265 results on '"Zhu, Shida"'
Search Results
2. Characteristics of germline DNA damage response gene mutations in ovarian cancer in Southwest China
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Fu, Kaiyu, Li, Qingli, Wang, Jie, Zhang, Mengpei, Yan, Xinyu, Li, Kemin, Song, Liang, Zhong, Lan, Ma, Yu, Chen, Jinghong, Zeng, Jing, Wang, Danqing, Shao, Di, Zhu, Shida, and Yin, Rutie
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- 2024
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3. The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science
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Lilly, Jena V, Rokita, Jo Lynne, Mason, Jennifer L, Patton, Tatiana, Stefankiewiz, Stephanie, Higgins, David, Trooskin, Gerri, Larouci, Carina A, Arya, Kamnaa, Appert, Elizabeth, Heath, Allison P, Zhu, Yuankun, Brown, Miguel A, Zhang, Bo, Farrow, Bailey K, Robins, Shannon, Morgan, Allison M, Nguyen, Thinh Q, Frenkel, Elizabeth, Lehmann, Kaitlin, Drake, Emily, Sullivan, Catherine, Plisiewicz, Alexa, Coleman, Noel, Patterson, Luke, Koptyra, Mateusz, Helili, Zeinab, Van Kuren, Nicholas, Young, Nathan, Kim, Meen Chul, Friedman, Christopher, Lubneuski, Alex, Blackden, Christopher, Williams, Marti, Baubet, Valerie, Tauhid, Lamiya, Galanaugh, Jamie, Boucher, Katie, Ijaz, Heba, Cole, Kristina A, Choudhari, Namrata, Santi, Mariarita, Moulder, Robert W, Waller, Jonathan, Rife, Whitney, Diskin, Sharon J, Mateos, Marion, Parsons, Donald W, Pollack, Ian F, Goldman, Stewart, Leary, Sarah, Caporalini, Chiara, Buccoliero, Anna Maria, Scagnet, Mirko, Haussler, David, Hanson, Derek, Firestein, Ron, Cain, Jason, Phillips, Joanna J, Gupta, Nalin, Mueller, Sabine, Grant, Gerald, Monje-Deisseroth, Michelle, Partap, Sonia, Greenfield, Jeffrey P, Hashizume, Rintaro, Smith, Amy, Zhu, Shida, Johnston, James M, Fangusaro, Jason R, Miller, Matthew, Wood, Matthew D, Gardner, Sharon, Carter, Claire L, Prolo, Laura M, Pisapia, Jared, Pehlivan, Katherine, Franson, Andrea, Niazi, Toba, Rubin, Josh, Abdelbaki, Mohamed, Ziegler, David S, Lindsay, Holly B, Stucklin, Ana Guerreiro, Gerber, Nicolas, Vaske, Olena M, Quinsey, Carolyn, Rood, Brian R, Nazarian, Javad, Raabe, Eric, Jackson, Eric M, Stapleton, Stacie, Lober, Robert M, Kram, David E, Koschmann, Carl, Storm, Phillip B, Lulla, Rishi R, Prados, Michael, Resnick, Adam C, and Waanders, Angela J
- Subjects
Neurosciences ,Pediatric Cancer ,Brain Disorders ,Pediatric Research Initiative ,Pediatric ,Brain Cancer ,Rare Diseases ,Cancer ,Good Health and Well Being ,Adult ,Humans ,Child ,Quality of Life ,Brain Neoplasms ,Collaborative international research infrastructure ,Pediatric brain tumors ,Multi-omic data ,Longitudinal clinical data ,Biospecimens ,Molecular clinical trials ,Clinical Sciences ,Oncology & Carcinogenesis - Abstract
Pediatric brain tumors are the leading cause of cancer-related death in children in the United States and contribute a disproportionate number of potential years of life lost compared to adult cancers. Moreover, survivors frequently suffer long-term side effects, including secondary cancers. The Children's Brain Tumor Network (CBTN) is a multi-institutional international clinical research consortium created to advance therapeutic development through the collection and rapid distribution of biospecimens and data via open-science research platforms for real-time access and use by the global research community. The CBTN's 32 member institutions utilize a shared regulatory governance architecture at the Children's Hospital of Philadelphia to accelerate and maximize the use of biospecimens and data. As of August 2022, CBTN has enrolled over 4700 subjects, over 1500 parents, and collected over 65,000 biospecimen aliquots for research. Additionally, over 80 preclinical models have been developed from collected tumors. Multi-omic data for over 1000 tumors and germline material are currently available with data generation for > 5000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors.
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- 2023
4. Homologous recombination deficiency status predicts response to platinum-based chemotherapy in Chinese patients with high-grade serous ovarian carcinoma
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Feng, Zheng, Shao, Di, Cai, Yuhang, Bi, Rui, Ju, Xingzhu, Chen, Dongju, Song, Chengcheng, Chen, Xiaojun, Li, Jin, An, Na, Li, Yunjin, Zhou, Qing, Xiu, Zhihui, Zhu, Shida, Wu, Xiaohua, and Wen, Hao
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- 2023
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5. Genomic basis for RNA alterations in cancer.
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PCAWG Transcriptome Core Group, Calabrese, Claudia, Davidson, Natalie R, Demircioğlu, Deniz, Fonseca, Nuno A, He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M, Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D, Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A, Hou, Yong, Huska, Matthew R, Kilpinen, Helena, Korbel, Jan O, Marin, Maximillian G, Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G, Su, Hong, Tan, Patrick, Waszak, Sebastian M, Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J, Meyerson, Matthew, Ouellette, BF Francis, Wu, Kui, Yang, Huanming, PCAWG Transcriptome Working Group, Brazma, Alvis, Brooks, Angela N, Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F, Stegle, Oliver, Zhang, Zemin, and PCAWG Consortium
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PCAWG Transcriptome Core Group ,PCAWG Transcriptome Working Group ,PCAWG Consortium ,Humans ,Neoplasms ,DNA ,Neoplasm ,RNA ,Genomics ,Gene Expression Regulation ,Neoplastic ,Genome ,Human ,DNA Copy Number Variations ,Transcriptome ,DNA ,Neoplasm ,Gene Expression Regulation ,Neoplastic ,Genome ,Human ,General Science & Technology - Abstract
Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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- 2020
6. The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science
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Lilly, Jena V., Rokita, Jo Lynne, Mason, Jennifer L., Patton, Tatiana, Stefankiewiz, Stephanie, Higgins, David, Trooskin, Gerri, Larouci, Carina A., Arya, Kamnaa, Appert, Elizabeth, Heath, Allison P., Zhu, Yuankun, Brown, Miguel A., Zhang, Bo, Farrow, Bailey K., Robins, Shannon, Morgan, Allison M., Nguyen, Thinh Q., Frenkel, Elizabeth, Lehmann, Kaitlin, Drake, Emily, Sullivan, Catherine, Plisiewicz, Alexa, Coleman, Noel, Patterson, Luke, Koptyra, Mateusz, Helili, Zeinab, Van Kuren, Nicholas, Young, Nathan, Kim, Meen Chul, Friedman, Christopher, Lubneuski, Alex, Blackden, Christopher, Williams, Marti, Baubet, Valerie, Tauhid, Lamiya, Galanaugh, Jamie, Boucher, Katie, Ijaz, Heba, Cole, Kristina A., Choudhari, Namrata, Santi, Mariarita, Moulder, Robert W., Waller, Jonathan, Rife, Whitney, Diskin, Sharon J., Mateos, Marion, Parsons, Donald W., Pollack, Ian F., Goldman, Stewart, Leary, Sarah, Caporalini, Chiara, Buccoliero, Anna Maria, Scagnet, Mirko, Haussler, David, Hanson, Derek, Firestein, Ron, Cain, Jason, Phillips, Joanna J., Gupta, Nalin, Mueller, Sabine, Grant, Gerald, Monje-Deisseroth, Michelle, Partap, Sonia, Greenfield, Jeffrey P., Hashizume, Rintaro, Smith, Amy, Zhu, Shida, Johnston, James M., Fangusaro, Jason R., Miller, Matthew, Wood, Matthew D., Gardner, Sharon, Carter, Claire L., Prolo, Laura M., Pisapia, Jared, Pehlivan, Katherine, Franson, Andrea, Niazi, Toba, Rubin, Josh, Abdelbaki, Mohamed, Ziegler, David S., Lindsay, Holly B., Stucklin, Ana Guerreiro, Gerber, Nicolas, Vaske, Olena M., Quinsey, Carolyn, Rood, Brian R., Nazarian, Javad, Raabe, Eric, Jackson, Eric M., Stapleton, Stacie, Lober, Robert M., Kram, David E., Koschmann, Carl, Storm, Phillip B., Lulla, Rishi R., Prados, Michael, Resnick, Adam C., and Waanders, Angela J.
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- 2023
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7. Evaluation of prognostic and predictive values of bespoke circulating tumor DNA assay in patients with advanced epithelial ovarian cancer.
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Wen, Hao, primary, Xu, Jing, additional, Chen, Yun, additional, Feng, Zheng, additional, Zhong, Yanping, additional, Sun, Lei, additional, Chen, Lin, additional, Zhu, Shida, additional, and Wu, Xiaohua, additional
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- 2024
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8. Circulating cell‐free DNA methylation‐based multi‐omics analysis allows early diagnosis of pancreatic ductal adenocarcinoma
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Zhao, Guochao, primary, Jiang, Ruijingfang, additional, Shi, Ying, additional, Gao, Suizhi, additional, Wang, Dansong, additional, Li, Zhilong, additional, Zhou, Yuhong, additional, Sun, Jianlong, additional, Wu, Wenchuan, additional, Peng, Jiaxi, additional, Kuang, Tiantao, additional, Rong, Yefei, additional, Yuan, Jie, additional, Zhu, Shida, additional, Jin, Gang, additional, Wang, Yuying, additional, and Lou, Wenhui, additional
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- 2024
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9. Genomic characterization of lymphomas in patients with inborn errors of immunity
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Ye, Xiaofei, Maglione, Paul J., Wehr, Claudia, Li, Xiaobo, Wang, Yating, Abolhassani, Hassan, Deripapa, Elena, Liu, Dongbing, Borte, Stephan, Du, Likun, Wan, Hui, Plötner, Andreas, Giannoula, Yvonne, Ko, Huai-Bin, Hou, Yong, Zhu, Shida, Grossman, Jennifer K., Sander, Birgitta, Grimbacher, Bodo, Hammarström, Lennart, Fedorova, Alina, Rosenzweig, Sergio D., Shcherbina, Anna, Wu, Kui, Warnatz, Klaus, Cunningham-Rundles, Charlotte, and Pan-Hammarström, Qiang
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- 2022
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10. Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome
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Liu, Xiaomin, Tong, Xin, Zou, Yuanqiang, Lin, Xiaoqian, Zhao, Hui, Tian, Liu, Jie, Zhuye, Wang, Qi, Zhang, Zhe, Lu, Haorong, Xiao, Liang, Qiu, Xuemei, Zi, Jin, Wang, Rong, Xu, Xun, Yang, Huanming, Wang, Jian, Zong, Yang, Liu, Weibin, Hou, Yong, Zhu, Shida, Jia, Huijue, and Zhang, Tao
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- 2022
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11. Genomic architecture of fetal central nervous system anomalies using whole-genome sequencing
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Yang, Ying, Zhao, Sheng, Sun, Guoqiang, Chen, Fang, Zhang, Tongda, Song, Jieping, Yang, Wenzhong, Wang, Lin, Zhan, Nianji, Yang, Xiaohong, Zhu, Xia, Rao, Bin, Yin, Zhenzhen, Zhou, Jing, Yan, Haisheng, Huang, Yushan, Ye, Jingyu, Huang, Hui, Cheng, Chen, Zhu, Shida, Guo, Jian, Xu, Xun, and Chen, Xinlin
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- 2022
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12. Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast
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Shi, Qianqian, Shao, Kang, Jia, Hongqin, Cao, Boyang, Li, Weidong, Dong, Shichen, Liu, Jian, Wu, Kailiang, Liu, Meng, Liu, Fangfang, Zhou, Hanlin, Lv, Jianke, Gu, Feng, Li, Luyuan, Zhu, Shida, Li, Shuai, Li, Guibo, and Fu, Li
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- 2022
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13. Personalized circulating tumor DNA monitoring improves recurrence surveillance and management after curative resection of colorectal liver metastases: A prospective cohort study
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Li, Yaqi, primary, Xu, Jing, additional, Hu, Xiang, additional, Chen, Yikuan, additional, Liu, Fangqi, additional, Chen, Yun, additional, Ma, Xiaoji, additional, Dong, Qiduo, additional, Sun, Lei, additional, Mo, Shaobo, additional, Zhang, Long, additional, He, Xingfeng, additional, Tong, Shanyou, additional, Wu, Huizi, additional, Li, Wenhua, additional, Cai, Sanjun, additional, Zhu, Shida, additional, Pan, Qi, additional, and Peng, Junjie, additional
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- 2024
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14. Population-based screening for colorectal cancer in Wuhan, China
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Liu, Song, primary, Wang, Yifan, additional, Wang, Yuying, additional, Duan, Chaofan, additional, Liu, Fan, additional, Zhang, Heng, additional, Tian, Xia, additional, Ding, Xiangwu, additional, Zhang, Manling, additional, Cao, Dan, additional, Liu, Yi, additional, Jiang, Ruijingfang, additional, Zhuo, Duan, additional, Peng, Jiaxi, additional, Zhu, Shida, additional, Zhao, Lijian, additional, Wang, Jian, additional, Wei, Li, additional, and Shi, Zhaohong, additional
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- 2024
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15. IL-17A deficiency inhibits lung cancer-induced osteoclastogenesis by promoting apoptosis of osteoclast precursor cells
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Wang, Hongkai, primary, Tang, Hao, additional, Yuan, Shujie, additional, Liang, Chuntao, additional, Li, Yuanxin, additional, Zhu, Shida, additional, and Chen, Kai, additional
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- 2024
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16. Single-cell atlas of domestic pig cerebral cortex and hypothalamus
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Zhu, Jiacheng, Chen, Fang, Luo, Lihua, Wu, Weiying, Dai, Jinxia, Zhong, Jixing, Lin, Xiumei, Chai, Chaochao, Ding, Peiwen, Liang, Langchao, Wang, Shiyou, Ding, Xiangning, Chen, Yin, Wang, Haoyu, Qiu, Jiaying, Wang, Feiyue, Sun, Chengcheng, Zeng, Yuying, Fang, Jian, Jiang, Xiaosen, Liu, Ping, Tang, Gen, Qiu, Xin, Zhang, Xingliang, Ruan, Yetian, Jiang, Sanjie, Li, Jiankang, Zhu, Shida, Xu, Xun, Li, Fang, Liu, Zhongmin, Cao, Gang, and Chen, Dongsheng
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- 2021
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17. Comparative analysis of clonal evolution among patients with right- and left-sided colon and rectal cancer
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Banerjee, Santasree, Zhang, Xianxiang, Kuang, Shan, Wang, Jigang, Li, Lei, Fan, Guangyi, Luo, Yonglun, Sun, Shuai, Han, Peng, Wu, Qingyao, Yang, Shujian, Ji, Xiaobin, Li, Yong, Deng, Li, Tian, Xiaofen, Wang, Zhiwei, Zhang, Yue, Wu, Kui, Zhu, Shida, Bolund, Lars, Yang, Huanming, Xu, Xun, Liu, Junnian, Lu, Yun, and Liu, Xin
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- 2021
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18. Author Correction: Genomic basis for RNA alterations in cancer
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Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, and Zhang, Zemin
- Published
- 2023
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19. Global Landscape of Clostridioides Difficile Phylogeography, Antibiotic Susceptibility, and Toxin Polymorphisms by Post-Hoc Whole-Genome Sequencing from the MODIFY I/II Studies
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Zhao, Hailong, Nickle, David C., Zeng, Zhen, Law, Pierra Y. T., Wilcox, Mark H., Chen, Lan, Peng, Ye, Meng, Jie, Deng, Ziqing, Albright, Andrew, Zhong, Huanzi, Xu, Xun, Zhu, Shida, Shen, Judong, Blanchard, Rebecca L., Dorr, Mary Beth, Shaw, Peter M., and Li, Junhua
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- 2021
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20. Sex- and age-related trajectories of the adult human gut microbiota shared across populations of different ethnicities
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Zhang, Xiuying, Zhong, Huanzi, Li, Yufeng, Shi, Zhun, Ren, Huahui, Zhang, Zhe, Zhou, Xianghai, Tang, Shanmei, Han, Xueyao, Lin, Yuxiang, Yang, Fangming, Wang, Dan, Fang, Chao, Fu, Zuodi, Wang, Lianying, Zhu, Shida, Hou, Yong, Xu, Xun, Yang, Huanming, Wang, Jian, Kristiansen, Karsten, Li, Junhua, and Ji, Linong
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- 2021
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21. Age‐dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging
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Sun, Liang, primary, Li, Zhiming, additional, Hu, Caiyou, additional, Ding, Jiahong, additional, Zhou, Qi, additional, Pang, Guofang, additional, Wu, Zhu, additional, Yang, Ruiyue, additional, Li, Shenghui, additional, Li, Jian, additional, Cai, Jianping, additional, Sun, Yuzhe, additional, Li, Rui, additional, Zhen, Hefu, additional, Sun, Shuqin, additional, Zhang, Jianmin, additional, Fang, Mingyan, additional, Chen, Zhihua, additional, Lv, Yuan, additional, Cao, Qizhi, additional, Sun, Yanan, additional, Gong, Ranhui, additional, Huang, Zezhi, additional, Duan, Yong, additional, Liu, Hengshuo, additional, Dong, Jun, additional, Li, Junchun, additional, Ruan, Jie, additional, Lu, Haorong, additional, He, Benjin, additional, Li, Ninghu, additional, Li, Tao, additional, Xue, Wenbin, additional, Li, Yan, additional, Shen, Juan, additional, Yang, Fan, additional, Zhao, Cheng, additional, Liang, Qinghua, additional, Zhang, Mingrong, additional, Chen, Chen, additional, Gong, Huan, additional, Hou, Yong, additional, Wang, Jian, additional, Zhang, Ying, additional, Yang, Huanming, additional, Zhu, Shida, additional, Xiao, Liang, additional, Jin, Zhen, additional, Guo, Haiyun, additional, Zhao, Peng, additional, Brix, Susanne, additional, Xu, Xun, additional, Jia, Huijue, additional, Kristiansen, Karsten, additional, Yang, Ze, additional, and Nie, Chao, additional
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- 2023
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22. Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome
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Liu, Xiaomin, Tong, Xin, Zhu, Jie, Tian, Liu, Jie, Zhuye, Zou, Yuanqiang, Lin, Xiaoqian, Liang, Hewei, Li, Wenxi, Ju, Yanmei, Qin, Youwen, Zou, Leying, Lu, Haorong, Zhu, Shida, Jin, Xin, Xu, Xun, Yang, Huanming, Wang, Jian, Zong, Yang, Liu, Weibin, Hou, Yong, Jia, Huijue, and Zhang, Tao
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- 2021
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23. Non-invasive lung cancer diagnosis and prognosis based on multi-analyte liquid biopsy
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Chen, Kezhong, Sun, Jianlong, Zhao, Heng, Jiang, Ruijingfang, Zheng, Jianchao, Li, Zhilong, Peng, Jiaxi, Shen, Haifeng, Zhang, Kai, Zhao, Jin, Zhu, Shida, Wang, Yuying, Yang, Fan, and Wang, Jun
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- 2021
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24. Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients
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Zhong, Huanzi, Wang, Yanqun, Shi, Zhun, Zhang, Lu, Ren, Huahui, He, Weiqun, Zhang, Zhaoyong, Zhu, Airu, Zhao, Jingxian, Xiao, Fei, Yang, Fangming, Liang, Tianzhu, Ye, Feng, Zhong, Bei, Ruan, Shicong, Gan, Mian, Zhu, Jiahui, Li, Fang, Li, Fuqiang, Wang, Daxi, Li, Jiandong, Ren, Peidi, Zhu, Shida, Yang, Huanming, Wang, Jian, Kristiansen, Karsten, Tun, Hein Min, Chen, Weijun, Zhong, Nanshan, Xu, Xun, Li, Yi-min, Li, Junhua, and Zhao, Jincun
- Published
- 2021
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25. Genomic basis for RNA alterations in cancer
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Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, and Zhang, Zemin
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- 2020
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26. Nationwide population genetic screening improves outcomes of newborn screening for hearing loss in China
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Wang, Qiuju, Xiang, Jiale, Sun, Jun, Yang, Yun, Guan, Jing, Wang, Dayong, Song, Cui, Guo, Ling, Wang, Hongyang, Chen, Yaqiu, Leng, Junhong, Wang, Xiaman, Zhang, Junqing, Han, Bing, Zou, Jing, Yan, Chengbin, Zhao, Lidong, Luo, Hongyu, Han, Yuan, Yuan, Wen, Zhang, Hongyun, Wang, Wei, Wang, Jian, Yang, Huanming, Xu, Xun, Yin, Ye, Morton, Cynthia C., Zhao, Lijian, Zhu, Shida, Shen, Jun, and Peng, Zhiyu
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- 2019
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27. Characterization and validation of somatic mutation spectrum to reveal heterogeneity in gastric cancer by single cell sequencing
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Peng, Lihua, Xing, Rui, Liu, Dongbing, Bao, Li, Cheng, Wenxiang, Wang, Hongyi, Yu, Yuan, Liu, Xiaofeng, Jiang, Lu, Wu, Yan, An, Zhongxue, Liang, Qiaoyi, Kim, Ryong Nam, Shin, Young Kee, Yang, Huanming, Wang, Jian, Yu, Jun, Zhang, Xiuqing, Xu, Xun, Yang, Jiaan, Wu, Kui, Zhu, Shida, and Lu, Youyong
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- 2019
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28. Genetic landscape of hepatitis B virus–associated diffuse large B-cell lymphoma
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Ren, Weicheng, Ye, Xiaofei, Su, Hong, Li, Wei, Liu, Dongbing, Pirmoradian, Mohammad, Wang, Xianhuo, Zhang, Bo, Zhang, Qiang, Chen, Longyun, Nie, Man, Liu, Yao, Meng, Bin, Huang, Huiqiang, Jiang, Wenqi, Zeng, Yixin, Li, Wenyu, Wu, Kui, Hou, Yong, Wiman, Klas G., Li, Zhiming, Zhang, Huilai, Peng, Roujun, Zhu, Shida, and Pan-Hammarström, Qiang
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- 2018
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29. Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome
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Liu, Xiaomin, Tong, Xin, Zou, Yuanqiang, Lin, Xiaoqian, Zhao, Hui, Tian, Liu, Jie, Zhuye, Wang, Qi, Zhang, Zhe, Lu, Haorong, Xiao, Liang, Qiu, Xuemei, Zi, Jin, Wang, Rong, Xu, Xun, Yang, Huanming, Wang, Jian, Zong, Yang, Liu, Weibin, Hou, Yong, Zhu, Shida, Jia, Huijue, and Zhang, Tao
- Abstract
The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization analyses on 3,432 Chinese individuals with whole-genome, whole-metagenome, anthropometric and blood metabolic trait data. We identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 of them. Increased relative abundances of fecal Oscillibacterand Alistipeswere causally linked to decreased triglyceride concentration. Conversely, blood metabolites such as glutamic acid appeared to decrease fecal Oxalobacter, and members of Proteobacteriawere influenced by metabolites such as 5-methyltetrahydrofolic acid, alanine, glutamate and selenium. Two-sample Mendelian randomization with data from Biobank Japan partly corroborated results with triglyceride and with uric acid, and also provided causal support for published fecal bacterial markers for cancer and cardiovascular diseases. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies.
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- 2024
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30. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity
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Liu, Longqi, Liu, Chuanyu, Quintero, Andrés, Wu, Liang, Yuan, Yue, Wang, Mingyue, Cheng, Mengnan, Leng, Lizhi, Xu, Liqin, Dong, Guoyi, Li, Rui, Liu, Yang, Wei, Xiaoyu, Xu, Jiangshan, Chen, Xiaowei, Lu, Haorong, Chen, Dongsheng, Wang, Quanlei, Zhou, Qing, Lin, Xinxin, Li, Guibo, Liu, Shiping, Wang, Qi, Wang, Hongru, Fink, J. Lynn, Gao, Zhengliang, Liu, Xin, Hou, Yong, Zhu, Shida, Yang, Huanming, Ye, Yunming, Lin, Ge, Chen, Fang, Herrmann, Carl, Eils, Roland, Shang, Zhouchun, and Xu, Xun
- Published
- 2019
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31. An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos
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Liu, Longqi, Leng, Lizhi, Liu, Chuanyu, Lu, Changfu, Yuan, Yue, Wu, Liang, Gong, Fei, Zhang, Shuoping, Wei, Xiaoyu, Wang, Mingyue, Zhao, Lei, Hu, Liang, Wang, Jian, Yang, Huanming, Zhu, Shida, Chen, Fang, Lu, Guangxiu, Shang, Zhouchun, and Lin, Ge
- Published
- 2019
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32. IL-17A regulates autophagy and promotes osteoclast differentiation through the ERK/mTOR/Beclin1 pathway
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Tang, Hao, primary, Zhu, Shida, additional, Chen, Kai, additional, Yuan, Shujie, additional, Hu, Junzu, additional, and Wang, Hongkai, additional
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- 2023
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33. Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas
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Georgiou, Konstantinos, Chen, Longyun, Berglund, Mattias, Ren, Weicheng, de Miranda, Noel F.C.C., Lisboa, Susana, Fangazio, Marco, Zhu, Shida, Hou, Yong, Wu, Kui, Fang, Wenfeng, Wang, Xianhuo, Meng, Bin, Zhang, Li, Zeng, Yixin, Bhagat, Govind, Nordenskjöld, Magnus, Sundström, Christer, Enblad, Gunilla, Dalla-Favera, Riccardo, Zhang, Huilai, Teixeira, Manuel R., Pasqualucci, Laura, Peng, Roujun, and Pan-Hammarström, Qiang
- Published
- 2016
- Full Text
- View/download PDF
34. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, 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Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Villasante, Izar, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, 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Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zamora, Jorge, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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35. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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36. Integrative pathway enrichment analysis of multivariate omics data
- Author
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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
- Published
- 2023
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37. Pathway and network analysis of more than 2500 whole cancer genomes
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Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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38. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campbell, Peter J, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Getz, Gad, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hess, Julian M, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hornshøj, Henrik, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose MG, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Johnson, Rory, Johnson, Todd A, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kellis, Manolis, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K, Kim, Youngwook, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Sushant, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lawrence, Michael S, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Lou, Shaoke, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchal, Kathleen, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Meyerson, William, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Muiños, Ferran, Mularoni, Loris, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakagawa, Hidewaki, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nielsen, Morten Muhlig, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pedersen, Jakob Skou, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pulido-Tamayo, Sergio, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Raphael, Benjamin J, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reimand, Jüri, Reis-Filho, Jorge, Reuter, Victor, Reyes-Salazar, Iker, Reyna, Matthew A, Reynolds, Sheila M, Rheinbay, Esther, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rubin, Mark A, Rubio-Perez, Carlota, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Sahinalp, S Cenk, Saini, Natalie, Saito-Adachi, Mihoko, Saksena, Gordon, Salcedo, Adriana, Salgado, Roberto, Salichos, Leonidas, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sander, Chris, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schumacher, Steven E, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shackleton, Mark, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shrestha, Raunak, Shringarpure, Suyash S, Shriver, Craig, Shuai, Shimin, Sidiropoulos, Nikos, Siebert, Reiner, Sieuwerts, Anieta M, Sieverling, Lina, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sinnott-Armstrong, Nasa, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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39. Genomic footprints of activated telomere maintenance mechanisms in cancer
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Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Pulido-Tamayo, Sergio, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Raphael, Benjamin J, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reimand, Jüri, Reis-Filho, Jorge, Reuter, Victor, Reyes-Salazar, Iker, Reyna, Matthew A, Reynolds, Sheila M, Rheinbay, Esther, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Roach, Jeffrey, Roberts, Lewis R, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rubin, Mark A, Rubio-Perez, Carlota, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Sahinalp, S Cenk, Saini, Natalie, Saito-Adachi, Mihoko, Saksena, Gordon, Salcedo, Adriana, Salgado, Roberto, Salichos, Leonidas, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sander, Chris, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shrestha, Raunak, Shringarpure, Suyash S, Shriver, Craig, Shuai, Shimin, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sinnott-Armstrong, Nasa, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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40. The genomic landscape of Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma
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Hong, Shaodong, Liu, Dongbing, Luo, Shuzhen, Fang, Wenfeng, Zhan, Jianhua, Fu, Sha, Zhang, Yaxiong, Wu, Xuan, Zhou, Huaqiang, Chen, Xi, Chen, Gang, Zhang, Zhonghan, Zheng, Qiufan, Li, Xiaobo, Chen, Jinghao, Liu, Xingmin, Lei, Mengyue, Ye, Chen, Wang, Jian, Yang, Huanming, Xu, Xun, Zhu, Shida, Yang, Yunpeng, Zhao, Yuanyuan, Zhou, Ningning, Zhao, Hongyun, Huang, Yan, Zhang, Lanjun, Wu, Kui, and Zhang, Li
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- 2019
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41. The dual role of CD70 in B‐cell lymphomagenesis
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Nie, Man, primary, Ren, Weicheng, additional, Ye, Xiaofei, additional, Berglund, Mattias, additional, Wang, Xianhuo, additional, Fjordén, Karin, additional, Du, Likun, additional, Giannoula, Yvonne, additional, Lei, Dexin, additional, Su, Wenjia, additional, Li, Wei, additional, Liu, Dongbing, additional, Linderoth, Johan, additional, Jiang, Chengyi, additional, Bao, Huijing, additional, Jiang, Wenqi, additional, Huang, Huiqiang, additional, Hou, Yong, additional, Zhu, Shida, additional, Enblad, Gunilla, additional, Jerkeman, Mats, additional, Wu, Kui, additional, Zhang, Huilai, additional, Amini, Rose‐Marie, additional, Li, Zhi‐Ming, additional, and Pan‐Hammarström, Qiang, additional
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- 2022
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42. The Influence of Vaginal Microbiome and Clinical Factors on HPV Clearance: A Prospective Study
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Yang, Zhongzhou, primary, Wu, Hao, additional, Wang, Xiaohan, additional, Tong, Guoqing, additional, Huang, Zhuoqi, additional, Wang, Jie, additional, Jiang, Yuxin, additional, Cao, Min, additional, Wang, Yue, additional, Deng, Xingxing, additional, Liu, Na, additional, Qi, Le, additional, Liu, Mengping, additional, Hutchins, Andrew, additional, Yao, Bin, additional, Shi, Mang, additional, Li, Yantao, additional, and Zhu, Shida, additional
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- 2022
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43. A cost-effectiveness of Fecal DNA methylation test for colorectal cancer screening in Saudi Arabia
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Yang, Zhongzhou, primary, Shi, Mang, additional, Liu, Mengping, additional, Wang, Zhe, additional, Huang, Hui, additional, Wang, Shunyao, additional, Zheng, Xiaoyuan, additional, Liu, Yanyan, additional, Liu, Na, additional, Li, Yantao, additional, Lau, Eric, additional, and Zhu, Shida, additional
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- 2022
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44. Identification of multi-omic biomarkers from Fecal DNA for improved Detection of Colorectal Cancer and precancerous lesions
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Fang, Yujing, primary, Peng, Jiaxi, additional, Li, Zhilong, additional, Jiang, Ruijingfang, additional, Lin, Yuxiang, additional, Shi, Ying, additional, Sun, Jianlong, additional, Zhuo, Duan, additional, Ou, Qingjian, additional, Chen, Jiali, additional, Wang, Xiaohan, additional, Cai, Jielun, additional, Zhu, Shida, additional, Wan, Desen, additional, Wang, Yuying, additional, and Lu, Zhenhai, additional
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- 2022
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45. The Children’s Brain Tumor Network (CBTN) - Accelerating Research in Pediatric Central Nervous System Tumors through Collaboration and Open Science
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Lilly, Jena V., primary, Rokita, Jo Lynne, additional, Mason, Jennifer L., additional, Patton, Tatiana, additional, Stefankiewiz, Stephanie, additional, Higgins, David, additional, Trooskin, Gerri, additional, Larouci, Carina A., additional, Arya, Kamnaa, additional, Appert, Elizabeth, additional, Heath, Allison P., additional, Zhu, Yuankun, additional, Brown, Miguel A., additional, Zhang, Bo, additional, Farrow, Bailey K., additional, Robins, Shannon, additional, Morgan, Allison M., additional, Nguyen, Thinh Q., additional, Frenkel, Elizabeth, additional, Lehmann, Kaitlin, additional, Drake, Emily, additional, Sullivan, Catherine, additional, Plisiewicz, Alexa, additional, Coleman, Noel, additional, Patterson, Luke, additional, Koptyra, Mateusz, additional, Helili, Zeinab, additional, Van Kuren, Nicholas, additional, Young, Nathan, additional, Kim, Meen Chul, additional, Friedman, Christopher, additional, Lubneuski, Alex, additional, Blackden, Christopher, additional, Williams, Marti, additional, Baubet, Valerie, additional, Tauhid, Lamiya, additional, Galanaugh, Jamie, additional, Boucher, Katie, additional, Ijaz, Heba, additional, Cole, Kristina A., additional, Choudhari, Namrata, additional, Santi, Mariarita, additional, Moulder, Robert W., additional, Waller, Jonathan, additional, Rife, Whitney, additional, Diskin, Sharon J., additional, Mateos, Marion, additional, Parsons, Donald W., additional, Pollack, Ian F., additional, Goldman, Stewart, additional, Leary, Sarah, additional, Caporalini, Chiara, additional, Buccoliero, Anna Maria, additional, Scagnet, Mirko, additional, Haussler, David, additional, Hanson, Derek, additional, Firestein, Ron, additional, Cain, Jason, additional, Phillips, Joanna J., additional, Gupta, Nalin, additional, Mueller, Sabine, additional, Grant, Gerald, additional, Monje-Deisseroth, Michelle, additional, Partap, Sonia, additional, Greenfield, Jeffrey P., additional, Hashizume, Rintaro, additional, Smith, Amy, additional, Zhu, Shida, additional, Johnston, James M., additional, Fangusaro, Jason R, additional, Miller, Matthew, additional, Wood, Matthew D., additional, Gardner, Sharon, additional, Carter, Claire L., additional, Prolo, Laura M., additional, Pisapia, Jared, additional, Pehlivan, Katherine, additional, Franson, Andrea, additional, Niazi, Toba, additional, Rubin, Josh, additional, Abdelbaki, Mohamed, additional, Ziegler, David S., additional, Lindsay, Holly B., additional, Stucklin, Ana Guerreiro, additional, Gerber, Nicolas, additional, Vaske, Olena M., additional, Quinsey, Carolyn, additional, Rood, Brian R., additional, Nazarian, Javad, additional, Raabe, Eric, additional, Jackson, Eric M., additional, Stapleton, Stacie, additional, Lober, Robert M., additional, Kram, David E., additional, Koschmann, Carl, additional, Storm, Phillip B., additional, Lulla, Rishi R., additional, Prados, Michael, additional, Resnick, Adam C., additional, and Waanders, Angela J., additional
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- 2022
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46. Characterization of genomic clones by targeted deep sequencing of ctDNA to monitor liver cancer
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Chunna Fan, Shuang Zeng, Shi Taiping, Yun Yang, Zhu Shida, Siming Xue, Lijie Song, Na An, Min Xia, Xie Ying, Mufei Lin, Xiaoyu Kong, Wang Hui, Xiaolin Zheng, Liangjun Gao, Zhonghai Fang, Xia Wei, Fengxia Liu, Yan Sun, Jing Yu, and Cheng Zhengyu
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Cancer Research ,business.industry ,BGISEQ-500 ,CIRCULATING TUMOR DNA ,Computational biology ,medicine.disease ,Deep sequencing ,liver cancer ,RECURRENT MUTATIONS ,monitoring ,targeted next-generation sequencing ,Oncology ,HEPATOCELLULAR-CARCINOMA ,Medicine ,Original Article ,Radiology, Nuclear Medicine and imaging ,Circulating tumor DNA (ctDNA) ,business ,Liver cancer - Abstract
Background: In recent years, the morbidity and mortality of cancer patients have continued to increase in China, and there is an urgent need to develop an effective method to monitor tumor dynamics and measure tumor burden. Derived from the cell-free fraction of blood in cancer patients, circulating tumor DNA (ctDNA) has been regarded as a promising surrogate for tumor tissue biopsies. With the development of sequencing technology, ctDNA has been recognized as a specific and highly sensitive biomarker, and it has become a hot research spot in recent years. Methods: In this paper, we investigated clonal changes before and after surgery in liver cancer patients using ctDNA. Results: First, we evaluated the accuracy and stability of the method in ctDNA detection using virtual tumor samples with known mutations. The results showed that our method detected variants with an allelic frequency of at least 0.5%. We then applied this method to 34 liver cancer patients. A total of 266 clinically relevant mutations were identified in the pretreatment plasma samples. Through the analysis of plasma DNA samples at different treatment time points, we also investigated the possibility of using ctDNA as a prognostic factor to reflect tumor dynamics and to evaluate clinical responses. Conclusions: The results demonstrated that targeted high-depth next-generation sequencing can be used in ctDNA detection. Compared to traditional biopsy, the detection of ctDNA provides more information for human liver cancer, which is essential to guide the selection of therapy and predict prognosis.
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- 2021
47. Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids
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Liu, Zhongzhen, primary, Wang, Taifu, additional, Yang, Xi, additional, Zhou, Qing, additional, Zhu, Sujun, additional, Zeng, Juan, additional, Chen, Haixiao, additional, Sun, Jinghua, additional, Li, Liqiang, additional, Xu, Jinjin, additional, Geng, Chunyu, additional, Xu, Xun, additional, Wang, Jian, additional, Yang, Huanming, additional, Zhu, Shida, additional, Chen, Fang, additional, and Wang, Wen‐Jing, additional
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- 2022
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48. Characteristics of germline DNA damage response gene mutations in ovarian cancer in Southwest China.
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Yin, Rutie, primary, Chen, Jinghong, additional, Li, Qingli, additional, Yan, Xinyu, additional, Wang, Jie, additional, Li, Kemin, additional, Song, Liang, additional, Zhong, Lan, additional, Ma, Yu, additional, Zhang, Mengpei, additional, Zeng, Jing, additional, Wang, Danqing, additional, and Zhu, Shida, additional
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- 2022
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49. Comparison of double-stranded and single-stranded cfDNA library construction methods for targeted genome and methylation sequencing
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Zheng, Jianchao, primary, Li, Zhilong, additional, Zhang, Xiuqing, additional, Zhang, Hongyun, additional, Zhu, Shida, additional, Sun, Jianlong, additional, and Wang, Yuying, additional
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- 2022
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50. Genetic characteristics of human papillomavirus type 16, 18, 52 and 58 in southern China
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Zu, Yuee, primary, Ou, Zhihua, additional, Wu, Dan, additional, Liu, Wei, additional, Liu, Liwen, additional, Wu, Di, additional, Zhao, Yanping, additional, Ren, Peidi, additional, Zhang, Yanqing, additional, Li, Wangsheng, additional, Fu, Shujin, additional, Wen, Yongchun, additional, Cai, Xianchu, additional, Liao, Wenbo, additional, Geng, Chunyu, additional, Zhou, Hongcheng, additional, Wang, Xiaman, additional, Lu, Haorong, additional, Peng, Huanhuan, additional, Liu, Na, additional, Zhu, Shida, additional, Liu, Jiyang, additional, Wang, Dongbo, additional, and Li, Junhua, additional
- Published
- 2021
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