Search

Your search keyword '"Nakagawa, Hidewaki"' showing total 792 results
Start Over Author "Nakagawa, Hidewaki"
792 results on '"Nakagawa, Hidewaki"'

1. Deep whole-genome analysis of 494 hepatocellular carcinomas

Author

Chen, Lei, Zhang, Chong, Xue, Ruidong, Liu, Mo, Bai, Jian, Bao, Jinxia, Wang, Yin, Jiang, Nanhai, Li, Zhixuan, Wang, Wenwen, Wang, Ruiru, Zheng, Bo, Yang, Airong, Hu, Ji, Liu, Ke, Shen, Siyun, Zhang, Yangqianwen, Bai, Mixue, Wang, Yan, Zhu, Yanjing, Yang, Shuai, Gao, Qiang, Gu, Jin, Gao, Dong, Wang, Xin Wei, Nakagawa, Hidewaki, Zhang, Ning, Wu, Lin, Rozen, Steven G., Bai, Fan, and Wang, Hongyang

Published
2024
Full Text
View/download PDF

2. Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants

Author

Wang, Anqi, Shen, Jiayi, Rodriguez, Alex A., Saunders, Edward J., Chen, Fei, Janivara, Rohini, Darst, Burcu F., Sheng, Xin, Xu, Yili, Chou, Alisha J., Benlloch, Sara, Dadaev, Tokhir, Brook, Mark N., Plym, Anna, Sahimi, Ali, Hoffman, Thomas J., Takahashi, Atushi, Matsuda, Koichi, Momozawa, Yukihide, Fujita, Masashi, Laisk, Triin, Figuerêdo, Jéssica, Muir, Kenneth, Ito, Shuji, Liu, Xiaoxi, Uchio, Yuji, Kubo, Michiaki, Kamatani, Yoichiro, Lophatananon, Artitaya, Wan, Peggy, Andrews, Caroline, Lori, Adriana, Choudhury, Parichoy P., Schleutker, Johanna, Tammela, Teuvo L. J., Sipeky, Csilla, Auvinen, Anssi, Giles, Graham G., Southey, Melissa C., MacInnis, Robert J., Cybulski, Cezary, Wokolorczyk, Dominika, Lubinski, Jan, Rentsch, Christopher T., Cho, Kelly, Mcmahon, Benjamin H., Neal, David E., Donovan, Jenny L., Hamdy, Freddie C., Martin, Richard M., Nordestgaard, Borge G., Nielsen, Sune F., Weischer, Maren, Bojesen, Stig E., Røder, Andreas, Stroomberg, Hein V., Batra, Jyotsna, Chambers, Suzanne, Horvath, Lisa, Clements, Judith A., Tilly, Wayne, Risbridger, Gail P., Gronberg, Henrik, Aly, Markus, Szulkin, Robert, Eklund, Martin, Nordstrom, Tobias, Pashayan, Nora, Dunning, Alison M., Ghoussaini, Maya, Travis, Ruth C., Key, Tim J., Riboli, Elio, Park, Jong Y., Sellers, Thomas A., Lin, Hui-Yi, Albanes, Demetrius, Weinstein, Stephanie, Cook, Michael B., Mucci, Lorelei A., Giovannucci, Edward, Lindstrom, Sara, Kraft, Peter, Hunter, David J., Penney, Kathryn L., Turman, Constance, Tangen, Catherine M., Goodman, Phyllis J., Thompson, Jr., Ian M., Hamilton, Robert J., Fleshner, Neil E., Finelli, Antonio, Parent, Marie-Élise, Stanford, Janet L., Ostrander, Elaine A., Koutros, Stella, Beane Freeman, Laura E., Stampfer, Meir, Wolk, Alicja, Håkansson, Niclas, Andriole, Gerald L., Hoover, Robert N., Machiela, Mitchell J., Sørensen, Karina Dalsgaard, Borre, Michael, Blot, William J., Zheng, Wei, Yeboah, Edward D., Mensah, James E., Lu, Yong-Jie, Zhang, Hong-Wei, Feng, Ninghan, Mao, Xueying, Wu, Yudong, Zhao, Shan-Chao, Sun, Zan, Thibodeau, Stephen N., McDonnell, Shannon K., Schaid, Daniel J., West, Catharine M. L., Barnett, Gill, Maier, Christiane, Schnoeller, Thomas, Luedeke, Manuel, Kibel, Adam S., Drake, Bettina F., Cussenot, Olivier, Cancel-Tassin, Geraldine, Menegaux, Florence, Truong, Thérèse, Koudou, Yves Akoli, John, Esther M., Grindedal, Eli Marie, Maehle, Lovise, Khaw, Kay-Tee, Ingles, Sue A., Stern, Mariana C., Vega, Ana, Gómez-Caamaño, Antonio, Fachal, Laura, Rosenstein, Barry S., Kerns, Sarah L., Ostrer, Harry, Teixeira, Manuel R., Paulo, Paula, Brandão, Andreia, Watya, Stephen, Lubwama, Alexander, Bensen, Jeannette T., Butler, Ebonee N., Mohler, James L., Taylor, Jack A., Kogevinas, Manolis, Dierssen-Sotos, Trinidad, Castaño-Vinyals, Gemma, Cannon-Albright, Lisa, Teerlink, Craig C., Huff, Chad D., Pilie, Patrick, Yu, Yao, Bohlender, Ryan J., Gu, Jian, Strom, Sara S., Multigner, Luc, Blanchet, Pascal, Brureau, Laurent, Kaneva, Radka, Slavov, Chavdar, Mitev, Vanio, Leach, Robin J., Brenner, Hermann, Chen, Xuechen, Holleczek, Bernd, Schöttker, Ben, Klein, Eric A., Hsing, Ann W., Kittles, Rick A., Murphy, Adam B., Logothetis, Christopher J., Kim, Jeri, Neuhausen, Susan L., Steele, Linda, Ding, Yuan Chun, Isaacs, William B., Nemesure, Barbara, Hennis, Anselm J. M., Carpten, John, Pandha, Hardev, Michael, Agnieszka, De Ruyck, Kim, De Meerleer, Gert, Ost, Piet, Xu, Jianfeng, Razack, Azad, Lim, Jasmine, Teo, Soo-Hwang, Newcomb, Lisa F., Lin, Daniel W., Fowke, Jay H., Neslund-Dudas, Christine M., Rybicki, Benjamin A., Gamulin, Marija, Lessel, Davor, Kulis, Tomislav, Usmani, Nawaid, Abraham, Aswin, Singhal, Sandeep, Parliament, Matthew, Claessens, Frank, Joniau, Steven, Van den Broeck, Thomas, Gago-Dominguez, Manuela, Castelao, Jose Esteban, Martinez, Maria Elena, Larkin, Samantha, Townsend, Paul A., Aukim-Hastie, Claire, Bush, William S., Aldrich, Melinda C., Crawford, Dana C., Srivastava, Shiv, Cullen, Jennifer, Petrovics, Gyorgy, Casey, Graham, Wang, Ying, Tettey, Yao, Lachance, Joseph, Tang, Wei, Biritwum, Richard B., Adjei, Andrew A., Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Yamoah, Kosj, Govindasami, Koveela, Chokkalingam, Anand P., Keaton, Jacob M., Hellwege, Jacklyn N., Clark, Peter E., Jalloh, Mohamed, Gueye, Serigne M., Niang, Lamine, Ogunbiyi, Olufemi, Shittu, Olayiwola, Amodu, Olukemi, Adebiyi, Akindele O., Aisuodionoe-Shadrach, Oseremen I., Ajibola, Hafees O., Jamda, Mustapha A., Oluwole, Olabode P., Nwegbu, Maxwell, Adusei, Ben, Mante, Sunny, Darkwa-Abrahams, Afua, Diop, Halimatou, Gundell, Susan M., Roobol, Monique J., Jenster, Guido, van Schaik, Ron H. N., Hu, Jennifer J., Sanderson, Maureen, Kachuri, Linda, Varma, Rohit, McKean-Cowdin, Roberta, Torres, Mina, Preuss, Michael H., Loos, Ruth J. F., Zawistowski, Matthew, Zöllner, Sebastian, Lu, Zeyun, Van Den Eeden, Stephen K., Easton, Douglas F., Ambs, Stefan, Edwards, Todd L., Mägi, Reedik, Rebbeck, Timothy R., Fritsche, Lars, Chanock, Stephen J., Berndt, Sonja I., Wiklund, Fredrik, Nakagawa, Hidewaki, Witte, John S., Gaziano, J. Michael, Justice, Amy C., Mancuso, Nick, Terao, Chikashi, Eeles, Rosalind A., Kote-Jarai, Zsofia, Madduri, Ravi K., Conti, David V., and Haiman, Christopher A.

Published
2023
Full Text
View/download PDF

3. 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
Full Text
View/download PDF

4. Immuno-genomic analysis reveals eosinophilic feature and favorable prognosis of female non-smoking esophageal squamous cell carcinomas

Author

Okawa, Yuki, Sasagawa, Shota, Kato, Hiroaki, Johnson, Todd A., Nagaoka, Koji, Kobayashi, Yukari, Hayashi, Akimasa, Shibayama, Takahiro, Maejima, Kazuhiro, Tanaka, Hiroko, Miyano, Satoru, Shibahara, Junji, Nishizuka, Satoshi, Hirano, Satoshi, Seto, Yasuyuki, Iwaya, Takeshi, Kakimi, Kazuhiro, Yasuda, Takushi, and Nakagawa, Hidewaki

Published
2024
Full Text
View/download PDF

5. Prognostic significance of pathogenic variants in BRCA1, BRCA2, ATM and PALB2 genes in men undergoing hormonal therapy for advanced prostate cancer

Author

Kimura, Hiroko, Mizuno, Kei, Shiota, Masaki, Narita, Shintaro, Terada, Naoki, Fujimoto, Naohiro, Ogura, Keiji, Hatano, Shotaro, Iwasaki, Yusuke, Hakozaki, Nozomi, Ishitoya, Satoshi, Sumiyoshi, Takayuki, Goto, Takayuki, Kobayashi, Takashi, Nakagawa, Hidewaki, Kamoto, Toshiyuki, Eto, Masatoshi, Habuchi, Tomonori, Ogawa, Osamu, Momozawa, Yukihide, and Akamatsu, Shusuke

Published
2022
Full Text
View/download PDF

6. Pan-cancer analysis of whole genomes

Author

Campbell, Peter J, Getz, Gad, Korbel, Jan O, Stuart, Joshua M, Jennings, Jennifer L, Stein, Lincoln D, Perry, Marc D, Nahal-Bose, Hardeep K, Ouellette, BF Francis, Li, Constance H, Rheinbay, Esther, Nielsen, G Petur, Sgroi, Dennis C, Wu, Chin-Lee, Faquin, William C, Deshpande, Vikram, Boutros, Paul C, Lazar, Alexander J, Hoadley, Katherine A, Louis, David N, Dursi, L Jonathan, Yung, Christina K, Bailey, Matthew H, Saksena, Gordon, Raine, Keiran M, Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun, Wang, Wenyi, Wheeler, David A, Ding, Li, Simpson, Jared T, O'Connor, Brian D, Yakneen, Sergei, Ellrott, Kyle, Miyoshi, Naoki, Butler, Adam P, Royo, Romina, Shorser, Solomon I, Vazquez, Miguel, Rausch, Tobias, Tiao, Grace, Waszak, Sebastian M, Rodriguez-Martin, Bernardo, Shringarpure, Suyash, Wu, Dai-Ying, Demidov, German M, Delaneau, Olivier, Hayashi, Shuto, Imoto, Seiya, Habermann, Nina, Segre, Ayellet V, Garrison, Erik, Cafferkey, Andy, Alvarez, Eva G, Maria Heredia-Genestar, Jose, Muyas, Francesc, Drechsel, Oliver, Bruzos, Alicia L, Temes, Javier, Zamora, Jorge, Baez-Ortega, Adrian, Kim, Hyung-Lae, Mashl, R Jay, Ye, Kai, DiBiase, Anthony, Huang, Kuan-lin, Letunic, Ivica, McLellan, Michael D, Newhouse, Steven J, Shmaya, Tal, Kumar, Sushant, Wedge, David C, Wright, Mark H, Yellapantula, Venkata D, Gerstein, Mark, Khurana, Ekta, Marques-Bonet, Tomas, Navarro, Arcadi, Bustamante, Carlos D, Siebert, Reiner, Nakagawa, Hidewaki, Easton, Douglas F, Ossowski, Stephan, Tubio, Jose MC, De La Vega, Francisco M, Estivill, Xavier, Yuen, Denis, Mihaiescu, George L, Omberg, Larsson, Ferretti, Vincent, Sabarinathan, Radhakrishnan, Pich, Oriol, Gonzalez-Perez, Abel, Weiner, Amaro Taylor, Fittall, Matthew W, Demeulemeester, Jonas, Tarabichi, Maxime, and Roberts, Nicola D

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Cancer Genomics, Human Genome, Cancer, Biotechnology, Prevention, 2.1 Biological and endogenous factors, Cell Proliferation, Cellular Senescence, Chromothripsis, Cloud Computing, DNA Mutational Analysis, Evolution, Molecular, Female, Genome, Human, Genomics, Germ-Line Mutation, High-Throughput Nucleotide Sequencing, Humans, Information Dissemination, Male, Mutagenesis, Mutation, Neoplasms, Oncogenes, Promoter Regions, Genetic, RNA Splicing, Reproducibility of Results, Telomerase, Telomere, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, General Science & Technology
Abstract

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Published
2020

7. 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

8. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.

Author

Zhang, Yiqun, Chen, Fengju, Fonseca, Nuno A, He, Yao, Fujita, Masashi, Nakagawa, Hidewaki, Zhang, Zemin, Brazma, Alvis, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton, Chad J, and PCAWG Consortium

Subjects
PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, PCAWG Consortium, Humans, Neoplasms, DNA Methylation, Gene Expression Regulation, Neoplastic, Regulatory Sequences, Nucleic Acid, Genes, Tumor Suppressor, Oncogenes, Databases, Genetic, Enhancer Elements, Genetic, Genomic Structural Variation, Whole Genome Sequencing, Gene Expression Regulation, Neoplastic, Regulatory Sequences, Nucleic Acid, Genes, Tumor Suppressor, Databases, Genetic, Enhancer Elements
Abstract

The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. TERT-associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non-amplified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.

Published
2020

9. Genotype-phenotype mapping of a patient-derived lung cancer organoid biobank identifies NKX2-1-defined Wnt dependency in lung adenocarcinoma

Author

Ebisudani, Toshiki, Hamamoto, Junko, Togasaki, Kazuhiro, Mitsuishi, Akifumi, Sugihara, Kai, Shinozaki, Taro, Fukushima, Takahiro, Kawasaki, Kenta, Seino, Takashi, Oda, Mayumi, Hanyu, Hikaru, Toshimitsu, Kohta, Emoto, Katsura, Hayashi, Yuichiro, Asakura, Keisuke, Johnson, Todd A., Terai, Hideki, Ikemura, Shinnosuke, Kawada, Ichiro, Ishii, Makoto, Hishida, Tomoyuki, Asamura, Hisao, Soejima, Kenzo, Nakagawa, Hidewaki, Fujii, Masayuki, Fukunaga, Koichi, Yasuda, Hiroyuki, and Sato, Toshiro

Published
2023
Full Text
View/download PDF

14. Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers

Author

Jikuya, Ryosuke, Murakami, Koichi, Nishiyama, Akira, Kato, Ikuma, Furuya, Mitsuko, Nakabayashi, Jun, Ramilowski, Jordan A., Hamanoue, Haruka, Maejima, Kazuhiro, Fujita, Masashi, Mitome, Taku, Ohtake, Shinji, Noguchi, Go, Kawaura, Sachi, Odaka, Hisakazu, Kawahara, Takashi, Komeya, Mitsuru, Shinoki, Risa, Ueno, Daiki, Ito, Hiroki, Ito, Yusuke, Muraoka, Kentaro, Hayashi, Narihiko, Kondo, Keiichi, Nakaigawa, Noboru, Hatano, Koji, Baba, Masaya, Suda, Toshio, Kodama, Tatsuhiko, Fujii, Satoshi, Makiyama, Kazuhide, Yao, Masahiro, Shuch, Brian M., Schmidt, Laura S., Linehan, W. Marston, Nakagawa, Hidewaki, Tamura, Tomohiko, and Hasumi, Hisashi

Published
2022
Full Text
View/download PDF

15. Proteo-genomic characterization of virus-associated liver cancers reveals potential subtypes and therapeutic targets

Author

Fujita, Masashi, Chen, Mei-Ju May, Siwak, Doris Rieko, Sasagawa, Shota, Oosawa-Tatsuguchi, Ayako, Arihiro, Koji, Ono, Atsushi, Miura, Ryoichi, Maejima, Kazuhiro, Aikata, Hiroshi, Ueno, Masaki, Hayami, Shinya, Yamaue, Hiroki, Chayama, Kazuaki, Lee, Ju-Seog, Lu, Yiling, Mills, Gordon B., Liang, Han, Nishizuka, Satoshi S., and Nakagawa, Hidewaki

Published
2022
Full Text
View/download PDF

20. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, Heidi L., Page, Angela J.H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J.S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., Brudno, Michael, Brush, Matthew H., Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, L. Jonathan, Dyke, Stephanie O.M., Eddy, James A., Eilbeck, Karen, Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M., Ho, Calvin W.L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jené, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J.M., Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M., Kekesi-Lafrance, Kristina, Kelleher, Jerome, Kerry, Giselle, Khor, Seik-Soon, Knoppers, Bartha M., Konopko, Melissa A., Kosaki, Kenjiro, Kuba, Martin, Lawson, Jonathan, Leinonen, Rasko, Li, Stephanie, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Liyanage, Isuru Udara, Lopez, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Metke-Jimenez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Munoz-Torres, Monica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura A.D., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Rodriguez, Laura Lyman, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos, Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Guimera, Roman Valls, Vamathevan, Jessica, Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, North, Kathryn, and Birney, Ewan

Published
2021
Full Text
View/download PDF

22. 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
Full Text
View/download PDF

24. Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction

Author

Conti, David V., Darst, Burcu F., Moss, Lilit C., Saunders, Edward J., Sheng, Xin, Chou, Alisha, Schumacher, Fredrick R., Olama, Ali Amin Al, Benlloch, Sara, Dadaev, Tokhir, Brook, Mark N., Sahimi, Ali, Hoffmann, Thomas J., Takahashi, Atushi, Matsuda, Koichi, Momozawa, Yukihide, Fujita, Masashi, Muir, Kenneth, Lophatananon, Artitaya, Wan, Peggy, Le Marchand, Loic, Wilkens, Lynne R., Stevens, Victoria L., Gapstur, Susan M., Carter, Brian D., Schleutker, Johanna, Tammela, Teuvo L. J., Sipeky, Csilla, Auvinen, Anssi, Giles, Graham G., Southey, Melissa C., MacInnis, Robert J., Cybulski, Cezary, Wokołorczyk, Dominika, Lubiński, Jan, Neal, David E., Donovan, Jenny L., Hamdy, Freddie C., Martin, Richard M., Nordestgaard, Børge G., Nielsen, Sune F., Weischer, Maren, Bojesen, Stig E., Røder, Martin Andreas, Iversen, Peter, Batra, Jyotsna, Chambers, Suzanne, Moya, Leire, Horvath, Lisa, Clements, Judith A., Tilley, Wayne, Risbridger, Gail P., Gronberg, Henrik, Aly, Markus, Szulkin, Robert, Eklund, Martin, Nordström, Tobias, Pashayan, Nora, Dunning, Alison M., Ghoussaini, Maya, Travis, Ruth C., Key, Tim J., Riboli, Elio, Park, Jong Y., Sellers, Thomas A., Lin, Hui-Yi, Albanes, Demetrius, Weinstein, Stephanie J., Mucci, Lorelei A., Giovannucci, Edward, Lindstrom, Sara, Kraft, Peter, Hunter, David J., Penney, Kathryn L., Turman, Constance, Tangen, Catherine M., Goodman, Phyllis J., Thompson, Jr., Ian M., Hamilton, Robert J., Fleshner, Neil E., Finelli, Antonio, Parent, Marie-Élise, Stanford, Janet L., Ostrander, Elaine A., Geybels, Milan S., Koutros, Stella, Freeman, Laura E. Beane, Stampfer, Meir, Wolk, Alicja, Håkansson, Niclas, Andriole, Gerald L., Hoover, Robert N., Machiela, Mitchell J., Sørensen, Karina Dalsgaard, Borre, Michael, Blot, William J., Zheng, Wei, Yeboah, Edward D., Mensah, James E., Lu, Yong-Jie, Zhang, Hong-Wei, Feng, Ninghan, Mao, Xueying, Wu, Yudong, Zhao, Shan-Chao, Sun, Zan, Thibodeau, Stephen N., McDonnell, Shannon K., Schaid, Daniel J., West, Catharine M. L., Burnet, Neil, Barnett, Gill, Maier, Christiane, Schnoeller, Thomas, Luedeke, Manuel, Kibel, Adam S., Drake, Bettina F., Cussenot, Olivier, Cancel-Tassin, Géraldine, Menegaux, Florence, Truong, Thérèse, Koudou, Yves Akoli, John, Esther M., Grindedal, Eli Marie, Maehle, Lovise, Khaw, Kay-Tee, Ingles, Sue A., Stern, Mariana C., Vega, Ana, Gómez-Caamaño, Antonio, Fachal, Laura, Rosenstein, Barry S., Kerns, Sarah L., Ostrer, Harry, Teixeira, Manuel R., Paulo, Paula, Brandão, Andreia, Watya, Stephen, Lubwama, Alexander, Bensen, Jeannette T., Fontham, Elizabeth T. H., Mohler, James, Taylor, Jack A., Kogevinas, Manolis, Llorca, Javier, Castaño-Vinyals, Gemma, Cannon-Albright, Lisa, Teerlink, Craig C., Huff, Chad D., Strom, Sara S., Multigner, Luc, Blanchet, Pascal, Brureau, Laurent, Kaneva, Radka, Slavov, Chavdar, Mitev, Vanio, Leach, Robin J., Weaver, Brandi, Brenner, Hermann, Cuk, Katarina, Holleczek, Bernd, Saum, Kai-Uwe, Klein, Eric A., Hsing, Ann W., Kittles, Rick A., Murphy, Adam B., Logothetis, Christopher J., Kim, Jeri, Neuhausen, Susan L., Steele, Linda, Ding, Yuan Chun, Isaacs, William B., Nemesure, Barbara, Hennis, Anselm J. M., Carpten, John, Pandha, Hardev, Michael, Agnieszka, De Ruyck, Kim, De Meerleer, Gert, Ost, Piet, Xu, Jianfeng, Razack, Azad, Lim, Jasmine, Teo, Soo-Hwang, Newcomb, Lisa F., Lin, Daniel W., Fowke, Jay H., Neslund-Dudas, Christine, Rybicki, Benjamin A., Gamulin, Marija, Lessel, Davor, Kulis, Tomislav, Usmani, Nawaid, Singhal, Sandeep, Parliament, Matthew, Claessens, Frank, Joniau, Steven, Van den Broeck, Thomas, Gago-Dominguez, Manuela, Castelao, Jose Esteban, Martinez, Maria Elena, Larkin, Samantha, Townsend, Paul A., Aukim-Hastie, Claire, Bush, William S., Aldrich, Melinda C., Crawford, Dana C., Srivastava, Shiv, Cullen, Jennifer C., Petrovics, Gyorgy, Casey, Graham, Roobol, Monique J., Jenster, Guido, van Schaik, Ron H. N., Hu, Jennifer J., Sanderson, Maureen, Varma, Rohit, McKean-Cowdin, Roberta, Torres, Mina, Mancuso, Nicholas, Berndt, Sonja I., Van Den Eeden, Stephen K., Easton, Douglas F., Chanock, Stephen J., Cook, Michael B., Wiklund, Fredrik, Nakagawa, Hidewaki, Witte, John S., Eeles, Rosalind A., Kote-Jarai, Zsofia, and Haiman, Christopher A.

Published
2021
Full Text
View/download PDF

26. Postoperative recurrence detection using individualized circulating tumor DNA in upper tract urothelial carcinoma

Author

Tamura, Daichi, primary, Abe, Masakazu, additional, Hiraki, Hayato, additional, Sasaki, Noriyuki, additional, Yashima‐Abo, Akiko, additional, Ikarashi, Daiki, additional, Kato, Renpei, additional, Kato, Yoichiro, additional, Maekawa, Shigekatsu, additional, Kanehira, Mitsugu, additional, Takata, Ryo, additional, Maejima, Kazuhiro, additional, Sasagawa, Shota, additional, Fujita, Masashi, additional, Suzuki, Yutaka, additional, Nakagawa, Hidewaki, additional, Iwaya, Takeshi, additional, Nishizuka, Satoshi S., additional, and Obara, Wataru, additional

Published
2023
Full Text
View/download PDF

28. Regulation of the innate immune response and gut microbiome by p53

Author

Khor, Amy Hui Ping, primary, Koguchi, Tomoyuki, additional, Liu, Hao, additional, Kakuta, Masanori, additional, Matsubara, Daisuke, additional, Wen, Ruimeng, additional, Sagiya, Yoji, additional, Imoto, Seiya, additional, Nakagawa, Hidewaki, additional, Matsuda, Koichi, additional, and Tanikawa, Chizu, additional

Published
2023
Full Text
View/download PDF

29. Immuno-genomic analysis reveals eosinophilic feature and favorable prognosis of female non-smoking esophageal squamous cell carcinomas

Author

Okawa, Yuki, primary, Sasagawa, Shota, additional, Kato, Hiroaki, additional, Johnson, Todd A., additional, Nagaoka, Koji, additional, Kobayashi, Yukari, additional, Hayashi, Akimasa, additional, Shibayama, Takahiro, additional, Maejima, Kazuhiro, additional, Tanaka, Hiroko, additional, Miyano, Satoru, additional, Shibahara, Junji, additional, Nishizuka, Satoshi, additional, Hirano, Satoshi, additional, Seto, Yasuyuki, additional, Iwaya, Takeshi, additional, Kakimi, Kazuhiro, additional, Yasuda, Takushi, additional, and Nakagawa, Hidewaki, additional

Published
2023
Full Text
View/download PDF

30. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Author

Alioto, Tyler S, Buchhalter, Ivo, Derdak, Sophia, Hutter, Barbara, Eldridge, Matthew D, Hovig, Eivind, Heisler, Lawrence E, Beck, Timothy A, Simpson, Jared T, Tonon, Laurie, Sertier, Anne-Sophie, Patch, Ann-Marie, Jäger, Natalie, Ginsbach, Philip, Drews, Ruben, Paramasivam, Nagarajan, Kabbe, Rolf, Chotewutmontri, Sasithorn, Diessl, Nicolle, Previti, Christopher, Schmidt, Sabine, Brors, Benedikt, Feuerbach, Lars, Heinold, Michael, Gröbner, Susanne, Korshunov, Andrey, Tarpey, Patrick S, Butler, Adam P, Hinton, Jonathan, Jones, David, Menzies, Andrew, Raine, Keiran, Shepherd, Rebecca, Stebbings, Lucy, Teague, Jon W, Ribeca, Paolo, Giner, Francesc Castro, Beltran, Sergi, Raineri, Emanuele, Dabad, Marc, Heath, Simon C, Gut, Marta, Denroche, Robert E, Harding, Nicholas J, Yamaguchi, Takafumi N, Fujimoto, Akihiro, Nakagawa, Hidewaki, Quesada, Víctor, Valdés-Mas, Rafael, Nakken, Sigve, Vodák, Daniel, Bower, Lawrence, Lynch, Andrew G, Anderson, Charlotte L, Waddell, Nicola, Pearson, John V, Grimmond, Sean M, Peto, Myron, Spellman, Paul, He, Minghui, Kandoth, Cyriac, Lee, Semin, Zhang, John, Létourneau, Louis, Ma, Singer, Seth, Sahil, Torrents, David, Xi, Liu, Wheeler, David A, López-Otín, Carlos, Campo, Elías, Campbell, Peter J, Boutros, Paul C, Puente, Xose S, Gerhard, Daniela S, Pfister, Stefan M, McPherson, John D, Hudson, Thomas J, Schlesner, Matthias, Lichter, Peter, Eils, Roland, Jones, David TW, and Gut, Ivo G

Subjects
Humans, Medulloblastoma, Mutation, Genome, Human, Leukemia, Lymphoid, High-Throughput Nucleotide Sequencing, Genome, Human, Leukemia, Lymphoid
Abstract

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.

Published
2015

31. Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions

Author

Han, Ying, Hazelett, Dennis J, Wiklund, Fredrik, Schumacher, Fredrick R, Stram, Daniel O, Berndt, Sonja I, Wang, Zhaoming, Rand, Kristin A, Hoover, Robert N, Machiela, Mitchell J, Yeager, Merideth, Burdette, Laurie, Chung, Charles C, Hutchinson, Amy, Yu, Kai, Xu, Jianfeng, Travis, Ruth C, Key, Timothy J, Siddiq, Afshan, Canzian, Federico, Takahashi, Atsushi, Kubo, Michiaki, Stanford, Janet L, Kolb, Suzanne, Gapstur, Susan M, Diver, W Ryan, Stevens, Victoria L, Strom, Sara S, Pettaway, Curtis A, Olama, Ali Amin Al, Kote-Jarai, Zsofia, Eeles, Rosalind A, Yeboah, Edward D, Tettey, Yao, Biritwum, Richard B, Adjei, Andrew A, Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P, Isaacs, William B, Chen, Constance, Lindstrom, Sara, Le Marchand, Loic, Giovannucci, Edward L, Pomerantz, Mark, Long, Henry, Li, Fugen, Ma, Jing, Stampfer, Meir, John, Esther M, Ingles, Sue A, Kittles, Rick A, Murphy, Adam B, Blot, William J, Signorello, Lisa B, Zheng, Wei, Albanes, Demetrius, Virtamo, Jarmo, Weinstein, Stephanie, Nemesure, Barbara, Carpten, John, Leske, M Cristina, Wu, Suh-Yuh, Hennis, Anselm JM, Rybicki, Benjamin A, Neslund-Dudas, Christine, Hsing, Ann W, Chu, Lisa, Goodman, Phyllis J, Klein, Eric A, Zheng, S Lilly, Witte, John S, Casey, Graham, Riboli, Elio, Li, Qiyuan, Freedman, Matthew L, Hunter, David J, Gronberg, Henrik, Cook, Michael B, Nakagawa, Hidewaki, Kraft, Peter, Chanock, Stephen J, Easton, Douglas F, Henderson, Brian E, Coetzee, Gerhard A, Conti, David V, and Haiman, Christopher A

Subjects
Cancer, Human Genome, Biotechnology, Genetics, Urologic Diseases, Prostate Cancer, 2.1 Biological and endogenous factors, Aetiology, Asian People, Black People, Chromosome Mapping, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Hispanic or Latino, Humans, Linkage Disequilibrium, Male, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Prostatic Neoplasms, Quantitative Trait Loci, White People, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.

Published
2015

34. Genetic and epigenetic basis of hepatoblastoma diversity

Author

Nagae, Genta, Yamamoto, Shogo, Fujita, Masashi, Fujita, Takanori, Nonaka, Aya, Umeda, Takayoshi, Fukuda, Shiro, Tatsuno, Kenji, Maejima, Kazuhiro, Hayashi, Akimasa, Kurihara, Sho, Kojima, Masato, Hishiki, Tomoro, Watanabe, Kenichiro, Ida, Kohmei, Yano, Michihiro, Hiyama, Yoko, Tanaka, Yukichi, Inoue, Takeshi, Ueda, Hiroki, Nakagawa, Hidewaki, Aburatani, Hiroyuki, and Hiyama, Eiso

Published
2021
Full Text
View/download PDF

35. Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

Author

Álvarez, Eva G., Demeulemeester, Jonas, Otero, Paula, Jolly, Clemency, García-Souto, Daniel, Pequeño-Valtierra, Ana, Zamora, Jorge, Tojo, Marta, Temes, Javier, Baez-Ortega, Adrian, Rodriguez-Martin, Bernardo, Oitaben, Ana, Bruzos, Alicia L., Martínez-Fernández, Mónica, Haase, Kerstin, Zumalave, Sonia, Abal, Rosanna, Rodríguez-Castro, Jorge, Rodriguez-Casanova, Aitor, Diaz-Lagares, Angel, Li, Yilong, Raine, Keiran M., Butler, Adam P., Otero, Iago, Ono, Atsushi, Aikata, Hiroshi, Chayama, Kazuaki, Ueno, Masaki, Hayami, Shinya, Yamaue, Hiroki, Maejima, Kazuhiro, Blanco, Miguel G., Forns, Xavier, Rivas, Carmen, Ruiz-Bañobre, Juan, Pérez-del-Pulgar, Sofía, Torres-Ruiz, Raúl, Rodriguez-Perales, Sandra, Garaigorta, Urtzi, Campbell, Peter J., Nakagawa, Hidewaki, Van Loo, Peter, and Tubio, Jose M. C.

Published
2021
Full Text
View/download PDF

36. 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
Full Text
View/download PDF

38. Genomic Heterogeneity Within Individual Prostate Cancer Foci Impacts Predictive Biomarkers of Targeted Therapy

Author

VanderWeele, David J., Finney, Richard, Katayama, Kotoe, Gillard, Marc, Paner, Gladell, Imoto, Seiya, Yamaguchi, Rui, Wheeler, David, Lack, Justin, Cam, Maggie, Pontier, Andrea, Nguyen, Yen Thi Minh, Maejima, Kazuhiro, Sasaki-Oku, Aya, Nakano, Kaoru, Tanaka, Hiroko, Vander Griend, Donald, Kubo, Michiaki, Ratain, Mark J., Miyano, Satoru, and Nakagawa, Hidewaki

Published
2019
Full Text
View/download PDF

39. Postoperative recurrence detection using individualized circulating tumor DNA in upper tract urothelial carcinoma.

Author

Tamura, Daichi, Abe, Masakazu, Hiraki, Hayato, Sasaki, Noriyuki, Yashima‐Abo, Akiko, Ikarashi, Daiki, Kato, Renpei, Kato, Yoichiro, Maekawa, Shigekatsu, Kanehira, Mitsugu, Takata, Ryo, Maejima, Kazuhiro, Sasagawa, Shota, Fujita, Masashi, Suzuki, Yutaka, Nakagawa, Hidewaki, Iwaya, Takeshi, Nishizuka, Satoshi S., and Obara, Wataru

Abstract

Biomarkers that could detect the postoperative recurrence of upper tract urothelial carcinoma (UTUC) have not been established. In this prospective study, we aim to evaluate the utility of individualized circulating tumor DNA (ctDNA) monitoring using digital PCR (dPCR) as a tumor recurrence biomarker for UTUC in the perioperative period. Twenty‐three patients who underwent radical nephroureterectomy (RNU) were included. In each patient, whole exome sequencing by next‐generation sequencing and TERT promoter sequencing of tumor DNA were carried out. Case‐specific gene mutations were selected from sequencing analysis to examine ctDNA by dPCR analysis. We also prospectively collected plasma and urine ctDNA from each patient. The longitudinal variant allele frequencies of ctDNA during the perioperative period were plotted. Case‐specific gene mutations were detected in 22 cases (96%) from ctDNA in the preoperative samples. Frequently detected genes were TERT (39%), FGFR3 (26%), TP53 (22%), and HRAS (13%). In all cases, we obtained plasma and urine samples for 241 time points and undertook individualized ctDNA monitoring for 2 years after RNU. Ten patients with intravesical recurrence had case‐specific ctDNA detected in urine at the time of recurrence. The mean lead time of urinary ctDNA in intravesical recurrence was 60 days (range, 0–202 days). Two patients with distal metastasis had case‐specific ctDNA in plasma at the time of metastasis. In UTUC, tumor‐specific gene mutations can be monitored postoperatively as ctDNA in plasma and urine. Individualized ctDNA might be a minimally invasive biomarker for the early detection of postoperative recurrence. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

40. Regulation of the innate immune response and gut microbiome by p53.

Author

Khor, Amy Hui Ping, Koguchi, Tomoyuki, Liu, Hao, Kakuta, Masanori, Matsubara, Daisuke, Wen, Ruimeng, Sagiya, Yoji, Imoto, Seiya, Nakagawa, Hidewaki, Matsuda, Koichi, and Tanikawa, Chizu

Abstract

p53 is a key tumor suppressor mutated in half of human cancers. In recent years, p53 was shown to regulate a wide variety of functions. From the transcriptome analysis of 24 tissues of irradiated mice, we identified 553 genes markedly induced by p53. Gene Ontology (GO) enrichment analysis found that the most associated biological process was innate immunity. 16S rRNA‐seq analysis revealed that Akkermansia, which has anti‐inflammatory properties and is involved in the regulation of intestinal barrier integrity, was decreased in p53‐knockout (p53−/−) mice after radiation. p53−/− mice were susceptible to radiation‐induced GI toxicity and had a significantly shorter survival time than p53‐wild‐type (p53+/+) mice following radiation. However, administration of antibiotics resulted in a significant improvement in survival and protection against GI toxicity. Mbl2 and Lcn2, which have antimicrobial activity, were identified to be directly transactivated by p53 and secreted by liver into the circulatory system. We also found the expression of MBL2 and LCN2 was decreased in liver cancer tissues with p53 mutations compared with those without p53 mutations. These results indicate that p53 is involved in shaping the gut microbiome through its downstream targets related to the innate immune system, thus protecting the intestinal barrier. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

41. Association of Hepatobiliary Phase of Gadoxetic-Acid-Enhanced MRI Imaging with Immune Microenvironment and Response to Atezolizumab Plus Bevacizumab Treatment

Author

Tamura, Yosuke, primary, Ono, Atsushi, additional, Nakahara, Hikaru, additional, Hayes, Clair Nelson, additional, Fujii, Yasutoshi, additional, Zhang, Peiyi, additional, Yamauchi, Masami, additional, Uchikawa, Shinsuke, additional, Teraoka, Yuji, additional, Uchida, Takuro, additional, Fujino, Hatsue, additional, Nakahara, Takashi, additional, Murakami, Eisuke, additional, Tsuge, Masataka, additional, Serikawa, Masahiro, additional, Miki, Daiki, additional, Kawaoka, Tomokazu, additional, Okamoto, Wataru, additional, Imamura, Michio, additional, Nakamura, Yuko, additional, Awai, Kazuo, additional, Kobayashi, Tsuyoshi, additional, Ohdan, Hideki, additional, Fujita, Masashi, additional, Nakagawa, Hidewaki, additional, Chayama, Kazuaki, additional, Aikata, Hiroshi, additional, and Oka, Shiro, additional

Published
2023
Full Text
View/download PDF

42. International network of cancer genome projects

Author

Hudson (Chairperson), Thomas J, Anderson, Warwick, Aretz, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusuda, Jun, Lane, David P, Laplace, Frank, Lu, Youyong, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers (Leader), Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter (Leader), Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Hudson, Thomas J, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal (Leader), P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Bowtell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman (Leader), Paul T, Bader, Gary D, Boutros, Paul C, and Flicek, Paul

Subjects
Cancer, Genetics, Human Genome, DNA Methylation, DNA Mutational Analysis, Databases, Genetic, Genes, Neoplasm, Genetics, Medical, Genome, Human, Genomics, Humans, Intellectual Property, International Cooperation, Mutation, Neoplasms, International Cancer Genome Consortium, General Science & Technology
Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

43. International network of cancer genome projects.

Author

International Cancer Genome Consortium, Hudson, Thomas J, Anderson, Warwick, Artez, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusada, Jun, Lane, David P, Laplace, Frank, Youyong, Lu, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers, Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Botwell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman, Paul T, Bader, Gary D, and Boutros, Paul C

Subjects
International Cancer Genome Consortium, Humans, Neoplasms, DNA Mutational Analysis, Genetics, Medical, Genomics, DNA Methylation, Mutation, Genome, Human, International Cooperation, Intellectual Property, Databases, Genetic, Genes, Neoplasm, Genetics, Medical, Genome, Human, Databases, Genetic, Genes, Neoplasm, General Science & Technology
Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

44. Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma

Author

Jikuya, Ryosuke, primary, Johnson, Todd A., additional, Maejima, Kazuhiro, additional, An, Jisong, additional, Ju, Young-Seok, additional, Lee, Hwajin, additional, Ha, Kyungsik, additional, Song, WooJeung, additional, Kim, Youngwook, additional, Okawa, Yuki, additional, Sasagawa, Shota, additional, Kanazashi, Yuki, additional, Fujita, Masashi, additional, Imoto, Seiya, additional, Mitome, Taku, additional, Ohtake, Shinji, additional, Noguchi, Go, additional, Kawaura, Sachi, additional, Iribe, Yasuhiro, additional, Aomori, Kota, additional, Tatenuma, Tomoyuki, additional, Komeya, Mitsuru, additional, Ito, Hiroki, additional, Ito, Yusuke, additional, Muraoka, Kentaro, additional, Furuya, Mitsuko, additional, Kato, Ikuma, additional, Fujii, Satoshi, additional, Hamanoue, Haruka, additional, Tamura, Tomohiko, additional, Baba, Masaya, additional, Suda, Toshio, additional, Kodama, Tatsuhiko, additional, Makiyama, Kazuhide, additional, Yao, Masahiro, additional, Shuch, Brian M., additional, Ricketts, Christopher J., additional, Schmidt, Laura S., additional, Linehan, W. Marston, additional, Nakagawa, Hidewaki, additional, and Hasumi, Hisashi, additional

Published
2023
Full Text
View/download PDF

45. Abstract 1416: Genomic features of renal cell carcinoma developed during end-stage renal disease and dialysis

Author

Maekawa, Shigekatsu, primary, Fujita, Masahi, additional, Takata, Ryo, additional, Ikarashi, Daiki, additional, Matsuura, Tomohiko, additional, Kato, Renpei, additional, Kato, Yoichiro, additional, Kanehira, Mitsugu, additional, Sugimura, Jun, additional, Abe, Takaya, additional, Nakagawa, Hidewaki, additional, and Obara, Wataru, additional

Published
2023
Full Text
View/download PDF

46. PD46-01 DETECTION OF INDIVIDUALIZED MUTATIONS AND MONITORING OF POSTOPERATIVE RECURRENCE USING CIRCULATING TUMOR DNA IN PATIENTS WITH UPPER TRACT UROTHELIAL CARCINOMA

Author

Tamura, Daichi, primary, Abe, Masakazu, additional, Ikarashi, Daiki, additional, Kato, Renpei, additional, Kato, Yoichiro, additional, Maekawa, Shigekatsu, additional, Kanehira, Mitsugu, additional, Takata, Ryo, additional, Suzuki, Yutaka, additional, Nakagawa, Hidewaki, additional, Nishizuka, Satoshi, additional, and Obara, Wataru, additional

Published
2023
Full Text
View/download PDF

47. MP69-02 CLINICAL IMPACT OF CANCER PREDISPOSING GENES ON UPPER URINARY TRACT UROTHELIAL CARCINOMA: A LARGE SCALE GENOME ANALYSIS IN JAPAN

Author

Sekine, Yuya, primary, Iwasaki, Yusuke, additional, Endo, Mikiko, additional, Sano, Takeshi, additional, Akamatsu, Shusuke, additional, Kobayashi, Takashi, additional, Nakagawa, Hidewaki, additional, Numakura, Kazuyuki, additional, Narita, Shintaro, additional, Momozawa, Yukihide, additional, and Habuchi, Tomonori, additional

Published
2023
Full Text
View/download PDF

48. Mutational signatures associated with tobacco smoking in human cancer

Author

Alexandrov, Ludmil B., Ju, Young Seok, Haase, Kerstin, Van Loo, Peter, Martincorena, Iñigo, Nik-Zainal, Serena, Totoki, Yasushi, Fujimoto, Akihiro, Nakagawa, Hidewaki, Shibata, Tatsuhiro, Campbell, Peter J., Vineis, Paolo, Phillips, David H., and Stratton, Michael R.

Published
2016

49. Publisher Correction: Integrated exome and RNA sequencing of dedifferentiated liposarcoma

Author

Hirata, Makoto, Asano, Naofumi, Katayama, Kotoe, Yoshida, Akihiko, Tsuda, Yusuke, Sekimizu, Masaya, Mitani, Sachiyo, Kobayashi, Eisuke, Komiyama, Motokiyo, Fujimoto, Hiroyuki, Goto, Takahiro, Iwamoto, Yukihide, Naka, Norifumi, Iwata, Shintaro, Nishida, Yoshihiro, Hiruma, Toru, Hiraga, Hiroaki, Kawano, Hirotaka, Motoi, Toru, Oda, Yoshinao, Matsubara, Daisuke, Fujita, Masashi, Shibata, Tatsuhiro, Nakagawa, Hidewaki, Nakayama, Robert, Kondo, Tadashi, Imoto, Seiya, Miyano, Satoru, Kawai, Akira, Yamaguchi, Rui, Ichikawa, Hitoshi, and Matsuda, Koichi

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results