-S5 　

    ISSN： 1471-2164

  31. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing Peer-reviewed

    Yukuto Sato, Kaname Kojima, Naoki Nariai, Yumi Yamaguchi-Kabata, Yosuke Kawai, Mamoru Takahashi, Takahiro Mimori, Masao Nagasaki

    BMC GENOMICS　15　664　2014/08

    DOI： 10.1186/1471-2164-15-664 　

    ISSN： 1471-2164

  32. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population Peer-reviewed

    Ikuko N. Motoike, Mitsuyo Matsumoto, Inaho Danjoh, Fumiki Katsuoka, Kaname Kojima, Naoki Nariai, Yukuto Sato, Yumi Yamaguchi-Kabata, Shin Ito, Hisaaki Kudo, Ichiko Nishijima, Satoshi Nishikawa, Xiaoqing Pan, Rumiko Saito, Sakae Saito, Tomo Saito, Matsuyuki Shirota, Kaoru Tsuda, Junji Yokozawa, Kazuhiko Igarashi, Naoko Minegishi, Osamu Tanabe, Nobuo Fuse, Masao Nagasaki, Kengo Kinoshita, Jun Yasuda, Masayuki Yamamoto

    BMC GENOMICS　15　673　2014/08

    DOI： 10.1186/1471-2164-15-673 　

    ISSN： 1471-2164

  33. Human genetic research, race, ethnicity and the labeling of populations: recommendations based on an interdisciplinary workshop in Japan Peer-reviewed

    Yasuko Takezawa, Kazuto Kato, Hiroki Oota, Timothy Caulfield, Akihiro Fujimoto, Shunwa Honda, Naoyuki Kamatani, Shoji Kawamura, Kohei Kawashima, Ryosuke Kimura, Hiromi Matsumae, Ayako Saito, Patrick E. Savage, Noriko Seguchi, Keiko Shimizu, Satoshi Terao, Yumi Yamaguchi-Kabata, Akira Yasukouchi, Minoru Yoneda, Katsushi Tokunaga

    BMC MEDICAL ETHICS　15　33　2014/04

    DOI： 10.1186/1472-6939-15-33 　

    ISSN： 1472-6939

  34. Transcriptome analysis of distinct mouse strains reveals kinesin light chain-1 splicing as an amyloid-beta accumulation modifier Peer-reviewed

    Takashi Morihara, Noriyuki Hayashi, Mikiko Yokokoji, Hiroyasu Akatsu, Michael A. Silverman, Nobuyuki Kimura, Masahiro Sato, Yuhki Saito, Toshiharu Suzuki, Kanta Yanagida, Takashi S. Kodama, Toshihisa Tanaka, Masayasu Okochi, Shinji Tagami, Hiroaki Kazui, Takashi Kudo, Ryota Hashimoto, Naohiro Itoh, Kouhei Nishitomi, Yumi Yamaguchi-Kabata, Tatsuhiko Tsunoda, Hironori Takamura, Taiichi Katayama, Ryo Kimura, Kouzin Kaminoa, Yoshio Hashizume, Masatoshi Takeda

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　111　(7)　2638-2643　2014/02

    DOI： 10.1073/pnas.1307345111 　

    ISSN： 0027-8424

  35. SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints Peer-reviewed

    Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Testuo Shibuya, Masao Nagasaki

    ALGORITHMS FOR COMPUTATIONAL BIOLOGY　8542　208-219　2014

    ISSN： 0302-9743

    eISSN： 1611-3349

  36. HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads Peer-reviewed

    Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai, Masao Nagasaki

    ALGORITHMS FOR COMPUTATIONAL BIOLOGY　8542　107-118　2014

    ISSN： 0302-9743

  37. iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data Peer-reviewed

    Takahiro Mimori, Naoki Nariai, Kaname Kojima, Mamoru Takahashi, Akira Ono, Yukuto Sato, Yumi Yamaguchi-Kabata, Masao Nagasaki

    BMC SYSTEMS BIOLOGY　7　S8　2013/12

    DOI： 10.1186/1752-0509-7-S6-S8 　

    ISSN： 1752-0509

  38. A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads Peer-reviewed

    Kaname Kojima, Naoki Nariai, Takahiro Mimori, Mamoru Takahashi, Yumi Yamaguchi-Kabata, Yukuto Sato, Masao Nagasaki

    BIOINFORMATICS　29　(22)　2835-2843　2013/11

    DOI： 10.1093/bioinformatics/btt503 　

    ISSN： 1367-4803

    eISSN： 1460-2059

  39. Prediction of Protein-Destabilizing Polymorphisms by Manual Curation with Protein Structure Peer-reviewed

    Craig Alan Gough, Keiichi Homma, Yumi Yamaguchi-Kabata, Makoto K. Shimada, Ranajit Chakraborty, Yasuyuki Fujii, Hisakazu Iwama, Shinsei Minoshima, Shigetaka Sakamoto, Yoshiharu Sato, Yoshiyuki Suzuki, Masahito Tada-Umezaki, Ken Nishikawa, Tadashi Imanishi, Takashi Gojobori

    PLOS ONE　7　(11)　e50445　2012/11

    DOI： 10.1371/journal.pone.0050445 　

    ISSN： 1932-6203

  40. Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes Peer-reviewed

    Yumi Yamaguchi-Kabata, Tatsuhiko Tsunoda, Natsuhiko Kumasaka, Atsushi Takahashi, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    JOURNAL OF HUMAN GENETICS　57　(5)　326-334　2012/05

    DOI： 10.1038/jhg.2012.26 　

    ISSN： 1434-5161

  41. A prioritization analysis of disease association by data-mining of functional annotation of human genes Peer-reviewed

    Takayuki Taniya, Susumu Tanaka, Yumi Yamaguchi-Kabata, Hideki Hanaoka, Chisato Yamasaki, Harutoshi Maekawa, Roberto A. Barrero, Boris Lenhard, Milton W. Datta, Mary Shimoyama, Roger Bumgarner, Ranajit Chakraborty, Ian Hopkinson, Libin Jia, Winston Hide, Charles Auffray, Shinsei Minoshima, Tadashi Imanishi, Takashi Gojobori

    GENOMICS　99　(1)　1-9　2012/01

    DOI： 10.1016/j.ygeno.2011.10.002 　

    ISSN： 0888-7543

  42. Identification of Nine Novel Loci Associated with White Blood Cell Subtypes in a Japanese Population Peer-reviewed

    Yukinori Okada, Tomomitsu Hirota, Yoichiro Kamatani, Atsushi Takahashi, Hiroko Ohmiya, Natsuhiko Kumasaka, Koichiro Higasa, Yumi Yamaguchi-Kabata, Naoya Hosono, Michael A. Nalls, Ming Huei Chen, Frank J. A. van Rooij, Albert V. Smith, Toshiko Tanaka, David J. Couper, Neil A. Zakai, Luigi Ferrucci, Dan L. Longo, Dena G. Hernandez, Jacqueline C. M. Witteman, Tamara B. Harris, Christopher J. O&apos;Donnell, Santhi K. Ganesh, Koichi Matsuda, Tatsuhiko Tsunoda, Toshihiro Tanaka, Michiaki Kubo, Yusuke Nakamura, Mayumi Tamari, Kazuhiko Yamamoto, Naoyuki Kamatani

    PLOS GENETICS　7　(6)　e1002067　2011/06

    DOI： 10.1371/journal.pgen.1002067 　

    ISSN： 1553-7390

  43. Making a haplotype catalog with estimated frequencies based on SNP homozygotes Peer-reviewed

    Yumi Yamaguchi-Kabata, Tatsuhiko Tsunoda, Atsushi Takahashi, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    JOURNAL OF HUMAN GENETICS　55　(8)　500-506　2010/08

    DOI： 10.1038/jhg.2010.56 　

    ISSN： 1434-5161

  44. Establishment of a standardized system to perform population structure analyses with limited sample size or with different sets of SNP genotypes Peer-reviewed

    Natsuhiko Kumasaka, Yumi Yamaguchi-Kabata, Atsushi Takahashi, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    JOURNAL OF HUMAN GENETICS　55　(8)　525-533　2010/08

    DOI： 10.1038/jhg.2010.63 　

    ISSN： 1434-5161

  45. VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts Peer-reviewed

    Makoto K. Shimada, Ryuzou Matsumoto, Yosuke Hayakawa, Ryoko Sanbonmatsu, Craig Gough, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Tadashi Imanishi, Takashi Gojobori

    NUCLEIC ACIDS RESEARCH　37　(Database issue)　D810-D815　2009/01

    DOI： 10.1093/nar/gkn798 　

    ISSN： 0305-1048

  46. Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies Peer-reviewed

    Yumi Yamaguchi-Kabata, Kazuyuki Nakazono, Atsushi Takahashi, Susumu Saito, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    AMERICAN JOURNAL OF HUMAN GENETICS　83　(4)　445-456　2008/10

    DOI： 10.1016/j.ajhg.2008.08.019 　

    ISSN： 0002-9297

  47. Distribution and Effects of Nonsense Polymorphisms in Human Genes Peer-reviewed

    Yumi Yamaguchi-Kabata, Makoto K. Shimada, Yosuke Hayakawa, Shinsei Minoshima, Ranajit Chakraborty, Takashi Gojobori, Tadashi Imanishi

    PLOS ONE　3　(10)　e3393　2008/10

    DOI： 10.1371/journal.pone.0003393 　

    ISSN： 1932-6203

  48. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts Peer-reviewed

    Chisato Yamasaki, Katsuhiko Murakami, Yasuyuki Fujii, Yoshiharu Sato, Erimi Harada, Jun-Ichi Takeda, Takayuki Taniya, Ryuichi Sakate, Shingo Kikugawa, Makoto Shimada, Motohiko Tanino, Kanako O. Koyanagi, Roberto A. Barrero, Craig Gough, Hong-Woo Chun, Takuya Habara, Hideki Hanaoka, Yosuke Hayakawa, Phillip B. Hilton, Yayoi Kaneko, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Akihiro Matsuya, Naoki Nagata, Kensaku Nishikata, Akiko Ogura Noda, Shin Nurimoto, Naomi Saichi, Hiroaki Sakai, Ryoko Sanbonmatsu, Rie Shiba, Mami Suzuki, Kazuhiko Takabayashi, Aiko Takahashi, Takuro Tamura, Masayuki Tanaka, Susumu Tanaka, Fusano Todokoro, Kaori Yamaguchi, Naoyuki Yamamoto, Toshihisa Okido, Jun Mashima, Aki Hashizume, Lihua Jin, Kyung-Bum Lee, Yi-Chueh Lin, Asami Nozaki, Katsunaga Sakai, Masahito Tada, Satoru Miyazaki, Takashi Makino, Hajime Ohyanagi, Naoki Osato, Nobuhiko Tanaka, Yoshiyuki Suzuki, Kazuho Ikeo, Naruya Saitou, Hideaki Sugawara, Claire O'Donovan, Tamara Kulikova, Eleanor Whitfield, Brian Halligan, Mary Shimoyama, Simon Twigger, Kei Yura, Kouichi Kimura, Tomohiro Yasuda, Tetsuo Nishikawa, Yutaka Akiyama, Chie Motono, Yuri Mukai, Hideki Nagasaki, Makiko Suwa, Paul Horton, Reiko Kikuno, Osamu Ohara, Doron Lancet, Eric Eveno, Esther Graudens, Sandrine Imbeaud, Marie Anne Debily, Yoshihide Hayashizaki, Clara Amid, Michael Han, Andreas Osanger, Toshinori Endo, Michael A. Thomas, Mika Hirakawa, Wojciech Makalowski, Mitsuteru Nakao, Nam-Soon Kim, Hyang-Sook Yoo, Sandro J. De Souza, Maria de Fatima Bonaldo, Yoshihito Niimura, Vladimir Kuryshev, Ingo Schupp, Stefan Wiemann, Matthew Bellgard, Masafumi Shionyu, Libin Jia, Danielle Thierry-Mieg, Jean Thierry-Mieg, Lukas Wagner, Qinghua Zhang, Mitiko Go, Shinsei Minoshima, Masafumi Ohtsubo, Kousuke Hanada, Peter Tonellato, Takao Isogai, Ji Zhang, Boris Lenhard, Sangsoo Kim, Zhu Chen, Ursula Hinz, Anne Estreicher, Kenta Nakai, Izabela Makalowska, Winston Hide, Nicola Tiffin, Laurens Wilming, Ranajit Chakraborty, Marcelo Bento Soares, Maria Luisa Chiusano, Yutaka Suzuki, Charles Auffray, Yumi Yamaguchi-Kabata, Takeshi Itoh, Teruyoshi Hishiki, Satoshi Fukuchi, Ken Nishikawa, Sumio Sugano, Nobuo Nomura, Yoshio Tateno, Tadashi Imanishi, Takashi Gojobori

    NUCLEIC ACIDS RESEARCH　36　(Database issue)　D793-D799　2008/01

    DOI： 10.1093/nar/gkm999 　

    ISSN： 0305-1048

    eISSN： 1362-4962

  49. Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB) Peer-reviewed

    C Yamasaki, KO Koyanagi, Y Fujii, T Itoh, R Barrero, T Tamura, Y Yamaguchi-Kabata, M Tanino, J Takeda, S Fukuchi, S Miyazaki, N Nomura, S Sugano, T Imanishi, T Gojobori

    GENE　364　99-107　2005/12

    DOI： 10.1016/j.gene.2005.05.036 　

    ISSN： 0378-1119

  50. A novel simian immunodeficiency virus from black mangabey (Lophocebus aterrimus) in the Democratic Republic of Congo Peer-reviewed

    T Takemura, M Ekwalanga, B Bikandou, E Ido, Y Yamaguchi-Kabata, S Ohkura, H Harada, J Takehisa, H Ichimura, HJ Parra, M Nende, E Mubwo, M Sepole, M Hayami, T Miura

    JOURNAL OF GENERAL VIROLOGY　86　(Pt 7)　1967-1971　2005/07

    DOI： 10.1099/vir.0.80697-0 　

    ISSN： 0022-1317

  51. Linkage of amino acid variation and evolution of human immunodeficiency virus type 1 gp120 envelope glycoprotein (subtype B) with usage of the second receptor Peer-reviewed

    Y Yamaguchi-Kabata, M Yamashita, S Ohkura, M Hayami, T Miura

    JOURNAL OF MOLECULAR EVOLUTION　58　(3)　333-340　2004/03

    DOI： 10.1007/s00239-003-2555-x 　

    ISSN： 0022-2844

    eISSN： 1432-1432

  52. Sequence variation of HIV and bioinformatics

    Yamaguchi-Kabata Yumi

    Uirusu　54　(1)　33-38　2004

    Publisher: The Japanese Society for Virology

    DOI： 10.2222/jsv.54.33 　

    More details Close

    The envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) interacts with receptors on the target cell and mediates virus entry by fusing the viral and cell membranes. To maintain the viral infectivity, amino acids that interact with receptors are expected to be more conserved than the other sites on the protein surface. In contrast to the functional constraint of amino acids for the receptor binding, some amino acid changes in this protein may produce antigenic variations that enable the virus to escape from recognition of the host immune system. Therefore, both positive selection (higher fitness) and negative selection (lower fitness) against amino acid changes are taking place during evolution of surface proteins of parasites To elucidate the evolutionary mechanisms of the whole HIV-1 gp120 envelope glycoprotein at the single site level, we collected and analyzed all available sequence data for the protein. By analyzing 186 sequences of the HIV-1 gp120 (subtype B), we reevaluated amino acid variability at the single site level, and estimated the numbers of synonymous and nonsynonymous substitutions at each codon position to detect positive and negative selection. We identified 33 amino acid positions which may be under positive selection. Some of these positions may form discontinuous epitopes. We also analyzed amino acid sequences to find amino acid positions responsible for usage of the second receptor. We found that, in addition to the V3 loop, amino acid variation at residue 440 in C4 region is clearly linked with the usage of CXCR 4.

  53. Integrative annotation of 21,037 human genes validated by full-length cDNA clones Peer-reviewed

    Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, Roberto A. Barrero, Takuro Tamura, Yumi Yamaguchi-Kabata, Motohiko Tanino, Kei Yura, Satoru Miyazaki, Kazuho Ikeo, Keiichi Homma, Arek Kasprzyk, Tetsuo Nishikawa, Mika Hirakawa, Jean Thierry-Mieg, Danielle Thierry-Mieg, Jennifer Ashurst, Libin Jia, Mitsuteru Nakao, Michael A. Thomas, Nicola Mulder, Youla Karavidopoulou, Lihua Jin, Sangsoo Kim, Tomohiro Yasuda, Boris Lenhard, Eric Eveno, Yoshiyuki Suzuki, Chisato Yamasaki, Jun-Ichi Takeda, Craig Gough, Phillip Hilton, Yasuyuki Fujii, Hiroaki Sakai, Susumu Tanaka, Clara Amid, Matthew Bellgard, Maria de Fatima Bonaldo, Hidemasa Bono, Susan K. Bromberg, Anthony J. Brookes, Elspeth Bruford, Piero Carninci, Claude Chelala, Christine Couillault, Sandro J. de Souza, Marie-Anne Debily, Marie-Dominique Devignes, Inna Dubchak, Toshinori Endo, Anne Estreicher, Eduardo Eyras, Kaoru Fukami-Kobayashi, Gopal R. Gopinath, Esther Graudens, Yoonsoo Hahn, Michael Han, Ze-Guang Han, Kousuke Hanada, Hideki Hanaoka, Erimi Harada, Katsuyuki Hashimoto, Ursula Hinz, Momoki Hirai, Teruyoshi Hishiki, Ian Hopkinson, Sandrine Imbeaud, Hidetoshi Inoko, Alexander Kanapin, Yayoi Kaneko, Takeya Kasukawa, Janet Kelso, Paul Kersey, Reiko Kikuno, Kouichi Kimura, Bernhard Korn, Vladimir Kuryshev, Izabela Makalowska, Takashi Makino, Shuhei Mano, Regine Mariage-Samson, Jun Mashima, Hideo Matsuda, Hans-Werner Mewes, Shinsei Minoshima, Keiichi Nagai, Hideki Nagasaki, Naoki Nagata, Rajni Nigam, Osamu Ogasawara, Osamu Ohara, Masafumi Ohtsubo, Norihiro Okada, Toshihisa Okido, Satoshi Oota, Motonori Ota, Toshio Ota, Tetsuji Otsuki, Dominique Piatier-Tonneau, Annemarie Poustka, Shuang-Xi Ren, Naruya Saitou, Katsunaga Sakai, Shigetaka Sakamoto, Ryuichi Sakate, Ingo Schupp, Florence Servant, Stephen Sherry, Rie Shiba, Nobuyoshi Shimizu, Mary Shimoyama, Andrew J. Simpson, Bento Soares, Charles Steward, Makiko Suwa, Mami Suzuki, Aiko Takahashi, Gen Tamiya, Hiroshi Tanaka, Todd Taylor, Joseph D. Terwilliger, Per Unneberg, Vamsi Veeramachaneni, Shinya Watanabe, Laurens Wilming, Norikazu Yasuda, Sook Hyang-Yoo, Marvin Stodolsky, Wojciech Makalowski, Mitiko Go, Kenta Nakai, Toshihisa Takagi, Minoru Kanehisa, Yoshiyuki Sakaki, John Quackenbush, Yasushi Okazaki, Yoshihide Hayashizaki, Winston Hide, Ranajit Chakraborty, Ken Nishikawa, Hideaki Sugawara, Yoshio Tateno, Zhu Chen, Michio Oishi, Peter Tonellato, Rolf Apweiler, Kousaku Okubo, Lukas Wagner, Stefan Wiemann, Robert L. Strausberg, Takao Isogai, Charles Auffray, Nobuo Nomura, Takashi Gojobori, Sumio Sugano

    PLoS Biology　2　(6)　e162　2004

    DOI： 10.1371/journal.pbio.0020162 　

    ISSN： 1544-9173

  54. Natural infection of wild-born mandrills (Mandrillus sphinx) with two different types of simian immunodeficiency virus Peer-reviewed

    J Takehisa, Y Harada, N Ndembi, Mboudjeka, I, Y Taniguchi, C Ngansop, S Kuate, L Zekeng, K Ibuki, T Shimada, B Bikandou, Y Yamaguchi-Kabata, T Miura, M Ikeda, H Ichimura, L Kaptue, M Hayami

    AIDS RESEARCH AND HUMAN RETROVIRUSES　17　(12)　1143-1154　2001/08

    DOI： 10.1089/088922201316912754 　

    ISSN： 0889-2229

  55. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes Peer-reviewed

    Y Yamaguchi-Kabata, T Gojobori

    JOURNAL OF VIROLOGY　74　(9)　4335-4350　2000/05

    DOI： 10.1128/JVI.74.9.4335-4350.2000 　

    ISSN： 0022-538X

  56. The genetic structure of the Raleigh natural population of Drosophila melanogaster revisited Peer-reviewed

    S Kusakabe, Y Yamaguchi, H Baba, T Mukai

    GENETICS　154　(2)　679-685　2000/02

    ISSN： 0016-6731

  57. Human immunodeficiency virus type 1 intergroup (M/O) recombination in Cameroon Peer-reviewed

    J Takehisa, L Zekeng, E Ido, Y Yamaguchi-Kabata, Mboudjeka, I, Y Harada, T Miura, L Kaptue, M Hayami

    JOURNAL OF VIROLOGY　73　(8)　6810-6820　1999/08

    ISSN： 0022-538X

  58. Natural infection of chimpanzees with new lentiviruses related to HIV-1/SIVcpz Peer-reviewed

    J Takehisa, B Bikandou, E Ido, Mboudjeka, I, R M'Vouenze, MY Nzoukoudi, Y Harada, Y Yamaguchi-Kabata, T Miura, M M'Pandi, HJ Parra, P M'Pele, M Hayami

    JOURNAL OF MEDICAL PRIMATOLOGY　28　(4-5)　169-173　1999/08

    ISSN： 0047-2565

  59. Genetic diversity of HIV-1 group M from Cameroon and Republic of Congo Peer-reviewed

    Mboudjeka, I, B Bikandou, L Zekeng, J Takehisa, Y Harada, Y Yamaguchi-Kabata, Y Taniguchi, E Ido, L Kaptue, P M'pelle, HJ Parra, M Ikeda, M Hayami, T Miura

    ARCHIVES OF VIROLOGY　144　(12)　2291-2311　1999

    DOI： 10.1007/s007050050645 　

    ISSN： 0304-8608

  60. Identification of regions in which positive selection may operate in S-RNase of Rosaceae: Implication for S-allele-specific recognition sites in S-RNase Peer-reviewed

    T Ishimizu, T Endo, Y Yamaguchi-Kabata, KT Nakamura, F Sakiyama, S Norioka

    FEBS LETTERS　440　(3)　337-342　1998/12

    DOI： 10.1016/S0014-5793(98)01470-7 　

    ISSN： 0014-5793

  61. Differences in the evolutionary pattern of feline panleukopenia virus and canine parvovirus Peer-reviewed

    M Horiuchi, Y Yamaguchi, T Gojobori, M Mochizuki, H Nagasawa, Y Toyoda, N Ishiguro, M Shinagawa

    VIROLOGY　249　(2)　440-452　1998/09

    DOI： 10.1006/viro.1998.9335 　

    ISSN： 0042-6822

  62. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts Peer-reviewed

    Y Yamaguchi, T Gojobori

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　94　(4)　1264-1269　1997/02

    DOI： 10.1073/pnas.94.4.1264 　

    ISSN： 0027-8424

  63. Molecular epidemiology of rubella by nucleotide sequences of the rubella virus E1 gene in three East Asian countries Peer-reviewed

    Shigetaka Katow, Hiroko Minahara, Masao Fukushima, Yumi Yamaguchi

    Journal of Infectious Diseases　176　(3)　602-616　1997

    Publisher: Oxford University Press

    DOI： 10.1086/514080 　

    ISSN： 0022-1899

  64. Father-to-mother-to-infant transmission of HIV-1: Clonally transmitted isolate of infant mutates more rapidly than that of the mother and rapidly loses reactivity with neutralizing antibody Peer-reviewed

    Y Okamoto, K Shiosaki, Y Eda, S Tokiyoshi, Y Yamaguchi, T Gojobori, T Hachimori, S Yamazaki, M Honda

    MICROBIOLOGY AND IMMUNOLOGY　41　(2)　131-138　1997

    ISSN： 0385-5600

  65. Evolutionary motif and its biological and structural significance Peer-reviewed

    Y Tateno, K Ikeo, T Imanishi, H Watanabe, T Endo, Y Yamaguchi, Y Suzuki, K Takahashi, K Tsunoyama, M Kawai, Y Kawanishi, K Naitou, T Gojobori

    JOURNAL OF MOLECULAR EVOLUTION　44　S38-S43　1997

    DOI： 10.1007/PL00000056 　

    ISSN： 0022-2844

  66. Identification of multiple HIV-1 cytotoxic T-cell epitopes presented by human leukocyte antigen B35 molecules Peer-reviewed

    Hajime Shiga, Tatsuo Shioda, Hiroko Tomiyama, Yuji Takamiya, Shinichi Oka, Satoshi Kimura, Yumi Yamaguchi, Takashi Gojoubori, Hans-Georg Rammensee, Kiyoshi Miwa, Masafumi Takiguchi

    AIDS　10　(10)　1075-1083　1996

    ISSN： 0269-9370

  67. MOLECULAR ANALYSIS OF GPDH NULL MUTATIONS THAT AROSE IN MUTATION ACCUMULATION EXPERIMENTS IN DROSOPHILA-MELANOGASTER Peer-reviewed

    Y YAMAGUCHI, TS TAKANO, T YAMAZAKI, K HARADA

    HEREDITY　73　397-404　1994/10

    ISSN： 0018-067X

  68. EVOLUTION OF PATHOGENIC VIRUSES WITH SPECIAL REFERENCE TO THE RATES OF SYNONYMOUS AND NONSYNONYMOUS SUBSTITUTIONS Peer-reviewed

    T GOJOBORI, Y YAMAGUCHI, K IKEO, M MIZOKAMI

    JAPANESE JOURNAL OF GENETICS　69　(5)　481-488　1994/10

    DOI： 10.1266/jjg.69.481 　

    ISSN： 0021-504X

  69. MOLECULAR-CLONING AND EXPRESSION OF A MEMBER OF THE AQUAPORIN FAMILY WITH PERMEABILITY TO GLYCEROL AND UREA IN ADDITION TO WATER EXPRESSED AT THE BASOLATERAL MEMBRANE OF KIDNEY COLLECTING DUCT CELLS Peer-reviewed

    K ISHIBASHI, S SASAKI, K FUSHIMI, S UCHIDA, M KUWAHARA, H SAITO, T FURUKAWA, K NAKAJIMA, Y YAMAGUCHI, T GOJOBORI, F MARUMO

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　91　(14)　6269-6273　1994/07

    DOI： 10.1073/pnas.91.14.6269 　

    ISSN： 0027-8424

Show all ︎Show first 5

Misc. 35

  1. Exploration of BRCA1/2 gene variants in a general population cohort and return of genomic results to the participants

    徳永英樹, 安田純, 島田宗昭, 濱中洋平, 重田昌吾, 布施昇男, 勝岡史城, 荻島創一, 荻島創一, 山口由美, 寳澤篤, 川目裕, 大根田絹子, 青木洋子, 山本雅之, 八重樫伸生

    日本癌学会学術総会抄録集(Web)　81st　2022

  2. ゲノムコホート研究におけるBRCA1/2遺伝情報返却とその後の医療機関との連携の取組み

    濱中 洋平, 多田 寛, 宮下 穣, 原田 成美, 佐藤 章子, 江幡 明子, 大根田 絹子, 布施 昇男, 川目 裕, 鈴木 洋一, 長神 風二, 鈴木 吉也, 佐藤 政文, 平塚 真弘, 櫻井 美佳, 宇留野 晃, 山口 由美, 平良 摩紀子, 山本 雅之, 石田 孝宣

    日本乳癌学会総会プログラム抄録集　29回　21-21　2021/07

    Publisher: (一社)日本乳癌学会

  3. 東北メディカル・メガバンク計画における遺伝情報返却の課題

    濱中洋平, 濱中洋平, 大根田絹子, 布施昇男, 川目裕, 川目裕, 長神風二, 鈴木吉也, 鈴木洋一, 鈴木洋一, 佐藤政文, 平塚真弘, 櫻井美佳, 宇留野晃, 山口由美, 平良摩紀子, 山本雅之, 濱中洋平, 濱中洋平

    日本人類遺伝学会大会プログラム・抄録集　65th (CD-ROM)　2020

  4. 大規模ゲノムコホート調査におけるBRCA1/2遺伝子の病的バリアント保持者への遺伝情報回付に関する課題

    濱中 洋平, 石田 孝宣, 布施 昇男, 川目 裕, 山口 由美, 安田 純, 多田 寛, 宮下 穣, 原田 成美, 佐藤 章子, 青木 洋子, 長神 風二, 八重樫 伸生, 木下 賢吾, 呉 繁夫, 山本 雅之

    日本乳癌学会総会プログラム抄録集　27回　332-332　2019/07

    Publisher: (一社)日本乳癌学会

  5. Estimating frequency of pathogenic variants in a Japanese population by using the whole-genome reference panel of ToMMo

    Yumi Yamaguchi-Kabata, Jun Yasuda, Osamu Tanabe, Yoichi Suzuki, Hiroshi Kawame, Nobuo Fuse, Masao Nagasaki, Yosuke Kawai, Kaname Kojima, Fumiki Katsuoka, Sakae Saito, Inaho Danjoh, Ikuko N. Motoike, Riu Yamashita, Seizo Koshiba, Daisuke Saigusa, Gen Tamiya, Shigeo Kure, Nobuo Yaegashi, Yoshio Kawaguchi, Fuji Nagami, Shinichi Kuriyama, Junichi Sugawara, Naoko Minegishi, Atsushi Hozawa, Soichi Ogishima, Hideyasu Kiyomoto, Takako Takai-Igarashi, Kengo Kinoshita, Masayuki Yamamoto

    HUMAN GENOMICS　12　2018/03

    ISSN： 1473-9542

    eISSN： 1479-7364

  6. 「遺伝の仕組み」と「多様性」を学ぶための小児を対象とした遺伝教育ツール開発の取り組み

    小林朋子, 小林朋子, 菅原美智子, 石原利乃, 本郷一夫, 相澤弥生, 山口由美, 齋藤さかえ, 田中由佳里, 栗木美穂, 長神風二, 安田純, 櫻井美佳, 栗山進一, 川目裕, 鈴木吉也, 山本雅之, 鈴木洋一, 鈴木洋一

    日本人類遺伝学会大会プログラム・抄録集　62nd　324　2017

  7. マルチオミクスが解き明かす疾患生物学 日本人多層オミックス参照パネルの拡張

    小柴 生造, 三枝 大輔, 元池 育子, 小島 要, 城田 松之, 齋藤 智, 勝岡 史城, 河合 洋介, 山口 由美, 田邉 修, 長崎 正郎, 安田 純, 木下 賢吾, 山本 雅之

    日本生化学会大会プログラム・講演要旨集　89回　[1S05-5]　2016/09

    Publisher: (公社)日本生化学会

  8. コルチコトロピン放出ホルモン受容体1,2遺伝子における一塩基多型と過敏性腸症候群との関連

    小室葉月, 佐藤菜保子, 佐々木彩加, 鈴木直輝, 鹿野理子, 鹿野理子, 田中由佳里, 田中由佳里, 山口由美, 山口由美, 金澤素, 割田仁, 青木正志, 福土審, 福土審

    心身医学　56　(6)　636-636　2016/06/01

    Publisher: (一社)日本心身医学会

    ISSN： 0385-0307

  9. Estimation of allele frequency of pathological variants based on whole-genome sequencing of 1070 Japanese individuals

    Yumi Yamaguchi-Kabata, Yosuke Kawai, Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yukuto Sato, Fumiki Katsuoka, Jun Yasuda, Masayuki Yamamoto, Masao Nagasaki

    GENES & GENETIC SYSTEMS　90　(6)　379-379　2015/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  10. Biological processes enriched in gene with long poly-Q may be commonly involved in pathogenesis of poly-Q diseases

    Makoto K. Shimada, Ryoko Sanbonmatsu, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Yoshiyuki Suzuki, Ranajit Chakraborty, Takashi Gojobori, Tadashi Imanishi

    GENES & GENETIC SYSTEMS　90　(6)　385-385　2015/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  11. Inference of negative selection on human genome from whole genome sequences of 1070 individuals

    Yosuke Kawai, Naoki Nariai, Kaname Kojima, Yumi Yamaguchi-Kabata, Yukuto Sato, Takahiro Mimori, Masaco Nagasaki

    GENES & GENETIC SYSTEMS　90　(6)　379-379　2015/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  12. ポリグルタミン病発症機序には共通して長いグルタミン反復が要求される過程を含んでいる

    嶋田誠, 三本松良子, 山口由美, 山崎千里, 鈴木善幸, CHAKRABORTY Ranajit, 五條堀孝, 今西規

    日本遺伝学会大会プログラム・予稿集　87th　83　2015/09

  13. 日本人全ゲノムファレンスパネルの構築と今後

    日本遺伝学会大会プログラム・予稿集　87th　73　2015/09

  14. SUGAR: graphical user interface-based high-resolution data cleaning tool for high-throughput sequencing data

    Yukuto Sato, Kaname Kojima, Naoki Nariai, Yumi Yamaguchi-Kabata, Yosuke Kawai, Masao Nagasaki

    GENES & GENETIC SYSTEMS　89　(6)　329-329　2014/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  15. Nonparametric inference of population demography from SNP data

    Yosuke Kawai, Yukuto Sato, Yumi Yamaguchi, Naoki Nariai, Sachiyo Sugimoto, Takahiro Mimori, Kaname Kojima, Masao Nagasaki

    GENES & GENETIC SYSTEMS　89　(6)　314-314　2014/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  16. Evolutionary analysis on glutamine repeats using database integration between transcripts and polymorphism

    Makoto K. Shimada, Ryoko Sanbonmatsu, Chisato Yamasaki, Yumi Yamaguchi-Kabata, Takashi Gojobori, Tadashi Imanishi

    GENES & GENETIC SYSTEMS　88　(6)　383-383　2013/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  17. ヒト転写物と多型のデータベース統合による,グルタミン反復配列長大化への進化的解析

    嶋田誠, 三本松良子, 山崎千里, 山口由美, 五條堀孝, 今西規

    日本遺伝学会大会プログラム・予稿集　85th　117　2013/08/31

  18. Dual genetic structure of the Japanese population based on autosomal SNPs and haplotypes

    Yumi Yamaguchi, Tatsuhiko Tsunoda, Natsuhiko Kumasaka, Atsushi Takahashi, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    GENES & GENETIC SYSTEMS　86　(6)　441-441　2011/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  19. Making a haplotype catalog with estimated frequencies based on SNP homozygotes: an application to the Japanese population

    Yumi Yamaguchi, Natsuhiko Kumasaka, Tatsuhiko Tsunoda, Atsushi Takahashi, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    GENES & GENETIC SYSTEMS　85　(6)　440-440　2010/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  20. Determination of haplotypes and estimation of haplotype frequencies by detecting homozygotes with SNP genotypes of 3,397 individuals from the Japanese population

    Yumi Yamaguchi, Atsushi Takahashi, Tatsuhiko Tsunoda, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    GENES & GENETIC SYSTEMS　84　(6)　463-463　2009/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  21. Population structure of Japanese based on SNP genotypes from 7,003 individuals: Effects on population-based association studies

    Yumi Yamaguchi-Kabata, Kazuyuki Nakazono, Atsushi Takahashi, Naoya Hosono, Susumu Saito, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

    GENES & GENETIC SYSTEMS　83　(6)　524-524　2008/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  22. ヒトゲノム上のナンセンスSNPの網羅的探索

    山口 由美, 加畑, 嶋田 誠, 早川 陽介, 蓑島 伸生, チャクラバルティ・ラナジット, 五條堀 孝, 今西 規

    日本生化学会大会・日本分子生物学会年会合同大会講演要旨集　81回・31回　4T9-2　2008/11

    Publisher: (公社)日本生化学会

  23. Identification of polymorphic microsatellites on all human genes and their effects on human proteome

    Sanbonmatsu Ryoko, Shimada Makoto, Yamasaki Chisato, Yamaguchi-Kabata Yumi, Gojobori Takashi, Imanishi Tadashi

    GENES & GENETIC SYSTEMS　82　(6)　553-553　2007/12

    ISSN： 1341-7568

    eISSN： 1880-5779

  24. ヒト全遺伝子上の多型マイクロサテライトの検出とプロテオームへの効果

    三本松良子, 嶋田誠, 山崎千里, 山口由美, 五條堀孝, 今西規

    日本遺伝学会大会プログラム・予稿集　79th　86　2007/09/07

  25. Construction and in vivo analysis of R5 single tropic virus that shares the same genetic backbone with dual tropic SHIV-KS661. Peer-reviewed

    Matsuda K, Ibuki K, Inaba K, Matsuyama M, Hirai K, Yamaguchi-Kabata Y, Hayami M, Miura T

    25th annual Symposium on Nonhuman Primate Models for AIDS, Monterey, U.S.A., Sep. 10-13, 2007　2007

  26. 新規疾病感受性遺伝子予測のためのデータマイニングシステムの構築

    谷家貴之, 田中進, 花岡秀樹, 前川陽俊, 山崎千里, BARRERO Barrero, 金子弥生, LENHARD Boris, DATTA Milton, SHIMOYAMA Mary, 山口由美, 今西規, 五条堀孝

    日本分子生物学会年会講演要旨集　28th　369　2005/11/25

  27. 統合的ヒト遺伝子アノテーションデータベースH‐InvDB 2.0

    今西規, 山崎千里, 藤井康之, 山口由美, 伊藤剛, 五条堀孝

    日本分子生物学会年会講演要旨集　28th　358　2005/11/25

  28. ヒト遺伝子の統合アノテーションデータベース:H‐Invitational Database

    今西規, 藤井康之, 山崎千里, 伊藤剛, 小柳香奈子, BARRERO R, 田村卓郎, 山口由美, 谷野元彦

    日本分子生物学会年会プログラム・講演要旨集　27th　777　2004/11/25

  29. Integrative annotation of 21,037 human genes validated by full-length cDNA clones

    T Imanishi, T Itoh, Y Suzuki, C O'Donovan, S Fukuchi, KO Koyanagi, RA Barrero, T Tamura, Y Yamaguchi-Kabata, M Tanino, K Yura, S Miyazaki, K Ikeo, K Homma, A Kasprzyk, T Nishikawa, M Hirakawa, J Thierry-Mieg, D Thierry-Mieg, J Ashurst, LB Jia, M Nakao, MA Thomas, N Mulder, Y Karavidopoulou, LH Jin, S Kim, T Yasuda, B Lenhard, E Eveno, Y Suzuki, C Yamasaki, J Takeda, C Gough, P Hilton, Y Fujii, H Sakai, S Tanaka, C Amid, M Bellgard, MD Bonaldo, H Bono, SK Bromberg, AJ Brookes, E Bruford, P Carninci, C Chelala, C Couillault, SJ de Souza, MA Debily, MD Devignes, Dubchak, I, T Endo, A Estreicher, E Eyras, K Fukami-Kobayash, GR Gopinath, E Graudens, Y Hahn, M Han, ZG Han, K Hanada, H Hanaoka, E Harada, K Hashimoto, U Hinz, M Hirai, T Hishiki, Hopkinson, I, S Imbeaud, H Inoko, A Kanapin, Y Kaneko, T Kasukawa, J Kelso, P Kersey, R Kikuno, K Kimura, B Korn, Kuryshev, V, Makalowska, I, T Makino, S Mano, R Mariage-Samson, J Mashima, H Matsuda, HW Mewes, S Minoshima, K Nagai, H Nagasaki, N Nagata, R Nigam, O Ogasawara, O Ohara, M Ohtsubo, N Okada, T Okido, S Oota, M Ota, T Ota, T Otsuki, D Piatier-Tonneau, A Poustka, SX Ren, N Saitou, K Sakai, S Sakamoto, R Sakate, Schupp, I, F Servant, S Sherry, R Shiba, N Shimizu, M Shimoyama, AJ Simpson, B Soares, C Steward, M Suwa, M Suzuki, A Takahashi, G Tamiya, H Tanaka, T Taylor, JD Terwilliger, P Unneberg, Veeramachaneni, V, S Watanabe, L Wilming, N Yasuda, HS Yoo, M Stodolsky, W Makalowski, M Go, K Nakai, T Takagi, M Kanehisa, Y Sakaki, J Quackenbush, Y Okazaki, Y Hayashizaki, W Hide, R Chakraborty, K Nishikawa, H Sugawara, Y Tateno, Z Chen, M Oishi, P Tonellato, R Apweiler, K Okubo, L Wagner, S Wiemann, RL Strausberg, T Isogai, C Auffray, N Nomura, T Gojobori, S Sugano

    PLOS BIOLOGY　2　(6)　856-875　2004/06

    DOI： 10.1371/journal.pbio.0020162 　

    ISSN： 1545-7885

  30. Nucleotide substitution rates of HIV-1.

    SUZUKI, Y, YAMAGUCHI-KABATA, Y, GOJOBORI, T

    AIDS Reviews.　2　(1)　39-47　2000

  31. HIVのV3領域のアミノ酸置換のパターン

    山口 由美, 五條堀 孝

    日本分子生物学会年会プログラム・講演要旨集　19　738-738　1996/08/01

  32. AIDSウイルスと分子進化--HIVの遺伝情報が語るその進化過程と臨床への応用 (6月第5土曜特集 ウイルス病最前線) -- (話題になっているウイルス)

    山口 由美, 五条堀 孝

    医学のあゆみ　177　(13)　852-856　1996/06/29

    Publisher: 医歯薬出版

    ISSN： 0039-2359

  33. Molecular evolution of viruses

    YAMAGUCHI Yumi, GOJOBORI Takashi

    Virus　46　(1)　1-6　1996/06/01

    Publisher: 日本ウィルス学会

    ISSN： 0042-6857

  34. 病原性ウイルスの同義および非同義置換速度

    五條堀 孝, 山口 由美, 池尾 一穂

    The Japanese journal of genetics　69　(5)　481-488　1994/10

    Publisher: Genetics Society of Japan

    ISSN： 0021-504X

  35. Extraction of sequence motifs by molecular evolutionary method.

    池尾一穂, 川西祐一, 河合正人, 内藤公敏, 遠藤俊徳, 山口由美, 今西規, 館野義男, 五条堀孝

    日本分子生物学会年会プログラム・講演要旨集　17th　1994

Show all ︎Show first 5

Books and Other Publications 1

  1. ヒトゲノム事典

    山口由美

    株式会社 一色出版　2021/11/10

    ISBN: 9784910389127

Research Projects 2

  1. Molecular epidemiology of HIV in central Africa - Searching for the origin of AIDS virus and its future

    IDO Eiji, HAYAMI Masanori, HAYAMI Masanori, MIURA Tomoyuki, IBUKI Kentaro, MIURA Tomoyuki, IBUKI Kentaro, MUYEMBE Jean-jacques, PARRA Henri-joseph, RAPHAEL Taty-taty, NICAISE Ndembi, DORA Mbanya

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (A)

    Institution: Kyoto University

    2005 - 2008

  2. Exploration of functional non-coding sequences in the higher eukaryotic genomes.

    IMANISHI Tadashi, YAMAGUCHI Yumi, ITOH Takeshi, IKEO Kazuho, BARRERO Roberto

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: National Institute of Advanced Industrial Science and Technology

    2004 - 2005

    More details Close

    In order to explore functional non-coding sequences hidden in the higher eukaryotic genomes, we conducted bioinformatic analyses of whole genomic sequences of human and other major model animals. First, we conducted comparative genomics analyses of human and other mammalian species, and created a new database of genomic sequence alignments named as G-compass (http://www.jbirc.aist.go.jp/g-compass/). While creating the genomic alignments, we discovered 82 human genomic regions that were completely conserved between human and mouse. Some of these conserved regions overlapped with known genes, but others were suggested to contain unidentified functional elements in the human genome. These results were reported in a paper by Fujii et al. (2005). Furthermore, we compared whole genomic sequences of human, chimpanzee, mouse and rat, and found that only 16.4% of the human genome is conserved in all these four species. This result was reported in a paper by Sakate et al. (2006). Next, we explored functional non-coding elements in the human genome. By sequence analyses of human genome and human transcripts, we predicted many new candidates of human microRNAs and their potential target (regulated) genes. A part of these results was applied for patents. In conclusion, we developed methods for identifying functional non-coding elements in the genomes, and succeeded in identifying some of them.