Details of the Researcher

PHOTO

Satoshi Makino
Section
Graduate School of Medicine
Job title
Assistant Professor
Degree
e-Rad No.
30423403

Professional Memberships 1

  • American Society of Human Genetics

    2005/10 - Present

Research Areas 1

  • Life sciences / Molecular biology /

Papers 48

  1. JG2: an updated version of the Japanese population-specific reference genome Peer-reviewed

    Sirawit Sriwichaiin, Satoshi Makino, Takamitsu Funayama, Akihito Otsuki, Junko Kawashima, Yasunobu Okamura, Shu Tadaka, Fumiki Katsuoka, Kazuki Kumada, Shuichi Tsutsumi, Kengo Kinoshita, Masayuki Yamamoto, Gen Tamiya, Jun Takayama

    Human Genome Variation　12　(1)　2025/10/01

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41439-025-00326-y 　

    eISSN： 2054-345X

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    Abstract Here we present the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously used in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a substantial advancement over the collapsed assembly-based JG1, with improvements including a greater number of identified variants (3,115,695 variants, of which 298,644 had an allele frequency (AF) of 1.0 in the 3.5KJPNv2 AF panel) and a higher N50 value (152,668,378 bp). These enhancements provide researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website (https://jmorp.megabank.tohoku.ac.jp/).

  2. Profiling of runs of homozygosity from whole-genome sequence data in Japanese biobank Peer-reviewed

    Aye Ko Ko Minn, Motomichi Matsuzaki, Akira Narita, Takamitsu Funayama, Yurii Kotsar, Satoshi Makino, Jun Takayama, Hikaru Abe, Michiaki Abe, Momoka Abe, Naomi Abe, Noriko Abe, Tomomi Abe, Yuto Abe, Shizuko Ahiko, Kayo Aiki, Hiromi Aizawa, Yukari Akiyama, Hayato Anzawa, Eri Aoki, Yuichi Aoki, Hiroko Arai, Misaki Arakawa, Yukie Asano, Liam Baird, Ayano Chiba, Haruna Chiba, Ippei Chiba, Kenji Chiba, Keiko Chida, Inaho Danjoh, Hisako Endo, Reika Fue, Futaba Fujishiro, Yayoi Fujita, Waka Fukunaga, Takuo Fukushi, Mami Funata, Takamitsu Funayama, Sho Furuhashi, Nobuo Fuse, Kumiko Fushiya, Tomomi Gamo, Chinatsu Gocho, Katsuhiro Gonoi, Maki Goto, Takahiko Goto, Yukie Goto, Kaori Gouko, Michiko Haga, Yoko Haga, Yuko Hamada, Yohei Hamanaka, Mika Hanazawa, Yukari Hara, Hisano Hasebe, Atsushi Hasegawa, Hiroaki Hashizume, Asuka Hatakeyama, Sumika Hatakeyama, Nozomi Hatanaka, Rieko Hatanaka, Takanori Hidaka, Kenji Hino, Hiroe Hirama, Ikuo Hirano, Sachiko Hirano, Takumi Hirata, Masahiro Hiratsuka, Yuki Hiratsuka, Ikuko Hirayama, Eiji Hishinuma, Atsushi Hozawa, Keisuke Ido, Nobuko Igari, Chikako Iida, Katsuko Imai, Makiko Inoue, Marie Inoue, Reiko Inoue, Rumi Irie, Motoko Ishida, Noriko Ishida, Eri Ishigaka, Chihiro Ishii, Osamu Ishii, Tadashi Ishii, Tatsuro Ishikawa, Mami Ishikuro, Kazutoshi Ishimori, Ryosuke Ishiwata, Miho Itabashi, Maiko Ito, Masumi Ito, Mayumi Ito, Rie Ito, Saori Ito, Fumihiko Iwabuchi, Maki Iwabuchi, Yoko Izumi, Yoshiko Izumi, Masataka Kambe, Kanako Watanabe, Takanari Kanno, Mayu Kano, Naoko Kasahara, Hinako Kashiwa, Kiyomi Katahira, Mayumi Kato, Yukie Kato, Fumiki Katsuoka, Takeshi Kawabata, Rika Kawada, Aoi Kawagoe, Hiroshi Kawame, Junko Kawashima, Yukako Kawashima, Junko Kikuchi, Masahiro Kikuya, Masae Kimura, Kengo Kinoshita, Ikuko Kishi, Tomoko Kishimoto, Tamie Kitaura, Mika Kobayashi, Tadao Kobayashi, Tomoko Kobayashi, Eiichi N. Kodama, Shun Kodate, Mana Kogure, Toshisada Kohagizawa, Naomi Kohketsu, Noa Koida, Chie Koide, Mika Koide, Toshihiko Koike, Shohei Koiso, Kaname Kojima, Junko Komatsu, Ayumi Kondo, Yukie Konno, Sachie Koreeda, Seizo Koshiba, Takuya Koyama, Hisaaki Kudo, Kazuki Kumada, Ryoko Kumadaki, Rika Kumagai, Toshie Kumagai, Yuko Kumagai, Yasuto Kunii, Miho Kuriki, Shinichi Kuriyama, Miyuki Kuroda, Emiko Kurokawa, Seiko Kurota, Hisako Kusano, Bin Li, Donghan Li, Kanako Maeshibu, Keiko Maeta, Hiroko Matsubara, Naomi Matsukawa, Masako Matsumoto, Takako Matsuoka, Yuka Matsushita, Fumiko Matsuzaki, Motomichi Matsuzaki, Hirohito Metoki, Sayaka Minakawa, Yuki Minami, Kyoko Mitate, Satomi Mito, Ayako Miura, Noriko Miura, Ryo Miyagi, Akiko Miyazawa, Satoshi Mizuno, Akiko Mochida, Mika Momii, Hiroko Mori, Naoko Mori, Hozumi Motohashi, Ikuko N. Motoike, Shunji Mugikura, Keiko Murakami, Takahisa Murakami, Toshiro Muranishi, Masato Nagai, Satoshi Nagaie, Fuji Nagami, Tatsuo Nagasaka, Sachiko Nagase, Kumiko Nakagawa, Taku Nakai, Noriko Nakajo, Naoki Nakamura, Tomohiro Nakamura, Yuko Nakasato, Kumi Nakaya, Naoki Nakaya, Kei Nanatani, Natsuko Narisawa, Yuka Narita, Hafumi Nishi, Kohji Nishida, Ichiko Nishijima, Takahiro Nobukuni, Kotaro Nochioka, Aoi Noda, Kenichi Noguchi, Kiriko Nozoe, Rie Nunokawa, Taku Obara, Tomoko Obara, Kaori Ogasawara, Satoru Ogawa, Soichi Ogishima, Nahoko Ohi, Namiko Ohisa, Kinuko Ohneda, Hayami Ohori, Yumi Oikawa, Yumiko Ojima, Yumi Okada, Yasunobu Okamura, Hiroshi Okuda, Mitsuko Okuda, Ayako Okumoto, Akane Ono, Chiaki Ono, Genki Onodera, Kaname Onodera, Masako Onodera, Midori Onuma, Tomomi Onuma, Keiichiro Oohashi, Masumi Oomachi, Kazuya Ootomo, Yukie Oouchi, Kazuko Oowada, Masatsugu Orui, Mayumi Osada, Tamae Osanai, Reiko Ota, Noriko Otake, Sumie Otomo, Tatsui Otsuka, Akihito Otsuki, Yoko Otsuki, Yuki Oyama, Keiko Oyamada, Masahiro Ozawa, Yoko Ozawa, Satomi Obara, Daisuke Saigusa, Asami Saito, Asuka Saito, Hisako Saito, Kazue Saito, Manami Saito, Megumi Saito, Ritsumi Saito, Sakae Saito, Tomo Saito, Yoshinobu Saitoh, Hiroko Sakai, Masaki Sakaida, Hiroshi Sakamono, Hiromi Sakamoto, Kana Sakamoto, Mia Sakamoto, Kasumi Sakurai, Miyuki Sakurai, Rieko Sakurai, Mika Sakurai-Yageta, Eriko Sasaki, Kana Sasaki, Miho Sasaki, Tadashi Sasaki, Yukari Sasaki, Yukie Sasaki, Akemi Sato, Chika Sato, Hirokazu Sato, Mayumi Sato, Michiyo Sato, Miho Sato, Mitsuharu Sato, Miu Sato, Naoko Sato, Reiko Sato, Satoshi Sato, Shiho Sato, Taku Sato, Yoshiko Sato, Youko Sato, Yui Sato, Yuriko Sato, Michihiro Satoh, Ayako Sekiya, Koji Shibuya, Hirohito Shima, Yoshiko Shima, Muneaki Shimada, Atsushi Shimizu, Ritsuko Shimizu, Genki Shinoda, Nobuyuki Shirakawa, Matsuyuki Shirota, Hiroe Shoji, Ikuko Shoji, Mariko Shoji, Midori Shoji, Wakako Shoji, Satomi Someya, Shinya Sonobe, Itsumi Sou, Rie Suenaga, Yasuko Suenaga, Mayumi Suga, Rika Sugai, Junichi Sugawara, Megumi Sugawara, Michiko Sugawara, Nanako Sugawara, Saori Sugawara, Yuki Sugawara, Sachiyo Sugimoto, Yoshiko Suto, Airi Suzuki, Ayano Suzuki, Keiko P. Suzuki, Mariko Suzuki, Michirou Suzuki, Mikiko Suzuki, Norio Suzuki, Rie Suzuki, Ryoko Suzuki, Takafumi Suzuki, Tatsuya Suzuki, Yoichi Suzuki, Kaho Sato, Shu Tadaka, Keiko Taguchi, Nozomi Taiji, Makiko Taira, Kaori Takagi, Emi Takahashi, Harumi Takahashi, Junko Takahashi, Megumi Takahashi, Noriko Takahashi, Rieko Takahashi, Yukiko Takahashi, Mayuko Takasawa, Jun Takayama, Miho Takeuchi, Yoshinobu Takeyama, Sayaka Takita, Toru Tamahara, Gen Tamiya, Naomi Tamura, Akari Tanaka, Saiko Tanaka, Chihiro Tanno, Naoko Tanno, Keiko Tateno, Minoru Tateno, Chika Terui, Yuriko Tezuka, Mihoko Toki, Etsuko Tomita, Hiroaki Tomita, Mai Tomizuka, Akiko Toriyama, Naho Tsuchiya, Miyuki Tsuda, Tomomi Tsumuraya, Junko Tsunasawa, Issei Tsunoda, Juri Uchiya, Akiko Ueda, Yuriko Ueki, Fumihiko Ueno, Rumi Ujiie, Keiko Umeda, Akira Uruno, Ikuko Wada, Tomoko Wada, Mika Wagatsuma, Hitoshi Watanabe, Kazue Watanabe, Nobuo Yaegashi, Mika Yagyu, Etsuko Yamada, Yumi Yamaguchi-Kabata, Masayuki Yamamoto, Tomiko Yamauchi, Yukari Yamauchi, Mika Yamazaki, Kenji Yano, Jun Yasuda, Hang Yin, Hiroshi Yokota, Manami Yokoyama, Yuko Yoshida, Mizue Yoshino, Zhiqian Yu, Yoshiyuki Yukawa, Lin Zhang, Makoto Sasaki, Akimune Fukushima, Yasushi Ishigaki, Atsushi Shimizu, Koichi Asahi, Ryoichi Tanaka, Kozo Tanno, Kotaro Otsuka, Fumie Aizawa, Naoyuki Nishiya, Mitsuko Iwabuchi, Fumitaka Tanaka, Shinichi Omama, Kouhei Hashizume, Noriko Takebe, Kazuhiro Yoshikawa, Yuka Kotozaki, Masato Nagai, Takahiro Mikami, Takahito Nasu, Junko Akai, Yorihiro Koeda, Yohei Sawa, Nobuyuki Takanashi, Yayoi Yamasaki, Haruki Terui, Kasumi Hannokizawa, Hideki Ohmomo, Shohei Komaki, Mamoru Satoh, Yoichi Sutoh, Fumio Yamashita, Yutaka Hasegawa, Shiori Minabe, Tsuyoshi Hachiya, Tomoharu Tokutomi, Yukiko Toya, Akiko Yoshida, Satoshi Nishizuka, Ryujin Endo, Shinichi Kuriyama, Gen Tamiya

    Journal of Human Genetics　70　(6)　287-296　2025/04/03

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s10038-025-01331-3 　

    ISSN： 1434-5161

    eISSN： 1435-232X

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    Abstract Runs of homozygosity (ROHs) are widely observed across the genomes of various species and have been reported to be associated with many traits and common diseases, as well as rare recessive diseases, in human populations. Although single nucleotide polymorphism (SNP) array data have been used in previous studies on ROHs, recent advances in whole-genome sequencing (WGS) technologies and the development of nationwide cohorts/biobanks are making high-density genomic data increasingly available, and it is consequently becoming more feasible to detect ROHs at higher resolution. In the study, we searched for ROHs in two high-coverage WGS datasets from 3552 Japanese individuals and 192 three-generation families (consisting of 1120 family members) in prospective genomic cohorts. The results showed that a considerable number of ROHs, especially short ones that may have remained undetected in conventionally used SNP-array data, can be detected in the WGS data. By filtering out sequencing errors and leveraging pedigree information, longer ROHs are more likely to be detected in WGS data than in SNP-array data. Additionally, we identified gene families within ROH islands that are associated with enriched pathways related to sensory perception of taste and odors, suggesting potential signatures of selection in these key genomic regions.

  3. A fine‐scale genetic map of the Japanese population Peer-reviewed

    Jun Takayama, Satoshi Makino, Takamitsu Funayama, Masao Ueki, Akira Narita, Keiko Murakami, Masatsugu Orui, Mami Ishikuro, Taku Obara, Shinichi Kuriyama, Masayuki Yamamoto, Gen Tamiya

    Clinical Genetics　2024/05/08

    Publisher: Wiley

    DOI： 10.1111/cge.14536 　

    ISSN： 0009-9163

    eISSN： 1399-0004

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    Abstract Genetic maps are fundamental resources for linkage and association studies. A fine‐scale genetic map can be constructed by inferring historical recombination events from the genome‐wide structure of linkage disequilibrium—a non‐random association of alleles among loci—by using population‐scale sequencing data. We constructed a fine‐scale genetic map and identified recombination hotspots from 10 092 551 bi‐allelic high‐quality autosomal markers segregating among 150 unrelated Japanese individuals whose genotypes were determined by high‐coverage (30×) whole‐genome sequencing, and the genotype quality was carefully controlled by using their parents' and offspring's genotypes. The pedigree information was also utilized for haplotype phasing. The resulting genome‐wide recombination rate profiles were concordant with those of the worldwide population on a broad scale, and the resolution was much improved. We identified 9487 recombination hotspots and confirmed the enrichment of previously known motifs in the hotspots. Moreover, we demonstrated that the Japanese genetic map improved the haplotype phasing and genotype imputation accuracy for the Japanese population. The construction of a population‐specific genetic map will help make genetics research more accurate.

  4. Heterozygous calcyclin-binding protein/Siah1-interacting protein (CACYBP/SIP) gene pathogenic variant linked to a dominant family with paucity of interlobular bile duct Peer-reviewed

    Miyako Kanno, Mitsuyoshi Suzuki, Ken Tanikawa, Chikahiko Numakura, Shu-ichi Matsuzawa, Tetsuya Niihori, Yoko Aoki, Yoichi Matsubara, Satoshi Makino, Gen Tamiya, Satoshi Nakano, Ryo Funayama, Matsuyuki Shirota, Keiko Nakayama, Tetsuo Mitsui, Kiyoshi Hayasaka

    Journal of Human Genetics　67　(7)　393-397　2022/07

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s10038-022-01017-0 　

    ISSN： 1434-5161

    eISSN： 1435-232X

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

    Soichi Ogishima, Satoshi Nagaie, Satoshi Mizuno, Ryosuke Ishiwata, Keita Iida, Kazuro Shimokawa, Takako Takai-Igarashi, Naoki Nakamura, Sachiko Nagase, Tomohiro Nakamura, Naho Tsuchiya, Naoki Nakaya, Keiko Murakami, Fumihiko Ueno, Tomomi Onuma, Mami Ishikuro, Taku Obara, Shunji Mugikura, Hiroaki Tomita, Akira Uruno, Tomoko Kobayashi, Akito Tsuboi, Shu Tadaka, Fumiki Katsuoka, Akira Narita, Mika Sakurai, Satoshi Makino, Gen Tamiya, Yuichi Aoki, Ritsuko Shimizu, Ikuko N. Motoike, Seizo Koshiba, Naoko Minegishi, Kazuki Kumada, Takahiro Nobukuni, Kichiya Suzuki, Inaho Danjoh, Fuji Nagami, Kozo Tanno, Hideki Ohmomo, Koichi Asahi, Atsushi Shimizu, Atsushi Hozawa, Shinichi Kuriyama, Masayuki Yamamoto, Michiaki Abe, Yayoi Aizawa, Yuichi Aoki, Koichi Chida, Inaho Danjoh, Shinichi Egawa, Ai Eto, Takamitsu Funayama, Nobuo Fuse, Yohei Hamanaka, Yuki Harada, Hiroaki Hashizume, Shinichi Higuchi, Sachiko Hirano, Takumi Hirata, Masahiro Hiratsuka, Atsushi Hozawa, Kazuhiko Igarashi, Jin Inoue, Noriko Ishida, Naoto Ishii, Tadashi Ishii, Mami Ishikuro, Kiyoshi Ito, Sadayoshi Ito, Maiko Kageyama, Fumiki Katsuoka, Hiroshi Kawame, Junko Kawashima, Masahiro Kikuya, Kengo Kinoshita, Kazuyuki Kitatani, Tomomi Kiyama, Hideyasu Kiyomoto, Tomoko Kobayashi, Eiichi Kodama, Mana Kogure, Kaname Kojima, Sachie Koreeda, Seizo Koshiba, Shihoko Koyama, Hisaaki Kudo, Kazuki Kumada, Shigeo Kure, Miho Kuriki, Shinichi Kuriyama, Yoko Kuroki, Norihide Maikusa, Satoshi Makino, Hiroko Matsubara, Hiroyuki Matsui, Hirohito Metoki, Takahiro Mimori, Naoko Minegishi, Kazuharu Misawa, Masako Miyashita, Satoshi Mizuno, Hozumi Motohashi, Ikuko N. Motoike, Satoshi Nagaie, Masato Nagai, Fuji Nagami, Masao Nagasaki, Sachiko Nagase, Naoki Nakamura, Tomohiro Nakamura, Naoki Nakaya, Keiko Nakayama, Akira Narita, Ichiko Nishijima, Takahiro Nobukuni, Kotaro Nochioka, Taku Obara, Soichi Ogishima, Noriaki Ohuchi, Gervais Olivier, Noriko Osumi, Hiroshi Otsu, Akihito Otsuki, Daisuke Saigusa, Sakae Saito, Tomo Saito, Masaki Sakaida, Mika Sakurai-Yageta, Yuki Sato, Yukuto Sato, Atsushi Sekiguchi, Chen-Yang Shen, Tomoko F. Shibata, Ritsuko Shimizu, Kazuro Shimokawa, Matsuyuki Shirota, Junichi Sugawara, Kichiya Suzuki, Yoichi Suzuki, Shu Tadaka, Makiko Taira, Takako Takai-Igarashi, Yuji Takano, Yasuyuki Taki, Gen Tamiya, Osamu Tanabe, Hiroshi Tanaka, Yukari Tanaka, Shunsuke Teraguchi, Takahiro Terakawa, Teiji Tominaga, Hiroaki Tomita, Akito Tsuboi, Naho Tsuchiya, Ichiro Tsuji, Masao Ueki, Akira Uruno, Nobuo Yaegashi, Junya Yamagishi, Yumi Yamaguchi-Kabata, Chizuru Yamanaka, Riu Yamashita, Jun Yasuda, Junji Yokozawa, Kazunori Waki, Makoto Sasaki, Junko Akai, Ryujin Endo, Akimune Fukushima, Ryohei Furukawa, Tsuyoshi Hachiya, Kouhei Hashizume, Jiro Hitomi, Yasushi Ishigaki, Shohei Komaki, Yuka Kotozaki, Takahiro Mikami, Motoyuki Nakamura, Naoyuki Nishiya, Satoshi Nishizuka, Yoko Nomura, Kuniaki Ogasawara, Hideki Ohmomo, Shinichi Omama, Ryo Otomo, Kotaro Otsuka, Kotaro Oyama, Kiyomi Sakata, Ryohei Sasaki, Mamoru Satoh, Namie Sato, Atsushi Shimizu, Yu Shiwa, Yoichi Sutoh, Nobuyuki Takanashi, Noriko Takebe, Fumitaka Tanaka, Ryoichi Tanaka, Kozo Tanno, Tomoharu Tokutomi, Kayono Yamamoto, Fumio Yamashita, Nobuo Fuse, Teiji Tominaga, Shigeo Kure, Nobuo Yaegashi, Kengo Kinoshita, Makoto Sasaki, Hiroshi Tanaka, Masayuki Yamamoto

    Human Genome Variation　8　(1)　44　2021/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41439-021-00175-5 　

    eISSN： 2054-345X

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    <title>Abstract</title>To reveal gene-environment interactions underlying common diseases and estimate the risk for common diseases, the Tohoku Medical Megabank (TMM) project has conducted prospective cohort studies and genomic and multiomics analyses. To establish an integrated biobank, we developed an integrated database called “dbTMM” that incorporates both the individual cohort/clinical data and the genome/multiomics data of 157,191 participants in the Tohoku Medical Megabank project. To our knowledge, dbTMM is the first database to store individual whole-genome data on a variant-by-variant basis as well as cohort/clinical data for over one hundred thousand participants in a prospective cohort study. dbTMM enables us to stratify our cohort by both genome-wide genetic factors and environmental factors, and it provides a research and development platform that enables prospective analysis of large-scale data from genome cohorts.

  6. Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs Peer-reviewed

    Mika Sakurai-Yageta, Kazuki Kumada, Chinatsu Gocho, Satoshi Makino, Akira Uruno, Shu Tadaka, Ikuko N Motoike, Masae Kimura, Shin Ito, Akihito Otsuki, Akira Narita, Hisaaki Kudo, Yuichi Aoki, Inaho Danjoh, Jun Yasuda, Hiroshi Kawame, Naoko Minegishi, Seizo Koshiba, Nobuo Fuse, Gen Tamiya, Masayuki Yamamoto, Kengo Kinoshita

    The Journal of Biochemistry　170　(3)　399-410　2021/05/13

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/jb/mvab060 　

    ISSN： 0021-924X

    eISSN： 1756-2651

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    <title>Abstract</title> Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin &amp;gt;2.5–5% were &amp;gt;0.9 and &amp;gt;0.8, respectively, and &amp;gt;12 million markers were imputed with an INFO score &amp;gt;0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.

  7. ALOX12 mutation in a family with dominantly inherited bleeding diathesis Peer-reviewed

    Tetsuo Mitsui, Satoshi Makino, Gen Tamiya, Hiroko Sato, Yuki Kawakami, Yoshitaka Takahashi, Toru Meguro, Hiroko Izumino, Yosuke Sudo, Ikuo Norota, Kuniaki Ishii, Kiyoshi Hayasaka

    Journal of Human Genetics　2021/02/10

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s10038-020-00887-6 　

    ISSN： 1434-5161

    eISSN： 1435-232X

  8. Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference Peer-reviewed

    Jun Takayama, Shu Tadaka, Kenji Yano, Fumiki Katsuoka, Chinatsu Gocho, Takamitsu Funayama, Satoshi Makino, Yasunobu Okamura, Atsuo Kikuchi, Sachiyo Sugimoto, Junko Kawashima, Akihito Otsuki, Mika Sakurai-Yageta, Jun Yasuda, Shigeo Kure, Kengo Kinoshita, Masayuki Yamamoto, Gen Tamiya

    Nature Communications　12　(1)　226　2021/01

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41467-020-20146-8 　

    eISSN： 2041-1723

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    <title>Abstract</title>The complete human genome sequence is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the reference genome (e.g., GRCh37) due to its bias toward European and African ancestries. Here, we perform de novo assembly of three Japanese male genomes using &gt; 100× Pacific Biosciences long reads and Bionano Genomics optical maps per sample. We integrate the genomes using the major allele for consensus and anchor the scaffolds using genetic and radiation hybrid maps to reconstruct each chromosome. The resulting genome sequence, JG1, is contiguous, accurate, and carries the Japanese major allele at most loci. We adopt JG1 as the reference for confirmatory exome re-analyses of seven rare-disease Japanese families and find that re-analysis using JG1 reduces total candidate variant calls versus GRCh37 while retaining disease-causing variants. These results suggest that integrating multiple genomes from a single population can aid genome analyses of that population.

  9. Clustering by phenotype and genome-wide association study in autism Peer-reviewed

    Akira Narita, Masato Nagai, Satoshi Mizuno, Soichi Ogishima, Gen Tamiya, Masao Ueki, Rieko Sakurai, Satoshi Makino, Taku Obara, Mami Ishikuro, Chizuru Yamanaka, Hiroko Matsubara, Yasutaka Kuniyoshi, Keiko Murakami, Fumihiko Ueno, Aoi Noda, Tomoko Kobayashi, Mika Kobayashi, Takuma Usuzaki, Hisashi Ohseto, Atsushi Hozawa, Masahiro Kikuya, Hirohito Metoki, Shigeo Kure, Shinichi Kuriyama

    Translational Psychiatry　10　(1)　290　2020/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41398-020-00951-x 　

    eISSN： 2158-3188

  10. Genome-wide association study identifies new loci for albuminuria in the Japanese population Peer-reviewed

    Hiroshi Okuda, Koji Okamoto, Michiaki Abe, Kota Ishizawa, Satoshi Makino, Osamu Tanabe, Junichi Sugawara, Atsushi Hozawa, Kozo Tanno, Makoto Sasaki, Gen Tamiya, Masayuki Yamamoto, Sadayoshi Ito, Tadashi Ishii

    Clinical and Experimental Nephrology　24　(8)　1-9　2020/08

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1007/s10157-020-01884-x 　

    ISSN： 1342-1751

    eISSN： 1437-7799

  11. 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome Peer-reviewed

    Shu Tadaka, Fumiki Katsuoka, Masao Ueki, Kaname Kojima, Satoshi Makino, Sakae Saito, Akihito Otsuki, Chinatsu Gocho, Mika Sakurai-Yageta, Inaho Danjoh, Ikuko N. Motoike, Yumi Yamaguchi-Kabata, Matsuyuki Shirota, Seizo Koshiba, Masao Nagasaki, Naoko Minegishi, Atsushi Hozawa, Shinichi Kuriyama, Atsushi Shimizu, Jun Yasuda, Nobuo Fuse, Gen Tamiya, Masayuki Yamamoto, Kengo Kinoshita

    Human Genome Variation　6　(1)　2019/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41439-019-0059-5 　

    eISSN： 2054-345X

  12. Outlier detection for questionnaire data in biobanks Peer-reviewed

    Rieko Sakurai, Masao Ueki, Satoshi Makino, Atsushi Hozawa, Shinichi Kuriyama, Takako Takai-Igarashi, Kengo Kinoshita, Masayuki Yamamoto, Gen Tamiya

    International Journal of Epidemiology　48　(4)　1305-1315　2019/08/01

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/ije/dyz012 　

    ISSN： 0300-5771

    eISSN： 1464-3685

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    <title>Abstract</title> <sec> <title>Background</title> Biobanks increasingly collect, process and store omics with more conventional epidemiologic information necessitating considerable effort in data cleaning. An efficient outlier detection method that reduces manual labour is highly desirable. </sec> <sec> <title>Method</title> We develop an unsupervised machine-learning method for outlier detection, namely kurPCA, that uses principal component analysis combined with kurtosis to ascertain the existence of outliers. In addition, we propose a novel regression adjustment approach to improve detection, namely the regression adjustment for data by systematic missing patterns (RAMP). </sec> <sec> <title>Result</title> Application to epidemiological record data in a large-scale biobank (Tohoku Medical Megabank Organization, Japan) shows that a combination of kurPCA and RAMP effectively detects known errors or inconsistent patterns. </sec> <sec> <title>Conclusions</title> We confirm through the results of the simulation and the application that our methods showed good performance. The proposed methods are useful for many practical analysis scenarios. </sec>

  13. 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 　

    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.

  14. Female Japanese quail visually differentiate testosterone-dependent male attractiveness for mating preferences Peer-reviewed

    Gen Hiyama, Shusei Mizushima, Mei Matsuzaki, Yasuko Tobari, Jae-Hoon Choi, Takashi Ono, Masaoki Tsudzuki, Satoshi Makino, Gen Tamiya, Naoki Tsukahara, Shoei Sugita, Tomohiro Sasanami

    Scientific Reports　8　(1)　2018/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41598-018-28368-z 　

    eISSN： 2045-2322

  15. Analysis of the genes responsible for steroid-resistant nephrotic syndrome and/or focal segmental glomerulosclerosis in Japanese patients by whole-exome sequencing analysis (vol 61, pg 137, 2016) International-journal

    Daisuke Ogino, Taeko Hashimoto, Motoshi Hattori, Noriko Sugawara, Yuko Akioka, Gen Tamiya, Satoshi Makino, Kentaro Toyota, Tetsuo Mitsui, Kiyoshi Hayasaka

    JOURNAL OF HUMAN GENETICS　61　(8)　771-772　2016/08

    DOI： 10.1038/jhg.2016.31 　

    ISSN： 1434-5161

    eISSN： 1435-232X

  16. Analysis of the genes responsible for steroid-resistant nephrotic syndrome and/or focal segmental glomerulosclerosis in Japanese patients by whole-exome sequencing analysis Peer-reviewed

    Daisuke Ogino, Taeko Hashimoto, Motoshi Hattori, Noriko Sugawara, Yuko Akioka, Gen Tamiya, Satoshi Makino, Kentaro Toyota, Tetsuo Mitsui, Kiyoshi Hayasaka

    JOURNAL OF HUMAN GENETICS　61　(2)　137-141　2016/02

    DOI： 10.1038/jhg.2015.122 　

    ISSN： 1434-5161

    eISSN： 1435-232X

  17. Waardenburg syndrome type IIE in a Japanese patient caused by a novel missense mutation in the SOX10 gene Peer-reviewed

    Ken Okamura, Naoki Oiso, Gen Tamiya, Satoshi Makino, Daishi Tsujioka, Yuko Abe, Masakazu Kawaguchi, Yutaka Hozumi, Yoshikazu Shimomura, Tamio Suzuki

    JOURNAL OF DERMATOLOGY　42　(12)　1211-1212　2015/12

    DOI： 10.1111/1346-8138.13095 　

    ISSN： 0385-2407

    eISSN： 1346-8138

  18. Whole-exome sequencing confirmation of a novel heterozygous mutation in RUNX1 in a pregnant woman with platelet disorder Peer-reviewed

    Miyuki Obata, Seiji Tsutsumi, Satoshi Makino, Kanako Takahashi, Norikazu Watanabe, Takayuki Yoshida, Gen Tamiya, Hirohisa Kurachi

    Platelets　26　(4)　364-369　2015/06/01

    Publisher: Informa Healthcare

    DOI： 10.3109/09537104.2014.912750 　

    ISSN： 1369-1635 0953-7104

  19. A Mutation of COX6A1 Causes a Recessive Axonal or Mixed Form of Charcot-Marie-Tooth Disease Peer-reviewed

    Gen Tamiya, Satoshi Makino, Makiko Hayashi, Akiko Abe, Chikahiko Numakura, Masao Ueki, Atsushi Tanaka, Chizuru Ito, Kiyotaka Toshimori, Nobuhiro Ogawa, Tomoya Terashima, Hiroshi Maegawa, Daijiro Yanagisawa, Ikuo Tooyama, Masayoshi Tada, Osamu Onodera, Kiyoshi Hayasaka

    AMERICAN JOURNAL OF HUMAN GENETICS　95　(3)　294-300　2014/09

    DOI： 10.1016/j.ajhg.2014.07.013 　

    ISSN： 0002-9297

    eISSN： 1537-6605

  20. Visualizing Hepatic Copper Release in Long–Evans Cinnamon Rats Using Single-Photon Emission Computed Tomography Peer-reviewed

    Eric M. Yezdimer, Tomohiro Umemoto, Hiroshi Yamada, Satoshi Makino, Ikuo Tooyama

    Applied Biochemistry and Biotechnology　170　(5)　1138-1150　2013/07

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1007/s12010-013-0252-9 　

    ISSN： 0273-2289

    eISSN： 1559-0291

  21. Generation of a Monoclonal Antibody Specifically Reacting with Neuron-specific TATA-Box Binding Protein-Associated Factor 1 (N-TAF1) Peer-reviewed

    Satoshi Makino, Chiaki Masuda, Satoshi Ando, Gen Tamiya, Ikuo Tooyama

    Antibodies　2　(4)　1-8　2012/12/21

    Publisher: MDPI AG

    DOI： 10.3390/antib2010001 　

    eISSN： 2073-4468

  22. In Vivo Detection of Copper Ions by Magnetic Resonance Imaging Using a Prion-Based Contrast Agent Peer-reviewed

    Satoshi Makino, Tomohiro Umemoto, Hiroshi Yamada, Eric M. Yezdimer, Ikuo Tooyama

    APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY　168　(3)　504-518　2012/10

    DOI： 10.1007/s12010-012-9792-7 　

    ISSN： 0273-2289

    eISSN： 1559-0291

  23. Sustained expression of a neuron-specific isoform of the Taf1 gene in development stages and aging in mice Peer-reviewed

    Jamiyansuren Jambaldorj, Satoshi Makino, Batmunkh Munkhbat, Gen Tamiya

    Biochemical and Biophysical Research Communications　425　(2)　273-277　2012/08

    Publisher: Elsevier BV

    DOI： 10.1016/j.bbrc.2012.07.081 　

    ISSN： 0006-291X

  24. UBR5 Gene Mutation Is Associated with Familial Adult Myoclonic Epilepsy in a Japanese Family Peer-reviewed

    Takeo Kato, Gen Tamiya, Shingo Koyama, Tomohiro Nakamura, Satoshi Makino, Shigeki Arawaka, Toru Kawanami, Ikuo Tooyama

    ISRN Neurology　2012　1-4　2012

    Publisher: Hindawi Limited

    DOI： 10.5402/2012/508308 　

    eISSN： 2090-5513

    More details Close

    The causal gene(s) for familial adult myoclonic epilepsy (FAME) remains undetermined. To identify it, an exome analysis was performed for the proband in a Japanese FAME family. Of the 383 missense/nonsense variants examined, only c.5720G&gt;A mutation (p.Arg1907His) in the <italic>UBR5</italic> gene was found in all of the affected individuals in the family, but not in the nonaffected members. Such mutation was not found in any of the 85 healthy individuals in the same community nor in any of the 24 individuals of various ethnicities. The present study demonstrated an FAME-associated mutation in the <italic>UBR5</italic> gene, which is located close to the reported locus linked to Japanese FAME families.

  25. Expression and Localization of TRK-Fused Gene Products in the Rat Brain and Retina Peer-reviewed

    Hisae Maebayashi, Shigako Takeuchi, Chiaki Masuda, Satoshi Makino, Kenji Fukui, Hiroshi Kimura, Ikuo Tooyama

    ACTA HISTOCHEMICA ET CYTOCHEMICA　45　(1)　15-23　2012

    Publisher: Japan Society of Histochemistry & Cytochemistry

    DOI： 10.1267/ahc.11015 　

    ISSN： 0044-5991

    eISSN： 1347-5800

  26. Infiltration of T Lymphocytes and Expression of ICAM-1 in the Hippocampus of Patients with Hippocampal Sclerosis Peer-reviewed

    Hiroaki Nakahara, Yoshihiro Konishi, Thomas G. Beach, Naoto Yamada, Satoshi Makino, Ikuo Tooyama

    ACTA HISTOCHEMICA ET CYTOCHEMICA　43　(6)　157-162　2010

    Publisher: Japan Society of Histochemistry & Cytochemistry

    DOI： 10.1267/ahc.10022 　

    ISSN： 0044-5991

    eISSN： 1347-5800

  27. The mRNA Distribution of C7orf24, a γ-Glutamyl Cyclotransferase, in Rat Tissues Peer-reviewed

    Keisuke Oda, Satoshi Makino, Chiaki Masuda, Tatsuhiro Yoshiki, Yoshihisa Kitamura, Kazuyuki Takata, Daijiro Yanagisawa, Takashi Taniguchi, Ikuo Tooyama

    Journal of Histochemistry & Cytochemistry　57　(12)　1121-1126　2009/12

    Publisher: SAGE Publications

    DOI： 10.1369/jhc.2009.953976 　

    ISSN： 0022-1554

    eISSN： 1551-5044

  28. Twenty-six new polymorphic microsatellite markers around the HLA-B, -C and -E loci in the human MHC class I region Peer-reviewed

    G. Tamiya, M. Ota, Y. Katsuyama, I. Shlina, A. Oka, S. Makino, M. Kimura, H. Inoko

    Tissue Antigens　51　(4)　337-346　2008/09/30

    Publisher: Wiley

    DOI： 10.1111/j.1399-0039.1998.tb02972.x 　

    ISSN： 0001-2815

    eISSN： 1399-0039

  29. Refinement of a locus for autosomal dominant hereditary motor and sensory neuropathy with proximal dominancy (HMSN-P) and genetic heterogeneity Peer-reviewed

    Kouji Maeda, Ryuji Kaji, Katsuhito Yasuno, Jamiyansuren Jambaldorj, Hiroyuki Nodera, Hiroshi Takashima, Masanori Nakagawa, Satoshi Makino, Gen Tamiya

    Journal of Human Genetics　52　(11)　907-914　2007/11

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1007/s10038-007-0193-7 　

    ISSN： 1434-5161

    eISSN： 1435-232X

  30. Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia Peer-reviewed

    Katsuhito Yasuno, Satoshi Ando, Shinnosuke Misumi, Satoshi Makino, Jerzy K Kulski, Tatsuyuki Muratake, Naoshi Kaneko, Hideki Amagane, Toshiyuki Someya, Hidetoshi Inoko, Hidemichi Suga, Kousuke Kanemoto, Gen Tamiya

    American Journal of Medical Genetics Part B: Neuropsychiatric Genetics　144B　(2)　250-253　2007/03/05

    Publisher: Wiley

    DOI： 10.1002/ajmg.b.30443 　

    ISSN： 1552-4841

    eISSN： 1552-485X

  31. Reduced Neuron-Specific Expression of the TAF1 Gene Is Associated with X-Linked Dystonia-Parkinsonism Peer-reviewed

    Satoshi Makino, Ryuji Kaji, Satoshi Ando, Maiko Tomizawa, Katsuhito Yasuno, Satoshi Goto, Shinnichi Matsumoto, Ma. Daisy Tabuena, Elma Maranon, Marita Dantes, Lillian V. Lee, Kazumasa Ogasawara, Ikuo Tooyama, Hiroyasu Akatsu, Masataka Nishimura, Gen Tamiya

    The American Journal of Human Genetics　80　(3)　393-406　2007/03

    Publisher: Elsevier BV

    DOI： 10.1086/512129 　

    ISSN： 0002-9297

  32. Tumour necrosis factor α signalling through activation of Kupffer cells plays an essential role in liver fibrosis of non-alcoholic steatohepatitis in mice Peer-reviewed

    K. Tomita, G. Tamiya, S. Ando, K. Ohsumi, T. Chiyo, A. Mizutani, N. Kitamura, K. Toda, T. Kaneko, Y. Horie, J. Y. Han, S. Kato, M. Shimoda, Y. Oike, M. Tomizawa, S. Makino, T. Ohkura, H. Saito, N. Kumagai, H. Nagata, H. Ishii, T. Hibi

    Gut　55　(3)　415-424　2006/03

    DOI： 10.1136/gut.2005.071118 　

    ISSN： 0017-5749

  33. Immunohistochemical study of TAFII250 in the rat laryngeal nervous system Peer-reviewed

    H Okano, H Bamba, Y Hisa, S Makino, S Ando, G Tamiya, S Goto, R Kaji, H Kimura, I Tooyama

    Histology and histopathology　20　(4)　1029-1035　2005/10

  34. Whole genome association study of rheumatoid arthritis using 27 039 microsatellites Peer-reviewed

    G Tamiya, M Shinya, T Imanishi, T Ikuta, S Makino, K Okamoto, K Furugaki, T Matsumoto, S Mano, S Ando, Y Nozaki, W Yukawa, R Nakashige, D Yamaguchi, H Ishibashi, M Yonekura, Y Nakami, S Takayama, T Endo, T Saruwatari, M Yagura, Y Yoshikawa, K Fujimoto, A Oka, S Chiku, SEV Linsen, MJ Giphart, JK Kulski, T Fukazawa, H Hashimoto, M Kimura, Y Hoshina, Y Suzuki, T Hotta, J Mochida, T Minezaki, K Komai, S Shiozawa, A Taniguchi, H Yamanaka, N Kamatani, T Gojobori, S Bahram, H Inoko

    HUMAN MOLECULAR GENETICS　14　(16)　2305-2321　2005/08

    DOI： 10.1093/hmg/ddi234 　

    ISSN： 0964-6906

  35. Functional anatomy of the basal ganglia in X-linked recessive dystonia-parkinsonism Peer-reviewed

    Satoshi Goto, Lillian V. Lee, Edwin L. Munoz, Ikuo Tooyama, Gen Tamiya, Satoshi Makino, Satoshi Ando, Marita B. Dantes, Kazumichi Yamada, Sadayuki Matsumoto, Hideki Shimazu, Jun-Ichi Kuratsu, Asao Hirano, Ryuji Kaji

    Annals of Neurology　58　(1)　7-17　2005/07

    Publisher: Wiley

    DOI： 10.1002/ana.20513 　

    ISSN： 0364-5134

  36. Novel algorithm for automated genotyping of microsatellites Peer-reviewed

    Toshiko Matsumoto, Wataru Yukawa, Yasuyuki Nozaki, Ryo Nakashige, Minori Shinya, Satoshi Makino, Masaru Yagura, Tomoki Ikuta, Tadashi Imanishi, Hidetoshi Inoko, Gen Tamiya, Takashi Gojobori

    Nucleic Acids Research　32　(20)　6069-6077　2004/11/16

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/nar/gkh946 　

    eISSN： 1362-4962

  37. Identification of two new C4 alleles by DNA sequencing and evidence for a historical recombination of serologically defined C4A and C4B alleles Peer-reviewed

    J. Hui, A. Oka, M. Tomizawa, G. K. Tay, J. K. Kulski, W. J. Penhale, S. P.A. Iaschi, S. Makino, G. Tamiya, H. Inoko

    Tissue Antigens　63　(3)　263-269　2004/03

    DOI： 10.1111/j.1399-0039.2004.0175.x 　

    ISSN： 0001-2815

  38. Identification of IκBL as the Second Major Histocompatibility Complex–Linked Susceptibility Locus for Rheumatoid Arthritis Peer-reviewed

    Koichi Okamoto, Satoshi Makino, Yoko Yoshikawa, Asumi Takaki, Yumie Nagatsuka, Masao Ota, Gen Tamiya, Akinori Kimura, Seiamak Bahram, Hidetoshi Inoko

    The American Journal of Human Genetics　72　(2)　303-312　2003/02

    Publisher: Elsevier BV

    DOI： 10.1086/346067 　

    ISSN： 0002-9297

  39. Identification of novel candidate genes in the diffuse panbronchiolitis critical region of the class I human MHC Peer-reviewed

    Y Matsuzaka, K Tounai, A Denda, M Tomizawa, S Makino, K Okamoto, N Keicho, A Oka, JK Kulski, G Tamiya, H Inoko

    IMMUNOGENETICS　54　(5)　301-309　2002/08

    DOI： 10.1007/s00251-002-0470-8 　

    ISSN： 0093-7711

  40. Susceptibility locus for non-obstructive azoospermia is localized within the HLA-DR/DQ subregion: Primary role of DQB1*0604 Peer-reviewed

    Y. Matsuzaka, S. Makino, K. Okamoto, A. Oka, A. Tsujimura, K. Matsumiya, S. Takahara, A. Okuyama, M. Sada, R. Gotoh, T. Nakatani, M. Ota, Y. Katsuyama, G. Tamiya, H. Inoko

    Tissue Antigens　60　(1)　53-63　2002/07/01

    DOI： 10.1034/j.1399-0039.2002.600107.x 　

    ISSN： 0001-2815

  41. Association of a determinant on mouse chromosome 18 with experimental severe Plasmodium berghei malaria Peer-reviewed

    Eiji Nagayasu, Koichi Nagakura, Mayumi Akaki, Gen Tamiya, Satoshi Makino, Yamaji Nakano, Minoru Kimura, Masamichi Aikawa

    Infection and Immunity　70　(2)　512-516　2002

    DOI： 10.1128/IAI.70.2.512-516.2002 　

    ISSN： 0019-9567

  42. New polymorphic microsatellite markers in the human MHC class III region Peer-reviewed

    Y. Matsuzaka, S. Makino, K. Nakajima, M. Tomizawa, A. Oka, S. Bahram, J. K. Kulski, G. Tamiya, H. Inoko

    Tissue Antigens　57　(5)　397-404　2001

    DOI： 10.1034/j.1399-0039.2001.057005397.x 　

    ISSN： 0001-2815

  43. Gene structure and promoter for Crad2 encoding mouse cis-retinol/3α-hydroxysterol short-chain dehydrogenase isozyme Peer-reviewed

    Kengo Tomita, Masahiro Sato, Kagemasa Kajiwara, Masafumi Tanaka, Gen Tamiya, Satoshi Makino, Maiko Tomizawa, Akiko Mizutani, Yuhko Kuwano, Takashi Shiina, Hiromasa Ishii, Minoru Kimura

    Gene　251　(2)　175-186　2000/06

    Publisher: Elsevier BV

    DOI： 10.1016/s0378-1119(00)00194-3 　

    ISSN： 0378-1119

  44. New polymorphic microsatellite markers in the human MHC class II region Peer-reviewed

    Y. Matsuzaka, S. Makino, K. Nakajima, M. Tomizawa, A. Oka, M. Kimura, S. Bahram, G. Tamiya, H. Inoko

    Tissue Antigens　56　(6)　492-500　2000

    DOI： 10.1034/j.1399-0039.2000.560602.x 　

    ISSN： 0001-2815

  45. Construction of a Linkage Map of the Medaka (Oryzias latipes) and Mapping of the Da Mutant Locus Defective in Dorsoventral Patterning Peer-reviewed

    M Ohtsuka, S Makino, K Yoda, H Wada, K Naruse, H Mitani, A Shima, K Ozato, M Kimura, H Inoko

    Genome Research　9　(12)　1277-1287　1999/12/01

    Publisher: Cold Spring Harbor Laboratory

    DOI： 10.1101/gr.9.12.1277 　

    eISSN： 1088-9051

  46. Association Analysis Using Refined Microsatellite Markers Localizes a Susceptibility Locus for Psoriasis Vulgaris Within a 111 kb Segment Telomeric to the HLA-C Gene Peer-reviewed

    A. Oka, G. Tamiya, M. Tomizawa, M. Ota, Y. Katsuyama, S. Makino, T. Shiina, M. Yoshitome, M. Iizuka, Y. Sasao, K. Iwashita, Y. Kawakubo, J. Sugai, A. Ozawa, M. Ohkido, M. Kimura, S. Bahram, H. Inoko

    Human Molecular Genetics　8　(12)　2165-2170　1999/11/01

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/hmg/8.12.2165 　

    ISSN： 0964-6906

    eISSN： 1460-2083

  47. New polymorphic microsatellite markers in the human MHC class I region Peer-reviewed

    G. Tamiya, T. Shiina, A. Oka, M. Tomizawa, M. Ota, Y. Katsuyama, M. Yoshitome, S. Makino, M. Kimura, H. Inoko

    Tissue Antigens　54　(3)　221-228　1999/09

    Publisher: Wiley

    DOI： 10.1034/j.1399-0039.1999.540302.x 　

    ISSN： 0001-2815

  48. Twenty-six new polymorphic microsatellite markers around the HLA-B, -C and -E loci in the human MHC class I region Peer-reviewed

    G Tamiya, M Ota, Y Katsuyama, T Shiina, A Oka, S Makino, M Kimura, H Inoko

    TISSUE ANTIGENS　51　(4)　337-346　1998/04

    ISSN： 0001-2815

Show all ︎Show first 5

Misc. 2

  1. Expression and Localization of TRK-Fused Gene Products in the Rat Brain and Retina (vol 45, pg 15, 2012)

    Hisae Maebayashi, Shigako Takeuchi, Chiaki Masuda, Satoshi Makino, Kenji Fukui, Hiroshi Kimura, Ikuo Tooyama

    ACTA HISTOCHEMICA ET CYTOCHEMICA　45　(4)　239-239　2012

    DOI： 10.1267/ahc.err.11015 　

    ISSN： 0044-5991

    eISSN： 1347-5800

  2. だれでも使えるバイオインフォマティクスリソース 「バイオインフォマティクスはじめの一歩｣

    牧野悟士

    分子精神医学　6　(1)　59-65　2006/01

Presentations 1

  1. Deficiency of a Neuron-specific Isoform of the TAF1 Gene Is Associated with X-linked Dystonia-Parkinsonism

    Makino S, Kaji R, Ando S, Tomizawa M, Ando H, Goto S, Matsumoto S, Tabuena D, Maranon E, Dantes M, Lee LV, Ogasawara K, Tooyama I, Akatsu H, Nishimura M, Tamiya G

    American Society of Human Genetics 2005 Annual Meeting　2005/10/27

Research Projects 5

  1. 大規模コホートの調査票における新規データクリーニング手法の開発

    牧野 悟士, 田宮 元, 櫻井 利恵子

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業 基盤研究(C)

    Category: 基盤研究(C)

    Institution: 東北大学

    2018/04 - 2021/03

    More details Close

    東北メディカル・メガバンク機構の大規模ゲノムコホート研究では、15万人の参加者について、各種の血液検査値や画像データ、健康診断結果が計測されると同時に、同意書、生活習慣などに関する調査票といった、紙媒体の形態で収集される情報を取り扱っている。適切な調査結果の還元と医療支援への貢献、そして学術的用途としての有用性を高めるために、データの信頼性確保が必須であり、そのためには、データ入力におけるモニタリングや論理チェック、データクリーニングが重要である。しかし、膨大なデータを全て人力で確認し、調査票原本に戻って修正の必要性を調べることは事実上不可能である。そこで本研究計画では、大規模なデータクリーニングにおいて、1) 集団からの外れ値を検出する際に既知の情報を利用して主成分分析（PCA）を拡張した統計的モデルを使用する、2) 検出されたエラー候補をその性質に基づいて分類・処理する、の二つの手法をあわせ用いることにより、この問題の本質的解決を目指している。 初年度においては、同意書および調査票と、関連する特定健診データなどにおいて、期待した通りの挙動をしないデータ及びパターン（ここではエラーと呼称する）の検出を一つ目の目的とした。そのために、これまで人力により行っていたエラーの検出を、主成分分析に基づいて自動化するアルゴリズムの開発を進めてきた。主成分分析を用いたエラー検出法はすでに多く提案されているが、エラー検出の自動化を行い、さらに検出の作業効率を上げるため、統計量の一つである尖度を用いたアルゴリズムを開発した。

  2. Analysis of mouse models of cytochrome c oxidase deficiency owing to mutations in COX6A1

    Makino Satoshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

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

    Institution: Tohoku University

    2015/04 - 2018/03

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    Charcot-Marie-Tooth disease (CMT) is the most common inherited neuropathy characterized by clinical and genetic heterogeneity. Whole-genome sequencing study in the probands, followed by mutation screening in the two families, revealed a disease-specific 5-bp deletion in a splicing element of intron 2 adjacent to the 3rd exon of COX6A1. Cox6a1 null mice showed significantly reduced COX activity and neurogenic muscular atrophy leading to a difficulty in walking. On the other hand, by electron microscope, no special findings were observed in nerve fibers. Therefore, we focused on the mitochondrial ferritin (FtMt) of metal binding protein present in mitochondria. Under oxidative stress conditions induced by hydrogen peroxide, the expression of FtMt were increased. This finding suggests that FtMt protects cells against oxidative stress by hydrogen peroxide.

  3. General transcription factor TAF1 is involved in transcriptional impairment and neurodegeneration

    MAKINO Satoshi, TOOYAMA Ikuo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

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

    2012/04 - 2015/03

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    We performed cell-cycle analysis in TAF1 or neuron-speciphic TAF1 (N-TAF1) transfected temperature-sensitive mutant hamster cell line, exhibits cell cycle arrest and apoptosis at the restrictive temperature. The aim is the comparison of the functional difference between TAF1 and N-TAF1 according to the view of possibilities that transcriptional impairment of subunit of general transcription factor causes neurodegeneration. Analysis of cell cycle by flow cytometry in TAF1 or neuron-speciphic TAF1 (N-TAF1) transfected mutant hamster cell line showed that the point mutation affects cell cycle in the cell line is less relevant to TAF1's neuron-specific functions.

  4. Neuron-Specific Function of N-TAF1, the disease causative gene of Hereditary Dystonia(DYT3)

    MAKINO Satoshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)

    Category: Grant-in-Aid for Young Scientists (B)

    Institution: Shiga University of Medical Science

    2010 - 2011

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    We previously found a neuron-specific isoform of the TAF1, which is the disease causative gene of X-linked recessive dystonia-parkinsonism. To investigate the function of the neuron-specific isoform of the TAF1 gene, we carried out over-expression of TAF1 in neuronal and non-neuronal cultured cell lines. We demonstrated that the localization pattern of TAF1 is different between neuronal and non-neuronal cell. And we performed knockdown of either TAF1 or N-TAF1 using siRNA. The microarray analysis showed some candidate gene which might be regulated by N-TAF1.

  5. Functional analysis of N-TAF1, the disease causative gene of X-linked recessive dystonia-parkinsonism

    MAKINO Satoshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)

    Category: Grant-in-Aid for Young Scientists (B)

    Institution: Shiga University of Medical Science

    2008 - 2009

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    We previously found a neuron-specific isoform of the TAF1, which is the disease causative gene of X-linked recessive dystonia-parkinsonism. To investigate the function of the neuron-specific isoform of the TAF1 gene, we carried out expression analysis in mouse brain and over-expression of N-TAF1 in cultured cell lines. We demonstrated that N-TAF1 varies from TAF1 gene in expression pattern, probably reflecting the difference in physiological roles between N-TAF1 and TAF1.