Details of the Researcher

PHOTO

Hayato Anzawa
Section
Graduate School of Information Sciences
Job title
Assistant Professor
Degree

  • 博士（情報科学）（東北大学）

  • 修士（情報科学）（東北大学）

Professional Memberships 1

  • Japanese Society for Bioinformatics

    2024 - Present

Research Areas 1

  • Informatics / Biological, health, and medical informatics /

Papers 10

  1. C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database

    Hayato Anzawa, Kengo Kinoshita

    Journal of Molecular Biology　435　(14)　168157-168157　2023/07/24

    Publisher: Elsevier {BV}

    DOI： 10.1016/j.jmb.2023.168157 　

    ISSN： 0022-2836

  2. Theoretical characterisation of strand cross-correlation in ChIP-seq International-journal Peer-reviewed

    Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita

    BMC Bioinformatics　21　(1)　2020/07/24

    Publisher: Springer Science and Business Media LLC

    DOI： 10.21203/rs.2.16602/v3 　

    ISSN： 1471-2105

    eISSN： 1471-2105

    More details Close

    Abstract Background Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) because of its peak calling independence, it remains unclear what aspects of quality such strand cross-correlation profiles actually measure. Results We introduced a simple model to simulate the mapped read-density of ChIP-seq and then derived the theoretical maximum and minimum of cross-correlation coefficients between strands. The results suggest that the maximum coefficient of typical ChIP-seq samples is directly proportional to the number of total mapped reads and the square of the ratio of signal reads, and inversely proportional to the number of peaks and the length of read-enriched regions. Simulation analysis supported our results and evaluation using 790 ChIP-seq data obtained from the public database demonstrated high consistency between calculated cross-correlation coefficients and estimated coefficients based on the theoretical relations and peak calling results. In addition, we found that the mappability-bias-correction improved sensitivity, enabling differentiation of maximum coefficients from the noise level. Based on these insights, we proposed virtual S/N (VSN), a novel peak call-free metric for S/N assessment. We also developed PyMaSC, a tool to calculate strand cross-correlation and VSN efficiently. VSN achieved most consistent S/N estimation for various ChIP targets and sequencing read depths. Furthermore, we demonstrated that a combination of VSN and pre-existing peak calling results enable the estimation of the numbers of detectable peaks for posterior experiments and assess peak calling results. Conclusions We present the first theoretical insights into the strand cross-correlation, and the results reveal the potential and the limitations of strand cross-correlation analysis. Our quality assessment framework using VSN provides peak call-independent QC and will help in the evaluation of peak call analysis in ChIP-seq experiments.

  3. PNPO–PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity

    Hiroki Sekine, Haruna Takeda, Norihiko Takeda, Akihiro Kishino, Hayato Anzawa, Takayuki Isagawa, Nao Ohta, Shohei Murakami, Hideya Iwaki, Nobufumi Kato, Shu Kimura, Zun Liu, Koichiro Kato, Fumiki Katsuoka, Masayuki Yamamoto, Fumihito Miura, Takashi Ito, Masatomo Takahashi, Yoshihiro Izumi, Hiroyuki Fujita, Hitoshi Yamagata, Takeshi Bamba, Takaaki Akaike, Norio Suzuki, Kengo Kinoshita, Hozumi Motohashi

    Nature Metabolism　2024/05/31

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s42255-024-01053-4 　

    eISSN： 2522-5812

  4. Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals

    Yu-ichi Aoki, Keiko Taguchi, Hayato Anzawa, Junko Kawashima, Noriko Ishida, Akihito Otsuki, Atsushi Hasegawa, Liam Baird, Takafumi Suzuki, Ikuko N Motoike, Kinuko Ohneda, Kazuki Kumada, Fumiki Katsuoka, Kengo Kinoshita, Masayuki Yamamoto

    The Journal of Biochemistry　2024/05/31

    DOI： 10.1093/jb/mvae008 　

  5. Identifying key genes in COPD risk via multiple population data integration and gene prioritization. International-journal

    Afeefa Zainab, Hayato Anzawa, Kengo Kinoshita

    PloS one　19　(11)　e0305803　2024

    DOI： 10.1371/journal.pone.0305803 　

    More details Close

    Chronic obstructive pulmonary disease (COPD) is a highly prevalent disease, making it a leading cause of death worldwide. Several genome-wide association studies (GWAS) have been conducted to identify loci associated with COPD. However, different ancestral genetic compositions for the same disease across various populations present challenges in studies involving multi-population data. In this study, we aimed to identify protein-coding genes associated with COPD by prioritizing genes for each population's GWAS data, and then combining these results instead of performing a common meta-GWAS due to significant sample differences in different population cohorts. Lung function measurements are often used as indicators for COPD risk prediction; therefore, we used lung function GWAS data from two populations, Japanese and European, and re-evaluated them using a multi-population gene prioritization approach. This study identified significant single nucleotide variants (SNPs) in both Japanese and European populations. The Japanese GWAS revealed nine significant SNPs and four lead SNPs in three genomic risk loci. In comparison, the European population showed five lead SNPs and 17 independent significant SNPs in 21 genomic risk loci. A comparative analysis of the results found 28 similar genes in the prioritized gene lists of both populations. We also performed a standard meta-analysis for comparison and identified 18 common genes in both populations. Our approach demonstrated that trans-ethnic linkage disequilibrium (LD) could detect some significant novel associations and genes that have yet to be reported or were missed in previous analyses. The study suggests that a gene prioritization approach for multi-population analysis using GWAS data may be a feasible method to identify new associations in data with genetic diversity across different populations. It also highlights the possibility of identifying generalized and population-specific treatment and diagnostic options.

  6. Deficiency of CHAMP1, a gene related to intellectual disability, causes impaired neuronal development and a mild behavioural phenotype Peer-reviewed

    Masayoshi Nagai, Kenji Iemura, Takako Kikkawa, Sharmin Naher, Satoko Hattori, Hideo Hagihara, Koh-ichi Nagata, Hayato Anzawa, Risa Kugisaki, Hideki Wanibuchi, Takaya Abe, Kenichi Inoue, Kengo Kinoshita, Tsuyoshi Miyakawa, Noriko Osumi, Kozo Tanaka

    Brain Communications　4　(5)　2022/09/01

    Publisher: Oxford University Press ({OUP})

    DOI： 10.1093/braincomms/fcac220 　

    ISSN： 2632-1297

    eISSN： 2632-1297

  7. High levels of chromosomal instability facilitate the tumor growth and sphere formation Peer-reviewed

    Iemura, K., Anzawa, H., Funayama, R., Iwakami, R., Nakayama, K., Kinoshita, K., Tanaka, K.

    Cancer Science　113　(8)　2727-2737　2022/06/05

    Publisher: Wiley

    DOI： 10.1111/cas.15457 　

    ISSN： 1349-7006 1347-9032

    eISSN： 1349-7006

  8. CEBPB is required for NRF2-mediated drug resistance in NRF2-activated non-small cell lung cancer cells Peer-reviewed

    Okazaki, K., Anzawa, H., Katsuoka, F., Kinoshita, K., Sekine, H., Motohashi, H.

    Journal of Biochemistry　171　(5)　567-578　2022/02/07

    Publisher: Oxford University Press ({OUP})

    DOI： 10.1093/jb/mvac013 　

    ISSN： 1756-2651 0021-924X

    eISSN： 1756-2651

  9. Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers Peer-reviewed

    Keito Okazaki, Hayato Anzawa, Zun Liu, Nao Ota, Hiroshi Kitamura, Yoshiaki Onodera, Md. Morshedul Alam, Daisuke Matsumaru, Takuma Suzuki, Fumiki Katsuoka, Shu Tadaka, Ikuko Motoike, Mika Watanabe, Kazuki Hayasaka, Akira Sakurada, Yoshinori Okada, Masayuki Yamamoto, Takashi Suzuki, Kengo Kinoshita, Hiroki Sekine, Hozumi Motohashi

    Nature Communications　11　(1)　2020/11/20

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41467-020-19593-0 　

    ISSN： 2041-1723

    eISSN： 2041-1723

  10. Landscape of electrophilic and inflammatory stress-mediated gene regulation in human lymphoblastoid cell lines Peer-reviewed

    Noriko Ishida, Yuichi Aoki, Fumiki Katsuoka, Ichiko Nishijima, Takahiro Nobukuni, Hayato Anzawa, Li Bin, Miyuki Tsuda, Kazuki Kumada, Hisaaki Kudo, Takahiro Terakawa, Akihito Otsuki, Kengo Kinoshita, Riu Yamashita, Naoko Minegishi, Masayuki Yamamoto

    Free Radical Biology and Medicine　161　71-83　2020/10/02

    Publisher: Elsevier {BV}

    DOI： 10.1016/j.freeradbiomed.2020.09.023 　

    ISSN： 0891-5849

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Misc. 2

  1. Genome-wide association study of central corneal thickness in the cohort Study

    布施昇男, 安澤隼人, 元池育子, 櫻井美由紀, 木下賢吾, 山本雅之

    日本眼科学会雑誌　128　2024

    ISSN： 0029-0203

  2. 転写因子NRF2の持続的活性化によるエンハンサーリモデリングと腫瘍幹細胞性の増強

    岡崎慶斗, 安澤隼人, 岡田克典, 鈴木貴, 木下賢吾, 関根弘樹, 本橋ほづみ

    日本生化学会大会(Web)　94th　2021

Presentations 5

  1. C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database

    Hayato Anzawa, Kengo Kinoshita

    1st Asia & Pacific Bioinformatics Joint Conference (APBJC 2024)　2024/10/23

  2. Large-scale assessment of ChIP-seq quality metrics toward peak call-free quality control

    Hayato Anzawa, Kengo Kinoshita

    29th Conference on Intelligent Systems for Molecular Biology and the 20th European Conference on Computational Biology　2021/07/27

  3. Theoretical estimation of the strand cross-correlation in ChIP-Seq data

    Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita

    Intelligent Systems for Molecular Biology and European Conference on Computational Biology, 2019　2019/07/22

  4. ChIP-Seqデータのクラスタリングによる実験条件・解析手法に起因するバイアスの可視化

    安澤隼人, 木下賢吾

    NGS現場の会第五回研究会　2017/05/22

  5. Model based discrimination method of ChIPed data from control data in ChIP-seq experiment dataset

    Hayato Anzawa, Kengo Kinoshita

    Informatics In Biology, Medicine and Pharmacology 2016　2016/09/30

Research Projects 1

  1. Development of a methodology for building secondary databases with incremental updates and its application to regulome data

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Early-Career Scientists

    Institution: Tohoku University

    2024/04/01 - 2027/03/31

Teaching Experience 4

  1. Programming A　Tohoku University Undergraduate (specialized)

  2. 創造工学研修　Tohoku University Undergraduate (specialized)

  3. Systems Bioinformatics　Tohoku University Postgraduate

  4. Laboratory C　Tohoku University Undergraduate (specialized)