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9. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Author

Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A, Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M, Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E, Shen, Ciyue, Amin, Samirkumar B, Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A, Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P, Haradhvala, Nicholas J, Hong, Chen, Isaev, Keren, Johnson, Todd A, Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D, Saksena, Gordon, Schumacher, Steven E, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose MC, Umer, Husen M, Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E, Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S, von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J, Rubin, Mark A, Sander, Chris, Stein, Lincoln D, Stuart, Joshua M, Tsunoda, Tatsuhiko, Wheeler, David A, Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J, López-Bigas, Núria, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad, and PCAWG Consortium

Subjects
PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, PCAWG Consortium, Humans, Neoplasms, Gene Expression Regulation, Neoplastic, Mutation, Genome, Human, Databases, Genetic, DNA Breaks, INDEL Mutation, Genome-Wide Association Study, Gene Expression Regulation, Neoplastic, Genome, Human, Databases, Genetic, General Science & Technology
Abstract

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.

Published
2020

10. The early neutrophil-committed progenitors aberrantly differentiate into immunoregulatory monocytes during emergency myelopoiesis

Author

Ikeda, Naoki, Kubota, Hiroaki, Suzuki, Risa, Morita, Mitsuki, Yoshimura, Ayana, Osada, Yuya, Kishida, Keigo, Kitamura, Daiki, Iwata, Ayaka, Yotsumoto, Satoshi, Kurotaki, Daisuke, Nishimura, Koutarou, Nishiyama, Akira, Tamura, Tomohiko, Kamatani, Takashi, Tsunoda, Tatsuhiko, Murakawa, Miyako, Asahina, Yasuhiro, Hayashi, Yoshihiro, Harada, Hironori, Harada, Yuka, Yokota, Asumi, Hirai, Hideyo, Seki, Takao, Kuwahara, Makoto, Yamashita, Masakatsu, Shichino, Shigeyuki, Tanaka, Masato, and Asano, Kenichi

Published
2023
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20. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Author

Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, and Getz, Gad

Published
2023
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21. Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels

Author

Spracklen, Cassandra N, Chen, Peng, Kim, Young Jin, Wang, Xu, Cai, Hui, Li, Shengxu, Long, Jirong, Wu, Ying, Wang, Ya Xing, Takeuchi, Fumihiko, Wu, Jer-Yuarn, Jung, Keum-Ji, Hu, Cheng, Akiyama, Koichi, Zhang, Yonghong, Moon, Sanghoon, Johnson, Todd A, Li, Huaixing, Dorajoo, Rajkumar, He, Meian, Cannon, Maren E, Roman, Tamara S, Salfati, Elias, Lin, Keng-Hung, Guo, Xiuqing, Sheu, Wayne HH, Absher, Devin, Adair, Linda S, Assimes, Themistocles L, Aung, Tin, Cai, Qiuyin, Chang, Li-Ching, Chen, Chien-Hsiun, Chien, Li-Hsin, Chuang, Lee-Ming, Chuang, Shu-Chun, Du, Shufa, Fan, Qiao, Fann, Cathy SJ, Feranil, Alan B, Friedlander, Yechiel, Gordon-Larsen, Penny, Gu, Dongfeng, Gui, Lixuan, Guo, Zhirong, Heng, Chew-Kiat, Hixson, James, Hou, Xuhong, Hsiung, Chao Agnes, Hu, Yao, Hwang, Mi Yeong, Hwu, Chii-Min, Isono, Masato, Juang, Jyh-Ming Jimmy, Khor, Chiea-Chuen, Kim, Yun Kyoung, Koh, Woon-Puay, Kubo, Michiaki, Lee, I-Te, Lee, Sun-Ju, Lee, Wen-Jane, Liang, Kae-Woei, Lim, Blanche, Lim, Sing-Hui, Liu, Jianjun, Nabika, Toru, Pan, Wen-Harn, Peng, Hao, Quertermous, Thomas, Sabanayagam, Charumathi, Sandow, Kevin, Shi, Jinxiu, Sun, Liang, Tan, Pok Chien, Tan, Shu-Pei, Taylor, Kent D, Teo, Yik-Ying, Toh, Sue-Anne, Tsunoda, Tatsuhiko, van Dam, Rob M, Wang, Aili, Wang, Feijie, Wang, Jie, Bin Wei, Wen, Xiang, Yong-Bing, Yao, Jie, Yuan, Jian-Min, Zhang, Rong, Zhao, Wanting, Chen, Yii-Der Ida, Rich, Stephen S, Rotter, Jerome I, Wang, Tzung-Dau, Wu, Tangchun, Lin, Xu, Han, Bok-Ghee, Tanaka, Toshihiro, Cho, Yoon Shin, Katsuya, Tomohiro, and Jia, Weiping

Subjects
Genetics, Human Genome, Atherosclerosis, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Adult, Alleles, Asian People, Cholesterol, Ethnicity, Female, Gene Frequency, Genetic Association Studies, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Lipids, Lipoproteins, HDL, Lipoproteins, LDL, Male, Middle Aged, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Triglycerides, White People, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P

Published
2017

23. Clinical usefulness of multigene screening with phenotype-driven bioinformatics analysis for the diagnosis of patients with monogenic diabetes or severe insulin resistance

Author

Hosoe, Jun, Miya, Fuyuki, Kadowaki, Hiroko, Fujiwara, Toyofumi, Suzuki, Ken, Kato, Takashi, Waki, Hironori, Sasako, Takayoshi, Aizu, Katsuya, Yamamura, Natsumi, Sasaki, Fusako, Kurano, Makoto, Hara, Kazuo, Tanaka, Masaki, Ishiura, Hiroyuki, Tsuji, Shoji, Honda, Kenjiro, Yoshimura, Jun, Morishita, Shinichi, Matsuzawa, Fumiko, Aikawa, Sei-Ichi, Boroevich, Keith A., Nangaku, Masaomi, Okada, Yukinori, Tsunoda, Tatsuhiko, Shojima, Nobuhiro, Yamauchi, Toshimasa, and Kadowaki, Takashi

Published
2020
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25. Subject-Specific-Frequency-Band for Motor Imagery EEG Signal Recognition Based on Common Spatial Spectral Pattern

Author

Kumar, Shiu, Sharma, Alok, Tsunoda, Tatsuhiko, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Nayak, Abhaya C., editor, and Sharma, Alok, editor

Published
2019
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26. Computational Prediction of Lysine Pupylation Sites in Prokaryotic Proteins Using Position Specific Scoring Matrix into Bigram for Feature Extraction

Author

Singh, Vineet, Sharma, Alok, Chandra, Abel, Dehzangi, Abdollah, Shigemizu, Daichi, Tsunoda, Tatsuhiko, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Nayak, Abhaya C., editor, and Sharma, Alok, editor

Published
2019
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27. Clustering of Small-Sample Single-Cell RNA-Seq Data via Feature Clustering and Selection

Author

Vans, Edwin, Sharma, Alok, Patil, Ashwini, Shigemizu, Daichi, Tsunoda, Tatsuhiko, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Nayak, Abhaya C., editor, and Sharma, Alok, editor

Published
2019
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29. A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa

Author

Nishiguchi, Koji M., Miya, Fuyuki, Mori, Yuka, Fujita, Kosuke, Akiyama, Masato, Kamatani, Takashi, Koyanagi, Yoshito, Sato, Kota, Takigawa, Toru, Ueno, Shinji, Tsugita, Misato, Kunikata, Hiroshi, Cisarova, Katarina, Nishino, Jo, Murakami, Akira, Abe, Toshiaki, Momozawa, Yukihide, Terasaki, Hiroko, Wada, Yuko, Sonoda, Koh-Hei, Rivolta, Carlo, Tsunoda, Tatsuhiko, Tsujikawa, Motokazu, Ikeda, Yasuhiro, and Nakazawa, Toru

Published
2021
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30. Profiling the inhibitory receptors LAG-3, TIM-3, and TIGIT in renal cell carcinoma reveals malignancy

Author

Takamatsu, Kimiharu, Tanaka, Nobuyuki, Hakozaki, Kyohei, Takahashi, Ryohei, Teranishi, Yu, Murakami, Tetsushi, Kufukihara, Ryohei, Niwa, Naoya, Mikami, Shuji, Shinojima, Toshiaki, Sasaki, Takashi, Sato, Yusuke, Kume, Haruki, Ogawa, Seishi, Kakimi, Kazuhiro, Kamatani, Takashi, Miya, Fuyuki, Tsunoda, Tatsuhiko, Aimono, Eriko, Nishihara, Hiroshi, Sawada, Kazuaki, Imamura, Takeshi, Mizuno, Ryuichi, and Oya, Mototsugu

Published
2021
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31. Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci

Author

He, Meian, Xu, Min, Zhang, Ben, Liang, Jun, Chen, Peng, Lee, Jong-Young, Johnson, Todd A, Li, Huaixing, Yang, Xiaobo, Dai, Juncheng, Liang, Liming, Gui, Lixuan, Qi, Qibin, Huang, Jinyan, Li, Yanping, Adair, Linda S, Aung, Tin, Cai, Qiuyin, Cheng, Ching-Yu, Cho, Myeong-Chan, Cho, Yoon Shin, Chu, Minjie, Cui, Bin, Gao, Yu-Tang, Go, Min Jin, Gu, Dongfeng, Gu, Weiqiong, Guo, Huan, Hao, Yongchen, Hong, Jie, Hu, Zhibin, Hu, Yanling, Huang, Jianfeng, Hwang, Joo-Yeon, Ikram, Mohammad Kamran, Jin, Guangfu, Kang, Dae-Hee, Khor, Chiea Chuen, Kim, Bong-Jo, Kim, Hung Tae, Kubo, Michiaki, Lee, Jeannette, Lee, Juyoung, Lee, Nanette R, Li, Ruoying, Li, Jun, Liu, JianJun, Longe, Jirong, Lu, Wei, Lu, Xiangfeng, Miao, Xiaoping, Okada, Yukinori, Ong, Rick Twee-Hee, Qiu, Gaokun, Seielstad, Mark, Sim, Xueling, Song, Huaidong, Takeuchi, Fumihiko, Tanaka, Toshihiro, Taylor, Phil R, Wang, Laiyuan, Wang, Weiqing, Wang, Yiqin, Wu, Chen, Wu, Ying, Xiang, Yong-Bing, Yamamoto, Ken, Yang, Handong, Liao, Ming, Yokota, Mitsuhiro, Young, Terri, Zhang, Xiaomin, Kato, Norihiro, Wang, Qing K, Zheng, Wei, Hu, Frank B, Lin, Dongxin, Shen, Hongbing, Teo, Yik Ying, Mo, Zengnan, Wong, Tien Yin, Lin, Xu, Mohlke, Karen L, Ning, Guang, Tsunoda, Tatsuhiko, Han, Bok-Ghee, Shu, Xiao-Ou, Tai, E Shyong, Wu, Tangchun, and Qi, Lu

Subjects
Prevention, Genetics, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Aged, Aged, 80 and over, Asian People, Body Height, Asia, Eastern, Female, Gene Frequency, Genetic Loci, Genome-Wide Association Study, Humans, Male, Metabolic Networks and Pathways, Middle Aged, Polymorphism, Single Nucleotide, Protein Tyrosine Phosphatases, White People, Young Adult, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Human height is associated with risk of multiple diseases and is profoundly determined by an individual's genetic makeup and shows a high degree of ethnic heterogeneity. Large-scale genome-wide association (GWA) analyses of adult height in Europeans have identified nearly 180 genetic loci. A recent study showed high replicability of results from Europeans-based GWA studies in Asians; however, population-specific loci may exist due to distinct linkage disequilibrium patterns. We carried out a GWA meta-analysis in 93 926 individuals from East Asia. We identified 98 loci, including 17 novel and 81 previously reported loci, associated with height at P < 5 × 10(-8), together explaining 8.89% of phenotypic variance. Among the newly identified variants, 10 are commonly distributed (minor allele frequency, MAF > 5%) in Europeans, with comparable frequencies with in Asians, and 7 single-nucleotide polymorphisms are with low frequency (MAF < 5%) in Europeans. In addition, our data suggest that novel biological pathway such as the protein tyrosine phosphatase family is involved in regulation of height. The findings from this study considerably expand our knowledge of the genetic architecture of human height in Asians.

Published
2015

34. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index

Author

Wen, Wanqing, Zheng, Wei, Okada, Yukinori, Takeuchi, Fumihiko, Tabara, Yasuharu, Hwang, Joo-Yeon, Dorajoo, Rajkumar, Li, Huaixing, Tsai, Fuu-Jen, Yang, Xiaobo, He, Jiang, Wu, Ying, He, Meian, Zhang, Yi, Liang, Jun, Guo, Xiuqing, Sheu, Wayne Huey-Herng, Delahanty, Ryan, Guo, Xingyi, Kubo, Michiaki, Yamamoto, Ken, Ohkubo, Takayoshi, Go, Min Jin, Liu, Jian Jun, Gan, Wei, Chen, Ching-Chu, Gao, Yong, Li, Shengxu, Lee, Nanette R, Wu, Chen, Zhou, Xueya, Song, Huaidong, Yao, Jie, Lee, I-Te, Long, Jirong, Tsunoda, Tatsuhiko, Akiyama, Koichi, Takashima, Naoyuki, Cho, Yoon Shin, Ong, Rick TH, Lu, Ling, Chen, Chien-Hsiun, Tan, Aihua, Rice, Treva K, Adair, Linda S, Gui, Lixuan, Allison, Matthew, Lee, Wen-Jane, Cai, Qiuyin, Isomura, Minoru, Umemura, Satoshi, Kim, Young Jin, Seielstad, Mark, Hixson, James, Xiang, Yong-Bing, Isono, Masato, Kim, Bong-Jo, Sim, Xueling, Lu, Wei, Nabika, Toru, Lee, Juyoung, Lim, Wei-Yen, Gao, Yu-Tang, Takayanagi, Ryoichi, Kang, Dae-Hee, Wong, Tien Yin, Hsiung, Chao Agnes, Wu, I-Chien, Juang, Jyh-Ming Jimmy, Shi, Jiajun, Choi, Bo Youl, Aung, Tin, Hu, Frank, Kim, Mi Kyung, Lim, Wei Yen, Wang, Tzung-Dao, Shin, Min-Ho, Lee, Jeannette, Ji, Bu-Tian, Lee, Young-Hoon, Young, Terri L, Shin, Dong Hoon, Chun, Byung-Yeol, Cho, Myeong-Chan, Han, Bok-Ghee, Hwu, Chii-Min, Assimes, Themistocles L, Absher, Devin, Yan, Xiaofei, Kim, Eric, Kuo, Jane Z, Kwon, Soonil, Taylor, Kent D, Chen, Yii-Der I, Rotter, Jerome I, Qi, Lu, Zhu, Dingliang, Wu, Tangchun, Mohlke, Karen L, and Gu, Dongfeng

Subjects
Biological Sciences, Genetics, Obesity, Nutrition, Human Genome, Women's Health, 5'-Nucleotidase, Aldehyde Dehydrogenase, Aldehyde Dehydrogenase, Mitochondrial, Asian People, Blood Proteins, Body Mass Index, Cardiac Myosins, Asia, Eastern, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Glycoproteins, Humans, KCNQ1 Potassium Channel, Male, Myosin Light Chains, Polymorphism, Single Nucleotide, Proteinase Inhibitory Proteins, Secretory, Medical and Health Sciences, Genetics & Heredity
Abstract

Recent genetic association studies have identified 55 genetic loci associated with obesity or body mass index (BMI). The vast majority, 51 loci, however, were identified in European-ancestry populations. We conducted a meta-analysis of associations between BMI and ∼2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 individuals of Asian ancestry, followed by in silico and de novo replication among 7488-47 352 additional Asian-ancestry individuals. We identified four novel BMI-associated loci near the KCNQ1 (rs2237892, P = 9.29 × 10(-13)), ALDH2/MYL2 (rs671, P = 3.40 × 10(-11); rs12229654, P = 4.56 × 10(-9)), ITIH4 (rs2535633, P = 1.77 × 10(-10)) and NT5C2 (rs11191580, P = 3.83 × 10(-8)) genes. The association of BMI with rs2237892, rs671 and rs12229654 was significantly stronger among men than among women. Of the 51 BMI-associated loci initially identified in European-ancestry populations, we confirmed eight loci at the genome-wide significance level (P < 5.0 × 10(-8)) and an additional 14 at P < 1.0 × 10(-3) with the same direction of effect as reported previously. Findings from this analysis expand our knowledge of the genetic basis of obesity.

Published
2014

35. Novel Genetic Markers Associate With Atrial Fibrillation Risk in Europeans and Japanese

Author

Lubitz, Steven A, Lunetta, Kathryn L, Lin, Honghuang, Arking, Dan E, Trompet, Stella, Li, Guo, Krijthe, Bouwe P, Chasman, Daniel I, Barnard, John, Kleber, Marcus E, Dörr, Marcus, Ozaki, Kouichi, Smith, Albert V, Müller-Nurasyid, Martina, Walter, Stefan, Agarwal, Sunil K, Bis, Joshua C, Brody, Jennifer A, Chen, Lin Y, Everett, Brendan M, Ford, Ian, Franco, Oscar H, Harris, Tamara B, Hofman, Albert, Kääb, Stefan, Mahida, Saagar, Kathiresan, Sekar, Kubo, Michiaki, Launer, Lenore J, Macfarlane, Peter W, Magnani, Jared W, McKnight, Barbara, McManus, David D, Peters, Annette, Psaty, Bruce M, Rose, Lynda M, Rotter, Jerome I, Silbernagel, Guenther, Smith, Jonathan D, Sotoodehnia, Nona, Stott, David J, Taylor, Kent D, Tomaschitz, Andreas, Tsunoda, Tatsuhiko, Uitterlinden, Andre G, Van Wagoner, David R, Völker, Uwe, Völzke, Henry, Murabito, Joanne M, Sinner, Moritz F, Gudnason, Vilmundur, Felix, Stephan B, März, Winfried, Chung, Mina, Albert, Christine M, Stricker, Bruno H, Tanaka, Toshihiro, Heckbert, Susan R, Jukema, J Wouter, Alonso, Alvaro, Benjamin, Emelia J, and Ellinor, Patrick T

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Genetics, Heart Disease, Cardiovascular, Clinical Research, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Adult, Aged, Aged, 80 and over, Asian People, Atrial Fibrillation, Chromosome Mapping, Chromosomes, Human, Pair 4, Europe, Female, Genetic Markers, Genetic Predisposition to Disease, Homeodomain Proteins, Humans, Japan, Male, Middle Aged, Polymorphism, Single Nucleotide, Transcription Factors, White People, atrial fibrillation, atrial flutter, genetic, prognosis, risk, Cardiorespiratory Medicine and Haematology, Public Health and Health Services, Cardiovascular System & Hematology, Cardiovascular medicine and haematology
Abstract

ObjectivesThis study sought to identify nonredundant atrial fibrillation (AF) genetic susceptibility signals and examine their cumulative relations with AF risk.BackgroundAF-associated loci span broad genomic regions that may contain multiple susceptibility signals. Whether multiple signals exist at AF loci has not been systematically explored.MethodsWe performed association testing conditioned on the most significant, independently associated genetic markers at 9 established AF loci using 2 complementary techniques in 64,683 individuals of European ancestry (3,869 incident and 3,302 prevalent AF cases). Genetic risk scores were created and tested for association with AF in Europeans and an independent sample of 11,309 individuals of Japanese ancestry (7,916 prevalent AF cases).ResultsWe observed at least 4 distinct AF susceptibility signals on chromosome 4q25 upstream of PITX2, but not at the remaining 8 AF loci. A multilocus score comprised 12 genetic markers demonstrated an estimated 5-fold gradient in AF risk. We observed a similar spectrum of risk associated with these markers in Japanese. Regions containing AF signals on chromosome 4q25 displayed a greater degree of evolutionary conservation than the remainder of the locus, suggesting that they may tag regulatory elements.ConclusionsThe chromosome 4q25 AF locus is architecturally complex and harbors at least 4 AF susceptibility signals in individuals of European ancestry. Similar polygenic AF susceptibility exists between Europeans and Japanese. Future work is necessary to identify causal variants, determine mechanisms by which associated loci predispose to AF, and explore whether AF susceptibility signals classify individuals at risk for AF and related morbidity.

Published
2014

39. Meta-analysis identifies multiple loci associated with kidney function–related traits in east Asian populations

Author

Okada, Yukinori, Sim, Xueling, Go, Min Jin, Wu, Jer-Yuarn, Gu, Dongfeng, Takeuchi, Fumihiko, Takahashi, Atsushi, Maeda, Shiro, Tsunoda, Tatsuhiko, Chen, Peng, Lim, Su-Chi, Wong, Tien-Yin, Liu, Jianjun, Young, Terri L, Aung, Tin, Seielstad, Mark, Teo, Yik-Ying, Kim, Young Jin, Lee, Jong-Young, Han, Bok-Ghee, Kang, Daehee, Chen, Chien-Hsiun, Tsai, Fuu-Jen, Chang, Li-Ching, Fann, S-J Cathy, Mei, Hao, Rao, Dabeeru C, Hixson, James E, Chen, Shufeng, Katsuya, Tomohiro, Isono, Masato, Ogihara, Toshio, Chambers, John C, Zhang, Weihua, Kooner, Jaspal S, Albrecht, Eva, Yamamoto, Kazuhiko, Kubo, Michiaki, Nakamura, Yusuke, Kamatani, Naoyuki, Kato, Norihiro, He, Jiang, Chen, Yuan-Tsong, Cho, Yoon Shin, Tai, E-Shyong, and Tanaka, Toshihiro

Subjects
Biological Sciences, Genetics, Kidney Disease, Human Genome, Renal and urogenital, Asian People, Blood Urea Nitrogen, Cohort Studies, Creatinine, Genetic Predisposition to Disease, Genome-Wide Association Study, Glomerular Filtration Rate, Humans, Kidney, Polymorphism, Single Nucleotide, Renal Insufficiency, Chronic, Uric Acid, KidneyGen Consortium, CKDGen Consortium, GUGC consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genome-wide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 × 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of ∼110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.

Published
2012

42. Unveiling synapse pathology in spinal bulbar muscular atrophy by genome-wide transcriptome analysis of purified motor neurons derived from disease specific iPSCs

Author

Onodera, Kazunari, Shimojo, Daisuke, Ishihara, Yasuharu, Yano, Masato, Miya, Fuyuki, Banno, Haruhiko, Kuzumaki, Naoko, Ito, Takuji, Okada, Rina, de Araújo Herculano, Bruno, Ohyama, Manabu, Yoshida, Mari, Tsunoda, Tatsuhiko, Katsuno, Masahisa, Doyu, Manabu, Sobue, Gen, Okano, Hideyuki, and Okada, Yohei

Published
2020
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48. Genome-wide association study suggests four variants influencing outcomes with ranibizumab therapy in exudative age-related macular degeneration

Author

Akiyama, Masato, Takahashi, Atsushi, Momozawa, Yukihide, Arakawa, Satoshi, Miya, Fuyuki, Tsunoda, Tatsuhiko, Ashikawa, Kyota, Oshima, Yuji, Yasuda, Miho, Yoshida, Shigeo, Enaida, Hiroshi, Tan, Xue, Yanagi, Yasuo, Yasukawa, Tsutomu, Ogura, Yuichiro, Nagai, Yoshimi, Takahashi, Kanji, Fujisawa, Kimihiko, Inoue, Maiko, Arakawa, Akira, Tanaka, Koji, Yuzawa, Mitsuko, Kadonosono, Kazuaki, Sonoda, Koh-Hei, Ishibashi, Tatsuro, and Kubo, Michiaki

Published
2018
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50. Integrated analysis of human genetic association study and mouse transcriptome suggests LBH and SHF genes as novel susceptible genes for amyloid-β accumulation in Alzheimer’s disease

Author

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

Published
2018
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