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1. Population-specific putative causal variants shape quantitative traits

Author

Koyama, Satoshi, Liu, Xiaoxi, Koike, Yoshinao, Hikino, Keiko, Koido, Masaru, Li, Wei, Akaki, Kotaro, Tomizuka, Kohei, Ito, Shuji, Otomo, Nao, Suetsugu, Hiroyuki, Yoshino, Soichiro, Akiyama, Masato, Saito, Kohei, Ishikawa, Yuki, Benner, Christian, Natarajan, Pradeep, Ellinor, Patrick T., Mushiroda, Taisei, Horikoshi, Momoko, Ikeda, Masashi, Iwata, Nakao, Matsuda, Koichi, Niida, Shumpei, Ozaki, Kouichi, Momozawa, Yukihide, Ikegawa, Shiro, Takeuchi, Osamu, Ito, Kaoru, and Terao, Chikashi

Published
2024
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2. A novel prognostic model of de novo metastatic hormone-sensitive prostate cancer to optimize treatment intensity

Author

Fujiwara, Hiroshi, Kubota, Masashi, Hidaka, Yu, Ito, Kaoru, Kawahara, Takashi, Kurahashi, Ryoma, Hattori, Yuto, Shiraishi, Yusuke, Hama, Yusuke, Makita, Noriyuki, Tashiro, Yu, Hatano, Shotaro, Ikeuchi, Ryosuke, Nakashima, Masakazu, Utsunomiya, Noriaki, Takashima, Yasushi, Somiya, Shinya, Nagahama, Kanji, Fujimoto, Takeru, Shimizu, Kosuke, Imai, Kazuto, Takahashi, Takehiro, Sumiyoshi, Takayuki, Goto, Takayuki, Morita, Satoshi, Kobayashi, Takashi, and Akamatsu, Shusuke

Published
2024
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4. Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease.

Author

Jang, Min, Patel, Parth, Pereira, Alexandre, Willcox, Jon, Haghighi, Alireza, Tai, Angela, Ito, Kaoru, Morton, Sarah, Gorham, Joshua, McKean, David, DePalma, Steven, Bernstein, Daniel, Brueckner, Martina, Chung, Wendy, Giardini, Alessandro, Goldmuntz, Elizabeth, Kaltman, Jonathan, Kim, Richard, Newburger, Jane, Shen, Yufeng, Tristani-Firouzi, Martin, Gelb, Bruce, Porter, George, Seidman, Christine, Seidman, Jonathan, and Srivastava, Deepak

Subjects
RNA splicing, algorithms, alleles, child, humans, Child, Humans, RNA, Heart Defects, Congenital, Mutation, RNA Splicing, Gene Frequency, RNA Splicing Factors, Repressor Proteins
Abstract

BACKGROUND: Known genetic causes of congenital heart disease (CHD) explain

Published
2023

9. Androgen receptor binding sites enabling genetic prediction of mortality due to prostate cancer in cancer-free subjects

Author

Ito, Shuji, Liu, Xiaoxi, Ishikawa, Yuki, Conti, David D., Otomo, Nao, Kote-Jarai, Zsofia, Suetsugu, Hiroyuki, Eeles, Rosalind A., Koike, Yoshinao, Hikino, Keiko, Yoshino, Soichiro, Tomizuka, Kohei, Horikoshi, Momoko, Ito, Kaoru, Uchio, Yuji, Momozawa, Yukihide, Kubo, Michiaki, Kamatani, Yoichiro, Matsuda, Koichi, Haiman, Christopher A., Ikegawa, Shiro, Nakagawa, Hidewaki, and Terao, Chikashi

Published
2023
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12. Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk

Author

Kojima, Shohei, Koyama, Satoshi, Ka, Mirei, Saito, Yuka, Parrish, Erica H., Endo, Mikiko, Takata, Sadaaki, Mizukoshi, Misaki, Hikino, Keiko, Takeda, Atsushi, Gelinas, Asami F., Heaton, Steven M., Koide, Rie, Kamada, Anselmo J., Noguchi, Michiya, Hamada, Michiaki, Kamatani, Yoichiro, Murakawa, Yasuhiro, Ishigaki, Kazuyoshi, Nakamura, Yukio, Ito, Kaoru, Terao, Chikashi, Momozawa, Yukihide, and Parrish, Nicholas F.

Published
2023
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13. Genome-wide analysis identifies novel susceptibility loci for myocardial infarction

Author

Hartiala, Jaana A, Han, Yi, Jia, Qiong, Hilser, James R, Huang, Pin, Gukasyan, Janet, Schwartzman, William S, Cai, Zhiheng, Biswas, Subarna, Trégouët, David-Alexandre, Smith, Nicholas L, Consortium, The INVENT, Group, The CHARGE Consortium Hemostasis Working, Consortium, The GENIUS-CHD, Seldin, Marcus, Pan, Calvin, Mehrabian, Margarete, Lusis, Aldons J, Bazeley, Peter, Sun, Yan V, Liu, Chang, Quyyumi, Arshed A, Scholz, Markus, Thiery, Joachim, Delgado, Graciela E, Kleber, Marcus E, März, Winfried, Howe, Laurence J, Asselbergs, Folkert W, van Vugt, Marion, Vlachojannis, Georgios J, Patel, Riyaz S, Lyytikäinen, Leo-Pekka, Kähönen, Mika, Lehtimäki, Terho, Nieminen, Tuomo VM, Kuukasjärvi, Pekka, Laurikka, Jari O, Chang, Xuling, Heng, Chew-Kiat, Jiang, Rong, Kraus, William E, Hauser, Elizabeth R, Ferguson, Jane F, Reilly, Muredach P, Ito, Kaoru, Koyama, Satoshi, Kamatani, Yoichiro, Komuro, Issei, Japan, Biobank, Stolze, Lindsey K, Romanoski, Casey E, Khan, Mohammad Daud, Turner, Adam W, Miller, Clint L, Aherrahrou, Redouane, Civelek, Mete, Ma, Lijiang, Björkegren, Johan LM, Kumar, S Ram, Tang, WH Wilson, Hazen, Stanley L, and Allayee, Hooman

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Clinical Sciences, Cardiovascular, Heart Disease, Clinical Research, Heart Disease - Coronary Heart Disease, Human Genome, Genetics, Aging, Atherosclerosis, Aetiology, 2.1 Biological and endogenous factors, Coronary Artery Disease, Endothelial Cells, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Japan, Myocardial Infarction, Polymorphism, Single Nucleotide, Risk Factors, Myocardial infarction, Genetic factors, Genome-wide association study, Meta-analysis, SLC44A3, INVENT Consortium, CHARGE Consortium Hemostasis Working Group, GENIUS-CHD Consortium, Biobank Japan, Cardiorespiratory Medicine and Haematology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology, Clinical sciences
Abstract

AimsWhile most patients with myocardial infarction (MI) have underlying coronary atherosclerosis, not all patients with coronary artery disease (CAD) develop MI. We sought to address the hypothesis that some of the genetic factors which establish atherosclerosis may be distinct from those that predispose to vulnerable plaques and thrombus formation.Methods and resultsWe carried out a genome-wide association study for MI in the UK Biobank (n∼472 000), followed by a meta-analysis with summary statistics from the CARDIoGRAMplusC4D Consortium (n∼167 000). Multiple independent replication analyses and functional approaches were used to prioritize loci and evaluate positional candidate genes. Eight novel regions were identified for MI at the genome wide significance level, of which effect sizes at six loci were more robust for MI than for CAD without the presence of MI. Confirmatory evidence for association of a locus on chromosome 1p21.3 harbouring choline-like transporter 3 (SLC44A3) with MI in the context of CAD, but not with coronary atherosclerosis itself, was obtained in Biobank Japan (n∼165 000) and 16 independent angiography-based cohorts (n∼27 000). Follow-up analyses did not reveal association of the SLC44A3 locus with CAD risk factors, biomarkers of coagulation, other thrombotic diseases, or plasma levels of a broad array of metabolites, including choline, trimethylamine N-oxide, and betaine. However, aortic expression of SLC44A3 was increased in carriers of the MI risk allele at chromosome 1p21.3, increased in ischaemic (vs. non-diseased) coronary arteries, up-regulated in human aortic endothelial cells treated with interleukin-1β (vs. vehicle), and associated with smooth muscle cell migration in vitro.ConclusionsA large-scale analysis comprising ∼831 000 subjects revealed novel genetic determinants of MI and implicated SLC44A3 in the pathophysiology of vulnerable plaques.

Published
2021

14. Cross-ancestry genome-wide analysis of atrial fibrillation unveils disease biology and enables cardioembolic risk prediction

Author

Miyazawa, Kazuo, Ito, Kaoru, Ito, Masamichi, Zou, Zhaonan, Kubota, Masayuki, Nomura, Seitaro, Matsunaga, Hiroshi, Koyama, Satoshi, Ieki, Hirotaka, Akiyama, Masato, Koike, Yoshinao, Kurosawa, Ryo, Yoshida, Hiroki, Ozaki, Kouichi, Onouchi, Yoshihiro, Takahashi, Atsushi, Matsuda, Koichi, Murakami, Yoshinori, Aburatani, Hiroyuki, Kubo, Michiaki, Momozawa, Yukihide, Terao, Chikashi, Oki, Shinya, Akazawa, Hiroshi, Kamatani, Yoichiro, and Komuro, Issei

Published
2023
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15. Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants

Author

Aragam, Krishna G., Jiang, Tao, Goel, Anuj, Kanoni, Stavroula, Wolford, Brooke N., Atri, Deepak S., Weeks, Elle M., Wang, Minxian, Hindy, George, Zhou, Wei, Grace, Christopher, Roselli, Carolina, Marston, Nicholas A., Kamanu, Frederick K., Surakka, Ida, Venegas, Loreto Muñoz, Sherliker, Paul, Koyama, Satoshi, Ishigaki, Kazuyoshi, Åsvold, Bjørn O., Brown, Michael R., Brumpton, Ben, de Vries, Paul S., Giannakopoulou, Olga, Giardoglou, Panagiota, Gudbjartsson, Daniel F., Güldener, Ulrich, Haider, Syed M. Ijlal, Helgadottir, Anna, Ibrahim, Maysson, Kastrati, Adnan, Kessler, Thorsten, Kyriakou, Theodosios, Konopka, Tomasz, Li, Ling, Ma, Lijiang, Meitinger, Thomas, Mucha, Sören, Munz, Matthias, Murgia, Federico, Nielsen, Jonas B., Nöthen, Markus M., Pang, Shichao, Reinberger, Tobias, Schnitzler, Gavin, Smedley, Damian, Thorleifsson, Gudmar, von Scheidt, Moritz, Ulirsch, Jacob C., Arnar, David O., Burtt, Noël P., Costanzo, Maria C., Flannick, Jason, Ito, Kaoru, Jang, Dong-Keun, Kamatani, Yoichiro, Khera, Amit V., Komuro, Issei, Kullo, Iftikhar J., Lotta, Luca A., Nelson, Christopher P., Roberts, Robert, Thorgeirsson, Gudmundur, Thorsteinsdottir, Unnur, Webb, Thomas R., Baras, Aris, Björkegren, Johan L. M., Boerwinkle, Eric, Dedoussis, George, Holm, Hilma, Hveem, Kristian, Melander, Olle, Morrison, Alanna C., Orho-Melander, Marju, Rallidis, Loukianos S., Ruusalepp, Arno, Sabatine, Marc S., Stefansson, Kari, Zalloua, Pierre, Ellinor, Patrick T., Farrall, Martin, Danesh, John, Ruff, Christian T., Finucane, Hilary K., Hopewell, Jemma C., Clarke, Robert, Gupta, Rajat M., Erdmann, Jeanette, Samani, Nilesh J., Schunkert, Heribert, Watkins, Hugh, Willer, Cristen J., Deloukas, Panos, Kathiresan, Sekar, and Butterworth, Adam S.

Published
2022
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16. Abstract 18244: A Multi-Ancestry GWAS of Calcific Aortic Stenosis Among 2.7 Million Individuals

Author

Small, Aeron M, Dufresne, Line, Farber-Eger, Eric, Abner, Erik, Corey, Kristin, Stefánsson, Kári, Nadauld, Lincoln, Bundgaard, Henning, Lee, Jiwoo, Schumacher, Johannes, Trenkwalder, Teresa, Soderberg, Stefan, Ganna, Andrea, Rader, Daniel J, Moksnes, Marta Riise, Lin, Meng, Laporte, Fabien, Larsson, Susanna, Smith, Gustav, Do, Ron, Ito, Kaoru, Holm, Hilma, Sun, Yan, Kim, Kelly, WILSON, PETER, Odonnell, Christopher J, Peloso, Gina, Engert, Jamie C, Thanassoulis, George, and Natarajan, Pradeep

Published
2023
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17. Large-scale genome-wide association study of coronary artery disease in genetically diverse populations

Author

Tcheandjieu, Catherine, Zhu, Xiang, Hilliard, Austin T., Clarke, Shoa L., Napolioni, Valerio, Ma, Shining, Lee, Kyung Min, Fang, Huaying, Chen, Fei, Lu, Yingchang, Tsao, Noah L., Raghavan, Sridharan, Koyama, Satoshi, Gorman, Bryan R., Vujkovic, Marijana, Klarin, Derek, Levin, Michael G., Sinnott-Armstrong, Nasa, Wojcik, Genevieve L., Plomondon, Mary E., Maddox, Thomas M., Waldo, Stephen W., Bick, Alexander G., Pyarajan, Saiju, Huang, Jie, Song, Rebecca, Ho, Yuk-Lam, Buyske, Steven, Kooperberg, Charles, Haessler, Jeffrey, Loos, Ruth J. F., Do, Ron, Verbanck, Marie, Chaudhary, Kumardeep, North, Kari E., Avery, Christy L., Graff, Mariaelisa, Haiman, Christopher A., Le Marchand, Loïc, Wilkens, Lynne R., Bis, Joshua C., Leonard, Hampton, Shen, Botong, Lange, Leslie A., Giri, Ayush, Dikilitas, Ozan, Kullo, Iftikhar J., Stanaway, Ian B., Jarvik, Gail P., Gordon, Adam S., Hebbring, Scott, Namjou, Bahram, Kaufman, Kenneth M., Ito, Kaoru, Ishigaki, Kazuyoshi, Kamatani, Yoichiro, Verma, Shefali S., Ritchie, Marylyn D., Kember, Rachel L., Baras, Aris, Lotta, Luca A., Kathiresan, Sekar, Hauser, Elizabeth R., Miller, Donald R., Lee, Jennifer S., Saleheen, Danish, Reaven, Peter D., Cho, Kelly, Gaziano, J. Michael, Natarajan, Pradeep, Huffman, Jennifer E., Voight, Benjamin F., Rader, Daniel J., Chang, Kyong-Mi, Lynch, Julie A., Damrauer, Scott M., Wilson, Peter W. F., Tang, Hua, Sun, Yan V., Tsao, Philip S., O’Donnell, Christopher J., and Assimes, Themistocles L.

Published
2022
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18. Genetic analysis of right heart structure and function in 40,000 people

Author

Pirruccello, James P., Di Achille, Paolo, Nauffal, Victor, Nekoui, Mahan, Friedman, Samuel F., Klarqvist, Marcus D. R., Chaffin, Mark D., Weng, Lu-Chen, Cunningham, Jonathan W., Khurshid, Shaan, Roselli, Carolina, Lin, Honghuang, Koyama, Satoshi, Ito, Kaoru, Kamatani, Yoichiro, Komuro, Issei, Jurgens, Sean J., Benjamin, Emelia J., Batra, Puneet, Natarajan, Pradeep, Ng, Kenney, Hoffmann, Udo, Lubitz, Steven A., Ho, Jennifer E., Lindsay, Mark E., Philippakis, Anthony A., and Ellinor, Patrick T.

Published
2022
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20. HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease

Author

Shimizu, Chisato, Kim, Jihoon, Eleftherohorinou, Hariklia, Wright, Victoria J, Hoang, Long T, Tremoulet, Adriana H, Franco, Alessandra, Hibberd, Martin L, Takahashi, Atsushi, Kubo, Michiaki, Ito, Kaoru, Tanaka, Toshihiro, Onouchi, Yoshihiro, Coin, Lachlan JM, Levin, Michael, Burns, Jane C, Shike, Hiroko, and Consortium, on behalf of International Kawasaki Disease Genetic

Subjects
Biomedical and Clinical Sciences, Immunology, Autoimmune Disease, Pediatric, Genetics, Prevention, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Alleles, Amino Acid Sequence, Amino Acid Substitution, Antigen Presentation, Binding Sites, Cohort Studies, Gene Frequency, Genetic Predisposition to Disease, Genotype, HLA-C Antigens, Histocompatibility Testing, Humans, Japan, Mucocutaneous Lymph Node Syndrome, Peptides, Polymorphism, Single Nucleotide, Protein Binding, Protein Domains, T-Lymphocytes, Cytotoxic, Kawasaki disease, HLA-C, Antigen presentation, Amino acid substitution, Cytotoxic T cells, International Kawasaki Disease Genetic Consortium
Abstract

Kawasaki disease (KD) is a pediatric vasculitis caused by an unknown trigger in genetically susceptible children. The incidence varies widely across genetically diverse populations. Several associations with HLA Class I alleles have been reported in single cohort studies. Using a genetic approach, from the nine single nucleotide variants (SNVs) associated with KD susceptibility in children of European descent, we identified SNVs near the HLA-C (rs6906846) and HLA-B genes (rs2254556) whose association was replicated in a Japanese descent cohort (rs6906846 p = 0.01, rs2254556 p = 0.005). The risk allele (A at rs6906846) was also associated with HLA-C*07:02 and HLA-C*04:01 in both US multi-ethnic and Japanese cohorts and HLA-C*12:02 only in the Japanese cohort. The risk A-allele was associated with eight non-conservative amino acid substitutions (amino acid positions); Asp or Ser (9), Arg (14), Ala (49), Ala (73), Ala (90), Arg (97), Phe or Ser (99), and Phe or Ser (116) in the HLA-C peptide binding groove that binds peptides for presentation to cytotoxic T cells (CTL). This raises the possibility of increased affinity to a "KD peptide" that contributes to the vasculitis of KD in genetically susceptible children.

Published
2019

22. Deep learning-based age estimation from chest X-rays indicates cardiovascular prognosis

Author

Ieki, Hirotaka, Ito, Kaoru, Saji, Mike, Kawakami, Rei, Nagatomo, Yuji, Takada, Kaori, Kariyasu, Toshiya, Machida, Haruhiko, Koyama, Satoshi, Yoshida, Hiroki, Kurosawa, Ryo, Matsunaga, Hiroshi, Miyazawa, Kazuo, Ozaki, Kouichi, Onouchi, Yoshihiro, Katsushika, Susumu, Matsuoka, Ryo, Shinohara, Hiroki, Yamaguchi, Toshihiro, Kodera, Satoshi, Higashikuni, Yasutomi, Fujiu, Katsuhito, Akazawa, Hiroshi, Iguchi, Nobuo, Isobe, Mitsuaki, Yoshikawa, Tsutomu, and Komuro, Issei

Published
2022
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23. Source File Set Search for Clone-and-Own Reuse Analysis

Author

Ishio, Takashi, Sakaguchi, Yusuke, Ito, Kaoru, and Inoue, Katsuro

Subjects
Computer Science - Software Engineering
Abstract

Clone-and-own approach is a natural way of source code reuse for software developers. To assess how known bugs and security vulnerabilities of a cloned component affect an application, developers and security analysts need to identify an original version of the component and understand how the cloned component is different from the original one. Although developers may record the original version information in a version control system and/or directory names, such information is often either unavailable or incomplete. In this research, we propose a code search method that takes as input a set of source files and extracts all the components including similar files from a software ecosystem (i.e., a collection of existing versions of software packages). Our method employs an efficient file similarity computation using b-bit minwise hashing technique. We use an aggregated file similarity for ranking components. To evaluate the effectiveness of this tool, we analyzed 75 cloned components in Firefox and Android source code. The tool took about two hours to report the original components from 10 million files in Debian GNU/Linux packages. Recall of the top-five components in the extracted lists is 0.907, while recall of a baseline using SHA-1 file hash is 0.773, according to the ground truth recorded in the source code repositories., Comment: 14th International Conference on Mining Software Repositories

Published
2017

24. Multi-ethnic genome-wide association study for atrial fibrillation

Author

Roselli, Carolina, Chaffin, Mark D, Weng, Lu-Chen, Aeschbacher, Stefanie, Ahlberg, Gustav, Albert, Christine M, Almgren, Peter, Alonso, Alvaro, Anderson, Christopher D, Aragam, Krishna G, Arking, Dan E, Barnard, John, Bartz, Traci M, Benjamin, Emelia J, Bihlmeyer, Nathan A, Bis, Joshua C, Bloom, Heather L, Boerwinkle, Eric, Bottinger, Erwin B, Brody, Jennifer A, Calkins, Hugh, Campbell, Archie, Cappola, Thomas P, Carlquist, John, Chasman, Daniel I, Chen, Lin Y, Chen, Yii-Der Ida, Choi, Eue-Keun, Choi, Seung Hoan, Christophersen, Ingrid E, Chung, Mina K, Cole, John W, Conen, David, Cook, James, Crijns, Harry J, Cutler, Michael J, Damrauer, Scott M, Daniels, Brian R, Darbar, Dawood, Delgado, Graciela, Denny, Joshua C, Dichgans, Martin, Dörr, Marcus, Dudink, Elton A, Dudley, Samuel C, Esa, Nada, Esko, Tonu, Eskola, Markku, Fatkin, Diane, Felix, Stephan B, Ford, Ian, Franco, Oscar H, Geelhoed, Bastiaan, Grewal, Raji P, Gudnason, Vilmundur, Guo, Xiuqing, Gupta, Namrata, Gustafsson, Stefan, Gutmann, Rebecca, Hamsten, Anders, Harris, Tamara B, Hayward, Caroline, Heckbert, Susan R, Hernesniemi, Jussi, Hocking, Lynne J, Hofman, Albert, Horimoto, Andrea RVR, Huang, Jie, Huang, Paul L, Huffman, Jennifer, Ingelsson, Erik, Ipek, Esra Gucuk, Ito, Kaoru, Jimenez-Conde, Jordi, Johnson, Renee, Jukema, J Wouter, Kääb, Stefan, Kähönen, Mika, Kamatani, Yoichiro, Kane, John P, Kastrati, Adnan, Kathiresan, Sekar, Katschnig-Winter, Petra, Kavousi, Maryam, Kessler, Thorsten, Kietselaer, Bas L, Kirchhof, Paulus, Kleber, Marcus E, Knight, Stacey, Krieger, Jose E, Kubo, Michiaki, Launer, Lenore J, Laurikka, Jari, Lehtimäki, Terho, Leineweber, Kirsten, Lemaitre, Rozenn N, Li, Man, Lim, Hong Euy, Lin, Henry J, and Lin, Honghuang

Subjects
Biological Sciences, Genetics, Heart Disease, Cardiovascular, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Atrial Fibrillation, Case-Control Studies, Ethnicity, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Quantitative Trait Loci, Transcriptome, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Atrial fibrillation (AF) affects more than 33 million individuals worldwide1 and has a complex heritability2. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.

Published
2018

25. Protein-Truncating Variants at the Cholesteryl Ester Transfer Protein Gene and Risk for Coronary Heart Disease

Author

Nomura, Akihiro, Won, Hong-Hee, Khera, Amit V, Takeuchi, Fumihiko, Ito, Kaoru, McCarthy, Shane, Emdin, Connor A, Klarin, Derek, Natarajan, Pradeep, Zekavat, Seyedeh M, Gupta, Namrata, Peloso, Gina M, Borecki, Ingrid B, Teslovich, Tanya M, Asselta, Rosanna, Duga, Stefano, Merlini, Piera A, Correa, Adolfo, Kessler, Thorsten, Wilson, James G, Bown, Matthew J, Hall, Alistair S, Braund, Peter S, Carey, David J, Murray, Michael F, Kirchner, H Lester, Leader, Joseph B, Lavage, Daniel R, Manus, J Neil, Hartze, Dustin N, Samani, Nilesh J, Schunkert, Heribert, Marrugat, Jaume, Elosua, Roberto, McPherson, Ruth, Farrall, Martin, Watkins, Hugh, Juang, Jyh-Ming J, Hsiung, Chao A, Lin, Shih-Yi, Wang, Jun-Sing, Tada, Hayato, Kawashiri, Masa-Aki, Inazu, Akihiro, Yamagishi, Masakazu, Katsuya, Tomohiro, Nakashima, Eitaro, Nakatochi, Masahiro, Yamamoto, Ken, Yokota, Mitsuhiro, Momozawa, Yukihide, Rotter, Jerome I, Lander, Eric S, Rader, Daniel J, Danesh, John, Ardissino, Diego, Gabriel, Stacey, Willer, Cristen J, Abecasis, Goncalo R, Saleheen, Danish, Kubo, Michiaki, Kato, Norihiro, Ida Chen, Yii-Der, Dewey, Frederick E, and Kathiresan, Sekar

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Clinical Sciences, Genetics, Cardiovascular, Heart Disease, Atherosclerosis, Heart Disease - Coronary Heart Disease, Adult, Aged, Case-Control Studies, Cholesterol Ester Transfer Proteins, Coronary Disease, Female, Genetic Variation, Humans, Male, Middle Aged, Risk Factors, case-control studies, cholesteryl ester transfer protein, coronary disease, lipids, Cardiorespiratory Medicine and Haematology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology, Clinical sciences
Abstract

RationaleTherapies that inhibit CETP (cholesteryl ester transfer protein) have failed to demonstrate a reduction in risk for coronary heart disease (CHD). Human DNA sequence variants that truncate the CETP gene may provide insight into the efficacy of CETP inhibition.ObjectiveTo test whether protein-truncating variants (PTVs) at the CETP gene were associated with plasma lipid levels and CHD.Methods and resultsWe sequenced the exons of the CETP gene in 58 469 participants from 12 case-control studies (18 817 CHD cases, 39 652 CHD-free controls). We defined PTV as those that lead to a premature stop, disrupt canonical splice sites, or lead to insertions/deletions that shift frame. We also genotyped 1 Japanese-specific PTV in 27561 participants from 3 case-control studies (14 286 CHD cases, 13 275 CHD-free controls). We tested association of CETP PTV carrier status with both plasma lipids and CHD. Among 58 469 participants with CETP gene-sequencing data available, average age was 51.5 years and 43% were women; 1 in 975 participants carried a PTV at the CETP gene. Compared with noncarriers, carriers of PTV at CETP had higher high-density lipoprotein cholesterol (effect size, 22.6 mg/dL; 95% confidence interval, 18-27; P

Published
2017

29. Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease

Author

Koyama, Satoshi, Ito, Kaoru, Terao, Chikashi, Akiyama, Masato, Horikoshi, Momoko, Momozawa, Yukihide, Matsunaga, Hiroshi, Ieki, Hirotaka, Ozaki, Kouichi, Onouchi, Yoshihiro, Takahashi, Atsushi, Nomura, Seitaro, Morita, Hiroyuki, Akazawa, Hiroshi, Kim, Changhoon, Seo, Jeong-sun, Higasa, Koichiro, Iwasaki, Motoki, Yamaji, Taiki, Sawada, Norie, Tsugane, Shoichiro, Koyama, Teruhide, Ikezaki, Hiroaki, Takashima, Naoyuki, Tanaka, Keitaro, Arisawa, Kokichi, Kuriki, Kiyonori, Naito, Mariko, Wakai, Kenji, Suna, Shinichiro, Sakata, Yasuhiko, Sato, Hiroshi, Hori, Masatsugu, Sakata, Yasushi, Matsuda, Koichi, Murakami, Yoshinori, Aburatani, Hiroyuki, Kubo, Michiaki, Matsuda, Fumihiko, Kamatani, Yoichiro, and Komuro, Issei

Published
2020
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30. Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases

Author

Ishigaki, Kazuyoshi, Akiyama, Masato, Kanai, Masahiro, Takahashi, Atsushi, Kawakami, Eiryo, Sugishita, Hiroki, Sakaue, Saori, Matoba, Nana, Low, Siew-Kee, Okada, Yukinori, Terao, Chikashi, Amariuta, Tiffany, Gazal, Steven, Kochi, Yuta, Horikoshi, Momoko, Suzuki, Ken, Ito, Kaoru, Koyama, Satoshi, Ozaki, Kouichi, Niida, Shumpei, Sakata, Yasushi, Sakata, Yasuhiko, Kohno, Takashi, Shiraishi, Kouya, Momozawa, Yukihide, Hirata, Makoto, Matsuda, Koichi, Ikeda, Masashi, Iwata, Nakao, Ikegawa, Shiro, Kou, Ikuyo, Tanaka, Toshihiro, Nakagawa, Hidewaki, Suzuki, Akari, Hirota, Tomomitsu, Tamari, Mayumi, Chayama, Kazuaki, Miki, Daiki, Mori, Masaki, Nagayama, Satoshi, Daigo, Yataro, Miki, Yoshio, Katagiri, Toyomasa, Ogawa, Osamu, Obara, Wataru, Ito, Hidemi, Yoshida, Teruhiko, Imoto, Issei, Takahashi, Takashi, Tanikawa, Chizu, Suzuki, Takao, Sinozaki, Nobuaki, Minami, Shiro, Yamaguchi, Hiroki, Asai, Satoshi, Takahashi, Yasuo, Yamaji, Ken, Takahashi, Kazuhisa, Fujioka, Tomoaki, Takata, Ryo, Yanai, Hideki, Masumoto, Akihide, Koretsune, Yukihiro, Kutsumi, Hiromu, Higashiyama, Masahiko, Murayama, Shigeo, Minegishi, Naoko, Suzuki, Kichiya, Tanno, Kozo, Shimizu, Atsushi, Yamaji, Taiki, Iwasaki, Motoki, Sawada, Norie, Uemura, Hirokazu, Tanaka, Keitaro, Naito, Mariko, Sasaki, Makoto, Wakai, Kenji, Tsugane, Shoichiro, Yamamoto, Masayuki, Yamamoto, Kazuhiko, Murakami, Yoshinori, Nakamura, Yusuke, Raychaudhuri, Soumya, Inazawa, Johji, Yamauchi, Toshimasa, Kadowaki, Takashi, Kubo, Michiaki, and Kamatani, Yoichiro

Published
2020
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31. ChaKi.NET liteの開発

Author

ITO, Kaoru and MORITA, Toshio

Subjects
コーパスツール, Universal Dependencies(UD), corpus tool, ChaKi.NET
Abstract

九州大学, 総和技研, Kyushu University, Sowa Research, 現代において，コーパスは言語研究に欠かせない資源となっている。言語学の分野では検索・閲覧・集計インターフェイスを備えたコーパスの利用が多いが，情報学等の分野で作成されたコーパスには必ずしもインターフェイスが提供されるわけではない。類型論研究での活用が期待されるUniversal Dependencies（UD）ツリーバンクもそのようなコーパスの1つである。そこで本研究では，既存の高機能コーパスツールであるChaKi.NETを情報抽出用に特化し，新規ユーザにも利用しやすい軽量版であるChaKi.NET liteを開発した。ChaKi.NETは高機能であるがゆえに利用者にとっての学習コストが高かったが，ChaKi.NET liteではUDに合わせたインターフェイスを提供し，アノテーション機能を省くことで目的の機能を利用しやすくした。本稿ではChaKi.NET lite開発の背景と機能について紹介する。, Corpora are indispensable resources for contemporary linguistic research. While corpora used for linguistics research usually have an interface, those developed for informatics research tend to lack one. Universal Dependencies (UD) Treebank, which has proved useful for linguistic typology studies, also lacks an interface. In this study, we developed a lightweight corpus tool named ChaKi.NET lite for new users, specialized from the existing sophisticated ChaKi.NET for information extraction. While one takes a long time to learn to use ChaKi.NET, ChaKi.NET lite reduces the required learning time by omitting the annotation function and providing an interface tailored to UD. This paper introduces the background of the development of ChaKi.NET lite and the new functions that this corpus tool provides., application/pdf

Published
2023

32. Association of Sickle Cell Trait With Chronic Kidney Disease and Albuminuria in African Americans

Author

Naik, Rakhi P, Derebail, Vimal K, Grams, Morgan E, Franceschini, Nora, Auer, Paul L, Peloso, Gina M, Young, Bessie A, Lettre, Guillaume, Peralta, Carmen A, Katz, Ronit, Hyacinth, Hyacinth I, Quarells, Rakale C, Grove, Megan L, Bick, Alexander G, Fontanillas, Pierre, Rich, Stephen S, Smith, Joshua D, Boerwinkle, Eric, Rosamond, Wayne D, Ito, Kaoru, Lanzkron, Sophie, Coresh, Josef, Correa, Adolfo, Sarto, Gloria E, Key, Nigel S, Jacobs, David R, Kathiresan, Sekar, Bibbins-Domingo, Kirsten, Kshirsagar, Abhijit V, Wilson, James G, and Reiner, Alexander P

Subjects
Epidemiology, Health Sciences, Cardiovascular, Aging, Clinical Research, Kidney Disease, Atherosclerosis, Rare Diseases, Renal and urogenital, Adult, Black or African American, Aged, Albuminuria, Cohort Studies, Female, Glomerular Filtration Rate, Humans, Male, Middle Aged, Prospective Studies, Renal Insufficiency, Chronic, Risk, Sickle Cell Trait, United States, Young Adult, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Abstract

ImportanceThe association between sickle cell trait (SCT) and chronic kidney disease (CKD) is uncertain.ObjectiveTo describe the relationship between SCT and CKD and albuminuria in self-identified African Americans.Design, setting, and participantsUsing 5 large, prospective, US population-based studies (the Atherosclerosis Risk in Communities Study [ARIC, 1987-2013; n = 3402], Jackson Heart Study [JHS, 2000-2012; n = 2105], Coronary Artery Risk Development in Young Adults [CARDIA, 1985-2006; n = 848], Multi-Ethnic Study of Atherosclerosis [MESA, 2000-2012; n = 1620], and Women's Health Initiative [WHI, 1993-2012; n = 8000]), we evaluated 15,975 self-identified African Americans (1248 participants with SCT [SCT carriers] and 14,727 participants without SCT [noncarriers]).Main outcomes and measuresPrimary outcomes were CKD (defined as an estimated glomerular filtration rate [eGFR] of 30 mg/g or albumin excretion rate >30 mg/24 hours), and decline in eGFR (defined as a decrease of >3 mL/min/1.73 m2 per year). Effect sizes were calculated separately for each cohort and were subsequently meta-analyzed using a random-effects model.ResultsA total of 2233 individuals (239 of 1247 SCT carriers [19.2%] vs 1994 of 14,722 noncarriers [13.5%]) had CKD, 1298 (140 of 675 SCT carriers [20.7%] vs 1158 of 8481 noncarriers [13.7%]) experienced incident CKD, 1719 (150 of 665 SCT carriers [22.6%] vs 1569 of 8249 noncarriers [19.0%]) experienced decline in eGFR, and 1322 (154 of 485 SCT carriers [31.8%] vs 1168 of 5947 noncarriers [19.6%]) had albuminuria during the study period. Individuals with SCT had an increased risk of CKD (odds ratio [OR], 1.57 [95% CI, 1.34-1.84]; absolute risk difference [ARD], 7.6% [95% CI, 4.7%-10.8%]), incident CKD (OR, 1.79 [95% CI, 1.45-2.20]; ARD, 8.5% [95% CI, 5.1%-12.3%]), and decline in eGFR (OR, 1.32 [95% CI, 1.07-1.61]; ARD, 6.1% [95% CI, 1.4%-13.0%]) compared with noncarriers. Sickle cell trait was also associated with albuminuria (OR, 1.86 [95% CI, 1.49-2.31]; ARD, 12.6% [95% CI, 7.7%-17.7%]).Conclusions and relevanceAmong African Americans in these cohorts, the presence of SCT was associated with an increased risk of CKD, decline in eGFR, and albuminuria, compared with noncarriers. These findings suggest that SCT may be associated with the higher risk of kidney disease in African Americans.

Published
2014

33. Increased Frequency of De Novo Copy Number Variants in Congenital Heart Disease by Integrative Analysis of Single Nucleotide Polymorphism Array and Exome Sequence Data

Author

Glessner, Joseph T, Bick, Alexander G, Ito, Kaoru, Homsy, Jason, Rodriguez-Murillo, Laura, Fromer, Menachem, Mazaika, Erica, Vardarajan, Badri, Italia, Michael, Leipzig, Jeremy, DePalma, Steven R, Golhar, Ryan, Sanders, Stephan J, Yamrom, Boris, Ronemus, Michael, Iossifov, Ivan, Willsey, A Jeremy, State, Matthew W, Kaltman, Jonathan R, White, Peter S, Shen, Yufeng, Warburton, Dorothy, Brueckner, Martina, Seidman, Christine, Goldmuntz, Elizabeth, Gelb, Bruce D, Lifton, Richard, Seidman, Jonathan, Hakonarson, Hakon, and Chung, Wendy K

Subjects
Human Genome, Pediatric, Congenital Structural Anomalies, Genetics, Cardiovascular, Heart Disease, Aetiology, 2.1 Biological and endogenous factors, Case-Control Studies, Cohort Studies, DNA Copy Number Variations, Exome, Gene Frequency, Gene Regulatory Networks, Heart Defects, Congenital, Humans, Molecular Sequence Data, Polymorphism, Single Nucleotide, DNA copy number variations, genomics, microarray analysis, polymorphism, single nucleotide, Cardiorespiratory Medicine and Haematology, Clinical Sciences, Cardiovascular System & Hematology
Abstract

RationaleCongenital heart disease (CHD) is among the most common birth defects. Most cases are of unknown pathogenesis.ObjectiveTo determine the contribution of de novo copy number variants (CNVs) in the pathogenesis of sporadic CHD.Methods and resultsWe studied 538 CHD trios using genome-wide dense single nucleotide polymorphism arrays and whole exome sequencing. Results were experimentally validated using digital droplet polymerase chain reaction. We compared validated CNVs in CHD cases with CNVs in 1301 healthy control trios. The 2 complementary high-resolution technologies identified 63 validated de novo CNVs in 51 CHD cases. A significant increase in CNV burden was observed when comparing CHD trios with healthy trios, using either single nucleotide polymorphism array (P=7×10(-5); odds ratio, 4.6) or whole exome sequencing data (P=6×10(-4); odds ratio, 3.5) and remained after removing 16% of de novo CNV loci previously reported as pathogenic (P=0.02; odds ratio, 2.7). We observed recurrent de novo CNVs on 15q11.2 encompassing CYFIP1, NIPA1, and NIPA2 and single de novo CNVs encompassing DUSP1, JUN, JUP, MED15, MED9, PTPRE SREBF1, TOP2A, and ZEB2, genes that interact with established CHD proteins NKX2-5 and GATA4. Integrating de novo variants in whole exome sequencing and CNV data suggests that ETS1 is the pathogenic gene altered by 11q24.2-q25 deletions in Jacobsen syndrome and that CTBP2 is the pathogenic gene in 10q subtelomeric deletions.ConclusionsWe demonstrate a significantly increased frequency of rare de novo CNVs in CHD patients compared with healthy controls and suggest several novel genetic loci for CHD.

Published
2014

34. 590. A New Thin-Film Transistor Image Sensor for Estimation of Bacterial Colony Species on Agar Plates

Author

Nakada, Mitsutaka, primary, Inagaki, Tsubasa, additional, Ariizumi, Reiichi, additional, Maeta, Shogo, additional, Ozaki, Hiroaki, additional, Fujisawa, Akihiko, additional, Tezen, Tomoya, additional, Tsunashima, Takanori, additional, Ito, Kaoru, additional, Abe, Daichi, additional, Yamaguchi, Kazunori, additional, Nakajima, Masakazu, additional, and Taketani, Makoto, additional

Published
2023
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35. 596. Image Sensor-based Real Time Monitoring of Bacterial Growth on Agar Plates

Author

Taketani, Makoto, primary, Inagaki, Tsubasa, additional, Nakada, Mitsutaka, additional, Ariizumi, Reiichi, additional, Nakajima, Masakazu, additional, Fujisawa, Akihiko, additional, Tezen, Tomoya, additional, Tsunashima, Takanori, additional, Ito, Kaoru, additional, Abe, Daichi, additional, Yamaguchi, Kazunori, additional, Ohnuma, Kenichiro, additional, Ishida, Nami, additional, Ebisawa, Kei Furui, additional, and Ohji, Goh, additional

Published
2023
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38. Epithelioid Angiomyolipoma with Tumor Thrombus into Inferior Vena Cava Presurgically Treated with Combination Therapy of Pembrolizumab and Axitinib: A Case Report

Author

Kawasoe, Chihiro, primary, Miyamoto, Yoshi, additional, Ito, Kaoru, additional, Murashima, Takaya, additional, Nagai, Takahiro, additional, Takamori, Hiroki, additional, Kiwaki, Takumi, additional, Kamimura, Toshio, additional, Mukai, Shoichiro, additional, and Kamoto, Toshiyuki, additional

Published
2023
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43. Population-specific reference panel improves imputation quality and enhances locus discovery and fine-mapping

Author

Terao, Chikashi, primary, Flanagan, Jack, additional, Tomizuka, Kohei, additional, Liu, Xiaoxi, additional, Ortega-Reyes, David, additional, Matoba, Nana, additional, Akiyama, Masato, additional, Ishigaki, Kazuyoshi, additional, Ashikawa, Kyota, additional, Takata, Sadaaki, additional, Aoi, Tomomi, additional, Momozawa, Yukihide, additional, Ito, Kaoru, additional, Murakami, Yoshinori, additional, Matsuda, Koichi, additional, Kamatami, Yoichiro, additional, Morris, Andrew, additional, and Horikoshi, Momoko, additional

Published
2023
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45. A Multi-Ancestry Polygenic Risk Score for Coronary Heart Disease Based on an Ancestrally Diverse Genome-Wide Association Study and Population-Specific Optimization

Author

Smith, Johanna L., primary, Tcheandjieu, Catherine, additional, Dikilitas, Ozan, additional, Iyer, Kruthika, additional, Miyazawa, Kazuo, additional, Hilliard, Austin, additional, Lynch, Julie, additional, Rotter, Jerome I., additional, Chen, Yii-Der Ida, additional, Sheu, Wayne Huey-Herng, additional, Chang, Kyong-Mi, additional, Kanoni, Stavroula, additional, Tsao, Philip, additional, Ito, Kaoru, additional, Kosel, Matthew, additional, Clarke, Shoa L., additional, Schaid, Daniel J., additional, Assimes, Themistocles L., additional, and Kullo, Iftikhar J., additional

Published
2023
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46. Use of the anterior prostatic urethral mucosa preservation technique during holmium laser enucleation of the prostate can reduce postoperative stress urinary incontinence.

Author

Fujisaki, Yukiya, Otsuka, Isamu, Kobayashi, Takahiko, Miyake, Nao, Ito, Kaoru, Terada, Naoki, Kamoto, Toshiyuki, and Iwamoto, Hideyasu

Subjects
URINARY stress incontinence, SURGICAL enucleation, HOLMIUM, ENUCLEATION of the eye, URINARY incontinence, BENIGN prostatic hyperplasia
Abstract

Introduction: Holmium laser enucleation of the prostate (HoLEP) is an effective and safe surgery for patients with benign prostatic hyperplasia. However, some patients exhibit postoperative urinary incontinence. Here, we compared surgical outcomes and incidence of stress urinary incontinence between HoLEP with and without anterior prostatic urethral mucosa preservation (APUMP). Methods: All patients in this study underwent HoLEP with APUMP technique (APUMP group) and without APUMP technique (no‐APUMP group). Enucleation weight, enucleation time, max flow rate increase at 3 months, and urinary incontinence rates immediately after catheter removal and at 1 month after surgery were compared between the groups. Results: In the APUMP (n = 340) and no‐APUMP (n = 75) groups, the median enucleation weights were 34.5 and 35.0 g, respectively (p =.982). The corresponding median enucleation times were 33.0 and 46.5 min (p <.01), and median max flow rate increases at 1 month were 10.5 and 9.9 mL/s (p =.89). The urinary incontinence rates immediately after catheter removal were 4.1% and 14.7% (p <.01), and were 3.8% and 12.0% (p <.01) at 1 month after surgery. Conclusion: HoLEP using the APUMP technique could be performed with a shorter operative time while maintaining efficacy. The incidence of postoperative urinary incontinence could be decreased by APUMP, indicating that such preservation facilitates the maintenance of urinary continence after surgery. [ABSTRACT FROM AUTHOR]

Published
2024
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47. Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants

Author

Aragam, Krishna G, Jiang, Tao, Goel, Anuj, Kanoni, Stavroula, Wolford, Brooke N, Atri, Deepak S, Weeks, Elle M, Wang, Minxian, Hindy, George, Zhou, Wei, Grace, Christopher, Roselli, Carolina, Marston, Nicholas A, Kamanu, Frederick K, Surakka, Ida, Venegas, Loreto Muñoz, Sherliker, Paul, Koyama, Satoshi, Ishigaki, Kazuyoshi, Åsvold, Bjørn O, Brown, Michael R, Brumpton, Ben, De Vries, Paul S, Giannakopoulou, Olga, Giardoglou, Panagiota, Gudbjartsson, Daniel F, Güldener, Ulrich, Haider, Syed M Ijlal, Helgadottir, Anna, Ibrahim, Maysson, Kastrati, Adnan, Kessler, Thorsten, Kyriakou, Theodosios, Konopka, Tomasz, Li, Ling, Ma, Lijiang, Meitinger, Thomas, Mucha, Sören, Munz, Matthias, Murgia, Federico, Nielsen, Jonas B, Nöthen, Markus M, Pang, Shichao, Reinberger, Tobias, Schnitzler, Gavin, Smedley, Damian, Thorleifsson, Gudmar, Von Scheidt, Moritz, Ulirsch, Jacob C, Danesh, John, Arnar, David O, Burtt, Noël P, Costanzo, Maria C, Flannick, Jason, Ito, Kaoru, Jang, Dong-Keun, Kamatani, Yoichiro, Khera, Amit V, Komuro, Issei, Kullo, Iftikhar J, Lotta, Luca A, Nelson, Christopher P, Roberts, Robert, Thorgeirsson, Gudmundur, Thorsteinsdottir, Unnur, Webb, Thomas R, Baras, Aris, Björkegren, Johan LM, Boerwinkle, Eric, Dedoussis, George, Holm, Hilma, Hveem, Kristian, Melander, Olle, Morrison, Alanna C, Orho-Melander, Marju, Rallidis, Loukianos S, Ruusalepp, Arno, Sabatine, Marc S, Stefansson, Kari, Zalloua, Pierre, Ellinor, Patrick T, Farrall, Martin, Ruff, Christian T, Finucane, Hilary K, Hopewell, Jemma C, Clarke, Robert, Gupta, Rajat M, Erdmann, Jeanette, Samani, Nilesh J, Schunkert, Heribert, Watkins, Hugh, Willer, Cristen J, Deloukas, Panos, Kathiresan, Sekar, Butterworth, Adam S, Aragam, Krishna G [0000-0003-3223-9131], Goel, Anuj [0000-0003-2307-4021], Kanoni, Stavroula [0000-0002-1691-9615], Wolford, Brooke N [0000-0003-3153-1552], Atri, Deepak S [0000-0001-8139-5419], Weeks, Elle M [0000-0002-4317-4444], Wang, Minxian [0000-0002-3753-508X], Zhou, Wei [0000-0001-7719-0859], Roselli, Carolina [0000-0001-5267-6756], Kamanu, Frederick K [0000-0001-7208-1047], Koyama, Satoshi [0000-0002-9286-0360], Ishigaki, Kazuyoshi [0000-0003-2881-0657], Åsvold, Bjørn O [0000-0003-3837-2101], Brumpton, Ben [0000-0002-3058-1059], Gudbjartsson, Daniel F [0000-0002-5222-9857], Güldener, Ulrich [0000-0001-5052-8610], Helgadottir, Anna [0000-0002-1806-2467], Kessler, Thorsten [0000-0003-3326-1621], Li, Ling [0000-0002-3280-9475], Mucha, Sören [0000-0002-1647-2526], Munz, Matthias [0000-0002-4728-3357], Murgia, Federico [0000-0002-3608-845X], Pang, Shichao [0000-0002-4111-2864], Smedley, Damian [0000-0002-5836-9850], Thorleifsson, Gudmar [0000-0003-4623-9087], von Scheidt, Moritz [0000-0001-7159-8271], Ulirsch, Jacob C [0000-0002-7947-0827], Costanzo, Maria C [0000-0001-9043-693X], Flannick, Jason [0000-0002-3618-795X], Ito, Kaoru [0000-0003-1843-773X], Khera, Amit V [0000-0001-6535-5839], Komuro, Issei [0000-0002-0714-7182], Kullo, Iftikhar J [0000-0002-6524-3471], Roberts, Robert [0000-0002-6792-4633], Webb, Thomas R [0000-0001-5998-8226], Baras, Aris [0000-0002-6830-3396], Björkegren, Johan LM [0000-0003-1945-7425], Holm, Hilma [0000-0002-9517-6636], Morrison, Alanna C [0000-0001-6381-4296], Orho-Melander, Marju [0000-0002-3578-2503], Stefansson, Kari [0000-0003-1676-864X], Farrall, Martin [0000-0003-4564-2165], Finucane, Hilary K [0000-0003-3864-9828], Clarke, Robert [0000-0002-9802-8241], Erdmann, Jeanette [0000-0002-4486-6231], Samani, Nilesh J [0000-0002-3286-8133], Schunkert, Heribert [0000-0001-6428-3001], Watkins, Hugh [0000-0002-5287-9016], Willer, Cristen J [0000-0001-5645-4966], Kathiresan, Sekar [0000-0002-3711-7101], Butterworth, Adam S [0000-0002-6915-9015], and Apollo - University of Cambridge Repository

Subjects
692/699/75/2, 631/208/205/2138, article, Humans, Coronary Artery Disease, Genome-Wide Association Study
Abstract

Funder: K.G.A. has received support from the American Heart Association Institute for Precision Cardiovascular Medicine (17IFUNP3384001), a KL2/Catalyst Medical Research Investigator Training (CMeRIT) award from the Harvard Catalyst (KL2 TR002542), and the NIH (1K08HL153937)., Funder: B.N.W is supported by the National Science Foundation Graduate Research Program (DGE 1256260)., Funder: I.S. is supported by a Precision Health Scholars Award from the University of Michigan Medical School., Funder: I.K., S.Ko., and K.It. are funded by the Japan Agency for Medical Research and Development, AMED, under Grant Numbers JP16ek0109070h0003, JP18kk0205008h0003, JP18kk0205001s0703, JP20km0405209, and JP20ek0109487. The BioBank Japan is supported by AMED under Grant Number JP20km0605001., Funder: J.L.M.B. acknowledges research support from NIH R01HL125863, American Heart Association (A14SFRN20840000), the Swedish Research Council (2018-02529) and Heart Lung Foundation (20170265) and the Foundation Leducq (PlaqueOmics: Novel Roles of Smooth Muscle and Other Matrix Producing Cells in Atherosclerotic Plaque Stability and Rupture, 18CVD02., Funder: P.S.dV was supported by American Heart Association grant number 18CDA34110116 and National Heart, Lung, and Blood Institute grant R01HL146860. The Atherosclerosis Risk in Communities study has been funded in whole or in part with Federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services (contract numbers HHSN268201700001I, HHSN268201700002I, HHSN268201700003I, HHSN268201700004I and HHSN268201700005I), R01HL087641, R01HL059367 and R01HL086694; National Human Genome Research Institute contract U01HG004402; and National Institutes of Health contract HHSN268200625226C. The authors thank the staff and participants of the ARIC study for their important contributions. Infrastructure was partly supported by Grant Number UL1RR025005, a component of the National Institutes of Health and NIH Roadmap for Medical Research., Funder: O.G. has received funding from the British Heart Foundation (BHF) (FS/14/66/3129)., Funder: T.K. is supported by the Corona-Foundation (Junior Research Group Translational Cardiovascular Genomics) and the German Research Foundation (DFG) as part of the Sonderforschungsbereich SFB 1123 (B02)., Funder: D.S.A. has received support from a training grant from the NIH (T32HL007604)., Funder: N.P.B., M.C.C., J.F., and D.-K.J. have been funded by the National Institute of Diabetes and Digestive and Kidney Diseases (2UM1DK105554)., Funder: A.V.K. has been funded by 1K08HG010155 from the National Human Genome Research Institute., Funder: C.P.N. and T.R.W received funding from the British Heart Foundation (SP/16/4/32697)., Funder: The Trøndelag Health Study (The HUNT Study) is a collaboration between HUNT Research Centre (Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology), Trøndelag County Council, Central Norway Regional Health Authority, and the Norwegian Institute of Public Health. The K.G. Jebsen Center for Genetic Epidemiology is financed by Stiftelsen Kristian Gerhard Jebsen; Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology; and Central Norway Regional Health Authority. Whole genome sequencing for the HUNT study was funded by HL109946., Funder: O.M. was funded by the Swedish Heart- and Lung Foundation, the Swedish Research Council, the European Research Council ERC-AdG-2019-885003 and Lund University Infrastructure grant ”Malmö population-based cohorts” (STYR 2019/2046)., Funder: This work was supported by the European Commission (HEALTH-F2–2013-601456) and the TriPartite Immunometabolism Consortium [TrIC]- NovoNordisk Foundation (NNF15CC0018486), VIAgenomics (SP/19/2/344612), the British Heart Foundation, a Wellcome Trust core award (M.F., H.W., 203141/Z/16/Z) and support from the NIHR Oxford Biomedical Research Centre. M.F. and H.W. are members of the Oxford BHF Centre of Research Excellence (RE/13/1/30181). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health., Funder: J.D. is a British Heart Foundation Professor, European Research Council Senior Investigator, and National Institute for Health Research (NIHR) Senior Investigator., Funder: J.C.H. acknowledges personal funding from the British Heart Foundation (FS/14/55/30806) and is a member of the Oxford BHF Centre of Research Excellence (RE/13/1/30181)., Funder: R.C. has received funding from the British Heart Foundation and British Heart Foundation Centre of Research Excellence., Funder: This research was supported by BHF (SP/13/2/30111) and conducted using the UK Biobank Resource (application number 9922)., Funder: The GerMIFs gratefully acknowledge the support of the Bavarian State Ministry of Health and Care, furthermore founded this work within its framework of DigiMed Bayern (grant No: DMB-1805-0001), the German Federal Ministry of Education and Research (BMBF) within the framework of ERA-NET on Cardiovascular Disease (Druggable-MI-genes: 01KL1802), within the scheme of target validation (BlockCAD: 16GW0198K), within the framework of the e:Med research and funding concept (AbCD-Net: 01ZX1706C), the British Heart Foundation (BHF)/German Centre of Cardiovascular Research (DZHK)-collaboration (VIAgenomics) and the German Research Foundation (DFG) as part of the Sonderforschungsbereich SFB 1123 (B02) and the Sonderforschungsbereich SFB TRR 267 (B05)., Funder: C.J.W. is funded by NIH grant R35-HL135824., Funder: This work was supported by the British Heart Foundation (BHF) grant RG/14/5/30893 (P.D.) and forms part of the research themes contributing to the translational research portfolios of the Barts Biomedical Research Centre funded by the UK National Institute for Health Research (NIHR)., The discovery of genetic loci associated with complex diseases has outpaced the elucidation of mechanisms of disease pathogenesis. Here we conducted a genome-wide association study (GWAS) for coronary artery disease (CAD) comprising 181,522 cases among 1,165,690 participants of predominantly European ancestry. We detected 241 associations, including 30 new loci. Cross-ancestry meta-analysis with a Japanese GWAS yielded 38 additional new loci. We prioritized likely causal variants using functionally informed fine-mapping, yielding 42 associations with less than five variants in the 95% credible set. Similarity-based clustering suggested roles for early developmental processes, cell cycle signaling and vascular cell migration and proliferation in the pathogenesis of CAD. We prioritized 220 candidate causal genes, combining eight complementary approaches, including 123 supported by three or more approaches. Using CRISPR–Cas9, we experimentally validated the effect of an enhancer in MYO9B, which appears to mediate CAD risk by regulating vascular cell motility. Our analysis identifies and systematically characterizes >250 risk loci for CAD to inform experimental interrogation of putative causal mechanisms for CAD.

Published
2022
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49. A genome-wide association analysis identifies NMNAT2 and HCP5 as susceptibility loci for Kawasaki disease

Author

Kim, Jae-Jung, Yun, Sin Weon, Yu, Jeong Jin, Yoon, Kyung Lim, Lee, Kyung-Yil, Kil, Hong-Ryang, Kim, Gi Beom, Han, Myung-Ki, Song, Min Seob, Lee, Hyoung Doo, Ha, Kee Soo, Sohn, Sejung, Johnson, Todd A, Takahashi, Atsushi, Kubo, Michiaki, Tsunoda, Tatsuhiko, Ito, Kaoru, Onouchi, Yoshihiro, Hong, Young Mi, Jang, Gi Young, and Lee, Jong-Keuk

Published
2017
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50. Cross-ancestry genome-wide analysis of atrial fibrillation unveils disease biology and enables cardioembolic risk prediction

Author

90452713, Miyazawa, Kazuo, Ito, Kaoru, Ito, Masamichi, Zou, Zhaonan, Kubota, Masayuki, Nomura, Seitaro, Matsunaga, Hiroshi, Koyama, Satoshi, Ieki, Hirotaka, Akiyama, Masato, Koike, Yoshinao, Kurosawa, Ryo, Yoshida, Hiroki, Ozaki, Kouichi, Onouchi, Yoshihiro, BioBank Japan Project, Takahashi, Atsushi, Matsuda, Koichi, Murakami, Yoshinori, Aburatani, Hiroyuki, Kubo, Michiaki, Momozawa, Yukihide, Terao, Chikashi, Oki, Shinya, Akazawa, Hiroshi, Kamatani, Yoichiro, Komuro, Issei, 90452713, Miyazawa, Kazuo, Ito, Kaoru, Ito, Masamichi, Zou, Zhaonan, Kubota, Masayuki, Nomura, Seitaro, Matsunaga, Hiroshi, Koyama, Satoshi, Ieki, Hirotaka, Akiyama, Masato, Koike, Yoshinao, Kurosawa, Ryo, Yoshida, Hiroki, Ozaki, Kouichi, Onouchi, Yoshihiro, BioBank Japan Project, Takahashi, Atsushi, Matsuda, Koichi, Murakami, Yoshinori, Aburatani, Hiroyuki, Kubo, Michiaki, Momozawa, Yukihide, Terao, Chikashi, Oki, Shinya, Akazawa, Hiroshi, Kamatani, Yoichiro, and Komuro, Issei

Abstract

Atrial fibrillation (AF) is a common cardiac arrhythmia resulting in increased risk of stroke. Despite highly heritable etiology, our understanding of the genetic architecture of AF remains incomplete. Here we performed a genome-wide association study in the Japanese population comprising 9, 826 cases among 150, 272 individuals and identified East Asian-specific rare variants associated with AF. A cross-ancestry meta-analysis of >1 million individuals, including 77, 690 cases, identified 35 new susceptibility loci. Transcriptome-wide association analysis identified IL6R as a putative causal gene, suggesting the involvement of immune responses. Integrative analysis with ChIP-seq data and functional assessment using human induced pluripotent stem cell-derived cardiomyocytes demonstrated ERRg as having a key role in the transcriptional regulation of AF-associated genes. A polygenic risk score derived from the cross-ancestry meta-analysis predicted increased risks of cardiovascular and stroke mortalities and segregated individuals with cardioembolic stroke in undiagnosed AF patients. Our results provide new biological and clinical insights into AF genetics and suggest their potential for clinical applications.

Published
2023

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