1,187 results on '"Stratton, Michael R"'
Search Results
2. Geographic variation of mutagenic exposures in kidney cancer genomes
- Author
-
Senkin, Sergey, Moody, Sarah, Díaz-Gay, Marcos, Abedi-Ardekani, Behnoush, Cattiaux, Thomas, Ferreiro-Iglesias, Aida, Wang, Jingwei, Fitzgerald, Stephen, Kazachkova, Mariya, Vangara, Raviteja, Le, Anh Phuong, Bergstrom, Erik N., Khandekar, Azhar, Otlu, Burçak, Cheema, Saamin, Latimer, Calli, Thomas, Emily, Atkins, Joshua Ronald, Smith-Byrne, Karl, Cortez Cardoso Penha, Ricardo, Carreira, Christine, Chopard, Priscilia, Gaborieau, Valérie, Keski-Rahkonen, Pekka, Jones, David, Teague, Jon W., Ferlicot, Sophie, Asgari, Mojgan, Sangkhathat, Surasak, Attawettayanon, Worapat, Świątkowska, Beata, Jarmalaite, Sonata, Sabaliauskaite, Rasa, Shibata, Tatsuhiro, Fukagawa, Akihiko, Mates, Dana, Jinga, Viorel, Rascu, Stefan, Mijuskovic, Mirjana, Savic, Slavisa, Milosavljevic, Sasa, Bartlett, John M. S., Albert, Monique, Phouthavongsy, Larry, Ashton-Prolla, Patricia, Botton, Mariana R., Silva Neto, Brasil, Bezerra, Stephania Martins, Curado, Maria Paula, Zequi, Stênio de Cássio, Reis, Rui Manuel, Faria, Eliney Ferreira, de Menezes, Nei Soares, Ferrari, Renata Spagnoli, Banks, Rosamonde E., Vasudev, Naveen S., Zaridze, David, Mukeriya, Anush, Shangina, Oxana, Matveev, Vsevolod, Foretova, Lenka, Navratilova, Marie, Holcatova, Ivana, Hornakova, Anna, Janout, Vladimir, Purdue, Mark P., Rothman, Nathaniel, Chanock, Stephen J., Ueland, Per Magne, Johansson, Mattias, McKay, James, Scelo, Ghislaine, Chanudet, Estelle, Humphreys, Laura, de Carvalho, Ana Carolina, Perdomo, Sandra, Alexandrov, Ludmil B., Stratton, Michael R., and Brennan, Paul
- Published
- 2024
- Full Text
- View/download PDF
3. An international report on bacterial communities in esophageal squamous cell carcinoma
- Author
-
Nomburg, Jason, Bullman, Susan, Nasrollahzadeh, Dariush, Collisson, Eric A, Abedi‐Ardekani, Behnoush, Akoko, Larry O, Atkins, Joshua R, Buckle, Geoffrey C, Gopal, Satish, Hu, Nan, Kaimila, Bongani, Khoshnia, Masoud, Malekzadeh, Reza, Menya, Diana, Mmbaga, Blandina T, Moody, Sarah, Mulima, Gift, Mushi, Beatrice P, Mwaiselage, Julius, Mwanga, Ally, Newton, Yulia, Ng, Dianna L, Radenbaugh, Amie, Rwakatema, Deogratias S, Selekwa, Msiba, Schüz, Joachim, Taylor, Philip R, Vaske, Charles, Goldstein, Alisa, Stratton, Michael R, McCormack, Valerie, Brennan, Paul, DeCaprio, James A, Meyerson, Matthew, Mmbaga, Elia J, and Van Loon, Katherine
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Human Genome ,Esophageal Cancer ,Microbiome ,Rare Diseases ,Cancer Genomics ,Clinical Research ,Dental/Oral and Craniofacial Disease ,Genetics ,Prevention ,Digestive Diseases ,Infectious Diseases ,Cancer ,Infection ,Bacteria ,Esophageal Neoplasms ,Esophageal Squamous Cell Carcinoma ,Humans ,Kenya ,Microbiota ,Africa ,esophageal cancer ,esophageal squamous cell carcinoma ,Fusobacterium ,microbiome ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
The incidence of esophageal squamous cell carcinoma (ESCC) is disproportionately high in the eastern corridor of Africa and parts of Asia. Emerging research has identified a potential association between poor oral health and ESCC. One possible link between poor oral health and ESCC involves the alteration of the microbiome. We performed an integrated analysis of four independent sequencing efforts of ESCC tumors from patients from high- and low-incidence regions of the world. Using whole genome sequencing (WGS) and RNA sequencing (RNAseq) of ESCC tumors from 61 patients in Tanzania, we identified a community of bacteria, including members of the genera Fusobacterium, Selenomonas, Prevotella, Streptococcus, Porphyromonas, Veillonella and Campylobacter, present at high abundance in ESCC tumors. We then characterized the microbiome of 238 ESCC tumor specimens collected in two additional independent sequencing efforts consisting of patients from other high-ESCC incidence regions (Tanzania, Malawi, Kenya, Iran, China). This analysis revealed similar ESCC-associated bacterial communities in these cancers. Because these genera are traditionally considered members of the oral microbiota, we next explored whether there was a relationship between the synchronous saliva and tumor microbiomes of ESCC patients in Tanzania. Comparative analyses revealed that paired saliva and tumor microbiomes were significantly similar with a specific enrichment of Fusobacterium and Prevotella in the tumor microbiome. Together, these data indicate that cancer-associated oral bacteria are associated with ESCC tumors at the time of diagnosis and support a model in which oral bacteria are present in high abundance in both saliva and tumors of some ESCC patients.
- Published
- 2022
4. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor
- Author
-
Islam, SM Ashiqul, Díaz-Gay, Marcos, Wu, Yang, Barnes, Mark, Vangara, Raviteja, Bergstrom, Erik N, He, Yudou, Vella, Mike, Wang, Jingwei, Teague, Jon W, Clapham, Peter, Moody, Sarah, Senkin, Sergey, Li, Yun Rose, Riva, Laura, Zhang, Tongwu, Gruber, Andreas J, Steele, Christopher D, Otlu, Burçak, Khandekar, Azhar, Abbasi, Ammal, Humphreys, Laura, Syulyukina, Natalia, Brady, Samuel W, Alexandrov, Boian S, Pillay, Nischalan, Zhang, Jinghui, Adams, David J, Martincorena, Iñigo, Wedge, David C, Landi, Maria Teresa, Brennan, Paul, Stratton, Michael R, Rozen, Steven G, and Alexandrov, Ludmil B
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Tobacco Smoke and Health ,Human Genome ,Cancer ,Prevention ,Tobacco ,Good Health and Well Being ,cancer genomics ,genomics ,mutagenesis ,mutational signatures - Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
- Published
- 2022
5. The Mutographs biorepository: A unique genomic resource to study cancer around the world
- Author
-
Perdomo, Sandra, Abedi-Ardekani, Behnoush, de Carvalho, Ana Carolina, Ferreiro-Iglesias, Aida, Gaborieau, Valérie, Cattiaux, Thomas, Renard, Hélène, Chopard, Priscilia, Carreira, Christine, Spanu, Andreea, Nikmanesh, Arash, Cardoso Penha, Ricardo Cortez, Antwi, Samuel O., Ashton-Prolla, Patricia, Canova, Cristina, Chitapanarux, Taned, Cox, Riley, Curado, Maria Paula, de Oliveira, José Carlos, Dzamalala, Charles, Fabianova, Elenora, Ferri, Lorenzo, Fitzgerald, Rebecca, Foretova, Lenka, Gallinger, Steven, Goldstein, Alisa M., Holcatova, Ivana, Huertas, Antonio, Janout, Vladimir, Jarmalaite, Sonata, Kaneva, Radka, Kowalski, Luiz Paulo, Kulis, Tomislav, Lagiou, Pagona, Lissowska, Jolanta, Malekzadeh, Reza, Mates, Dana, McCorrmack, Valerie, Menya, Diana, Mhatre, Sharayu, Mmbaga, Blandina Theophil, de Moricz, André, Nyirády, Péter, Ognjanovic, Miodrag, Papadopoulou, Kyriaki, Polesel, Jerry, Purdue, Mark P., Rascu, Stefan, Rebolho Batista, Lidia Maria, Reis, Rui Manuel, Ribeiro Pinto, Luis Felipe, Rodríguez-Urrego, Paula A., Sangkhathat, Surasak, Sangrajrang, Suleeporn, Shibata, Tatsuhiro, Stakhovsky, Eduard, Świątkowska, Beata, Vaccaro, Carlos, Vasconcelos de Podesta, Jose Roberto, Vasudev, Naveen S., Vilensky, Marta, Yeung, Jonathan, Zaridze, David, Zendehdel, Kazem, Scelo, Ghislaine, Chanudet, Estelle, Wang, Jingwei, Fitzgerald, Stephen, Latimer, Calli, Moody, Sarah, Humphreys, Laura, Alexandrov, Ludmil B., Stratton, Michael R., and Brennan, Paul
- Published
- 2024
- Full Text
- View/download PDF
6. APOBEC mutagenesis is a common process in normal human small intestine
- Author
-
Wang, Yichen, Robinson, Philip S., Coorens, Tim H. H., Moore, Luiza, Lee-Six, Henry, Noorani, Ayesha, Sanders, Mathijs A., Jung, Hyunchul, Katainen, Riku, Heuschkel, Robert, Brunton-Sim, Roxanne, Weston, Robyn, Read, Debbie, Nobbs, Beverley, Fitzgerald, Rebecca C., Saeb-Parsy, Kourosh, Martincorena, Iñigo, Campbell, Peter J., Rushbrook, Simon, Zilbauer, Matthias, Buczacki, Simon James Alexander, and Stratton, Michael R.
- Published
- 2023
- Full Text
- View/download PDF
7. The repertoire of mutational signatures in human cancer
- Author
-
Alexandrov, Ludmil B, Kim, Jaegil, Haradhvala, Nicholas J, Huang, Mi Ni, Tian Ng, Alvin Wei, Wu, Yang, Boot, Arnoud, Covington, Kyle R, Gordenin, Dmitry A, Bergstrom, Erik N, Islam, SM Ashiqul, Lopez-Bigas, Nuria, Klimczak, Leszek J, McPherson, John R, Morganella, Sandro, Sabarinathan, Radhakrishnan, Wheeler, David A, Mustonen, Ville, Getz, Gad, Rozen, Steven G, and Stratton, Michael R
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Cancer ,2.1 Biological and endogenous factors ,Aetiology ,Good Health and Well Being ,Age Factors ,Base Sequence ,Exome ,Genome ,Human ,Humans ,Mutation ,Neoplasms ,Sequence Analysis ,DNA ,PCAWG Mutational Signatures Working Group ,PCAWG Consortium ,General Science & Technology - Abstract
Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses3-15, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.
- Published
- 2020
8. Procarbazine-induced Genomic Toxicity in Hodgkin Lymphoma Survivors
- Author
-
Santarsieri, Anna, primary, Mitchell, Emily, additional, Pham, My H., additional, Sanghvi, Rashesh, additional, Jablonski, Janina, additional, Lee-Six, Henry, additional, Sturgess, Katherine, additional, Brice, Pauline, additional, Menne, Tobias F., additional, Osborne, Wendy, additional, Creasey, Thomas, additional, Ardeshna, Kirit M., additional, Baxter, Joanna, additional, Behan, Sarah, additional, Bhuller, Kaljit, additional, Booth, Stephen, additional, Chavda, Nikesh D., additional, Collins, Graham P., additional, Culligan, Dominic J., additional, Cwynarski, Kate, additional, Davies, Andrew, additional, Downing, Abigail, additional, Dutton, David, additional, Furtado, Michelle, additional, Gallop-Evans, Eve, additional, Hodson, Andrew, additional, Hopkins, David, additional, Hsu, Hannah, additional, Iyengar, Sunil, additional, Jones, Stephen G., additional, Karanth, Mamatha, additional, Linton, Kim M., additional, Lomas, Oliver C., additional, Martinez-Calle, Nicolas, additional, Mathur, Abhinav, additional, McKay, Pamela, additional, Nagumantry, Sateesh K., additional, Phillips, Elizabeth H., additional, Phillips, Neil, additional, Rudge, John F., additional, Shah, Nimish K., additional, Stafford, Gwyneth, additional, Sternberg, Alex, additional, Trickey, Rachel, additional, Uttenthal, Benjamin J., additional, Wetherall, Natasha, additional, Zhang, Xiao-Yin, additional, McMillan, Andrew K., additional, Coleman, Nicholas, additional, Stratton, Michael R., additional, Laurenti, Elisa, additional, Borchmann, Peter, additional, Borchmann, Sven, additional, Campbell, Peter J., additional, Rahbari, Raheleh, additional, and Follows, George A., additional
- Published
- 2024
- Full Text
- View/download PDF
9. Mechanisms of APOBEC3 mutagenesis in human cancer cells
- Author
-
Petljak, Mia, Dananberg, Alexandra, Chu, Kevan, Bergstrom, Erik N., Striepen, Josefine, von Morgen, Patrick, Chen, Yanyang, Shah, Hina, Sale, Julian E., Alexandrov, Ludmil B., Stratton, Michael R., and Maciejowski, John
- Published
- 2022
- Full Text
- View/download PDF
10. Clonal dynamics of haematopoiesis across the human lifespan
- Author
-
Mitchell, Emily, Spencer Chapman, Michael, Williams, Nicholas, Dawson, Kevin J., Mende, Nicole, Calderbank, Emily F., Jung, Hyunchul, Mitchell, Thomas, Coorens, Tim H. H., Spencer, David H., Machado, Heather, Lee-Six, Henry, Davies, Megan, Hayler, Daniel, Fabre, Margarete A., Mahbubani, Krishnaa, Abascal, Federico, Cagan, Alex, Vassiliou, George S., Baxter, Joanna, Martincorena, Inigo, Stratton, Michael R., Kent, David G., Chatterjee, Krishna, Parsy, Kourosh Saeb, Green, Anthony R., Nangalia, Jyoti, Laurenti, Elisa, and Campbell, Peter J.
- Published
- 2022
- Full Text
- View/download PDF
11. Somatic mutation rates scale with lifespan across mammals
- Author
-
Cagan, Alex, Baez-Ortega, Adrian, Brzozowska, Natalia, Abascal, Federico, Coorens, Tim H. H., Sanders, Mathijs A., Lawson, Andrew R. J., Harvey, Luke M. R., Bhosle, Shriram, Jones, David, Alcantara, Raul E., Butler, Timothy M., Hooks, Yvette, Roberts, Kirsty, Anderson, Elizabeth, Lunn, Sharna, Flach, Edmund, Spiro, Simon, Januszczak, Inez, Wrigglesworth, Ethan, Jenkins, Hannah, Dallas, Tilly, Masters, Nic, Perkins, Matthew W., Deaville, Robert, Druce, Megan, Bogeska, Ruzhica, Milsom, Michael D., Neumann, Björn, Gorman, Frank, Constantino-Casas, Fernando, Peachey, Laura, Bochynska, Diana, Smith, Ewan St. John, Gerstung, Moritz, Campbell, Peter J., Murchison, Elizabeth P., Stratton, Michael R., and Martincorena, Iñigo
- Published
- 2022
- Full Text
- View/download PDF
12. Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors
- Author
-
Herpers, Bram, Eppink, Berina, James, Mark I., Cortina, Carme, Cañellas-Socias, Adrià, Boj, Sylvia F., Hernando-Momblona, Xavier, Glodzik, Dominik, Roovers, Rob C., van de Wetering, Marc, Bartelink-Clements, Carina, Zondag-van der Zande, Vanessa, Mateos, Jara García, Yan, Kuan, Salinaro, Lucia, Basmeleh, Abdul, Fatrai, Szabolcs, Maussang, David, Lammerts van Bueren, Jeroen J., Chicote, Irene, Serna, Garazi, Cabellos, Laia, Ramírez, Lorena, Nuciforo, Paolo, Salazar, Ramon, Santos, Cristina, Villanueva, Alberto, Stephan-Otto Attolini, Camille, Sancho, Elena, Palmer, Hector G., Tabernero, Josep, Stratton, Michael R., de Kruif, John, Logtenberg, Ton, Clevers, Hans, Price, Leo S., Vries, Robert G. J., Batlle, Eduard, and Throsby, Mark
- Published
- 2022
- Full Text
- View/download PDF
13. Mutational landscape of normal epithelial cells in Lynch Syndrome patients
- Author
-
Lee, Bernard C. H., Robinson, Philip S., Coorens, Tim H. H., Yan, Helen H. N., Olafsson, Sigurgeir, Lee-Six, Henry, Sanders, Mathijs A., Siu, Hoi Cheong, Hewinson, James, Yue, Sarah S. K., Tsui, Wai Yin, Chan, Annie S. Y., Chan, Anthony K. W., Ho, Siu Lun, Campbell, Peter J., Martincorena, Inigo, Buczacki, Simon J. A., Yuen, Siu Tsan, Leung, Suet Yi, and Stratton, Michael R.
- Published
- 2022
- Full Text
- View/download PDF
14. Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells
- Author
-
Robinson, Philip S., Thomas, Laura E., Abascal, Federico, Jung, Hyunchul, Harvey, Luke M. R., West, Hannah D., Olafsson, Sigurgeir, Lee, Bernard C. H., Coorens, Tim H. H., Lee-Six, Henry, Butlin, Laura, Lander, Nicola, Truscott, Rebekah, Sanders, Mathijs A., Lensing, Stefanie V., Buczacki, Simon J. A., ten Hoopen, Rogier, Coleman, Nicholas, Brunton-Sim, Roxanne, Rushbrook, Simon, Saeb-Parsy, Kourosh, Lalloo, Fiona, Campbell, Peter J., Martincorena, Iñigo, Sampson, Julian R., and Stratton, Michael R.
- Published
- 2022
- Full Text
- View/download PDF
15. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
- Author
-
Garcia-Alonso, Luz, Handfield, Louis-François, Roberts, Kenny, Nikolakopoulou, Konstantina, Fernando, Ridma C., Gardner, Lucy, Woodhams, Benjamin, Arutyunyan, Anna, Polanski, Krzysztof, Hoo, Regina, Sancho-Serra, Carmen, Li, Tong, Kwakwa, Kwasi, Tuck, Elizabeth, Lorenzi, Valentina, Massalha, Hassan, Prete, Martin, Kleshchevnikov, Vitalii, Tarkowska, Aleksandra, Porter, Tarryn, Mazzeo, Cecilia Icoresi, van Dongen, Stijn, Dabrowska, Monika, Vaskivskyi, Vasyl, Mahbubani, Krishnaa T., Park, Jong-eun, Jimenez-Linan, Mercedes, Campos, Lia, Kiselev, Vladimir Yu., Lindskog, Cecilia, Ayuk, Paul, Prigmore, Elena, Stratton, Michael R., Saeb-Parsy, Kourosh, Moffett, Ashley, Moore, Luiza, Bayraktar, Omer A., Teichmann, Sarah A., Turco, Margherita Y., and Vento-Tormo, Roser
- Published
- 2021
- Full Text
- View/download PDF
16. The long-term effects of chemotherapy on normal blood cells
- Author
-
Mitchell, Emily, primary, Pham, My H., additional, Clay, Anna, additional, Sanghvi, Rashesh, additional, Pietsch, Sandra, additional, Hsu, Joanne I., additional, Jung, Hyunchul, additional, Vedi, Aditi, additional, Moody, Sarah, additional, Wang, Jingwei, additional, Leonganmornlert, Daniel, additional, Chapman, Michael Spencer, additional, Williams, Nicholas, additional, Dunstone, Ellie, additional, Santarsieri, Anna, additional, Cagan, Alex, additional, Machado, Heather E., additional, Baxter, Joanna, additional, Follows, George, additional, Hodson, Daniel J, additional, McDermott, Ultan, additional, Doherty, Gary J., additional, Martincorena, Inigo, additional, Humphreys, Laura, additional, Mahbubani, Krishnaa, additional, Parsy, Kourosh Saeb, additional, Takahashi, Koichi, additional, Goodell, Margaret A., additional, Kent, David, additional, Laurenti, Elisa, additional, Campbell, Peter J., additional, Rahbari, Raheleh, additional, Nangalia, Jyoti, additional, and Stratton, Michael R., additional
- Published
- 2024
- Full Text
- View/download PDF
17. The Complexity of Tobacco Smoke-Induced Mutagenesis in Head and Neck Cancer
- Author
-
Torrens, Laura, primary, Moody, Sarah, additional, de Carvalho, Ana Carolina, additional, Kazachkova, Mariya, additional, Abedi-Ardekani, Behnoush, additional, Cheema, Saamin, additional, Senkin, Sergey, additional, Cattiaux, Thomas, additional, Cortez Cardoso Penha, Ricardo, additional, Atkins, Joshua R, additional, Gaborieau, Valérie, additional, Chopard, Priscilia, additional, Carreira, Christine, additional, Abbasi, Ammal, additional, Bergstrom, Erik N, additional, Vangara, Raviteja, additional, Wang, Jingwei, additional, Fitzgerald, Stephen, additional, Latimer, Calli, additional, Diaz-Gay, Marcos, additional, Jones, David, additional, Teague, Jon, additional, Ribeiro Pinto, Felipe, additional, Kowalski, Luiz Paulo, additional, Polesel, Jerry, additional, Giudici, Fabiola, additional, de Oliveira, José Carlos, additional, Lagiou, Pagona, additional, Lagiou, Areti, additional, Vilensky, Marta, additional, Mates, Dana, additional, Mates, Ioan N, additional, Arantes, Lidia MRB, additional, Reis, Rui, additional, Podesta, Jose Roberto V, additional, von Zeidler, Sandra V, additional, Holcatova, Ivana, additional, Curado, Maria Paula, additional, Canova, Cristina, additional, Fabianova, Elenora, additional, Rodríguez-Urrego, Paula A, additional, Humphreys, Laura, additional, Alexandrov, Ludmil B, additional, Brennan, Paul, additional, Stratton, Michael R, additional, and Perdomo, Sandra, additional
- Published
- 2024
- Full Text
- View/download PDF
18. WCN24-1870 CHRONIC RENAL LESIONS IN PATIENTS WITH RENAL CELL CARCINOMA ARE ASSOCIATED WITH ARISTOLOCHIC ACID EXPOSURE AND FASTER ACCUMULATION OF DNA DAMAGE
- Author
-
ABEDI-ARDEKANI, Behnoush, primary, Martin, Fannie, additional, Senkin, Sergey, additional, Moody, Sarah, additional, Cattiaux, Thomas, additional, Wang, Yichen, additional, Ferreiro-Iglesias, Aida, additional, Gaborieau, Valerie, additional, Perdomo, Sandra, additional, Humphreys, Laura, additional, Stratton, Michael R., additional, Brennan, Paul, additional, Foll, Matthieu, additional, and Alcala, Nicolas, additional
- Published
- 2024
- Full Text
- View/download PDF
19. Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence
- Author
-
Moody, Sarah, Senkin, Sergey, Islam, S. M. Ashiqul, Wang, Jingwei, Nasrollahzadeh, Dariush, Cortez Cardoso Penha, Ricardo, Fitzgerald, Stephen, Bergstrom, Erik N., Atkins, Joshua, He, Yudou, Khandekar, Azhar, Smith-Byrne, Karl, Carreira, Christine, Gaborieau, Valerie, Latimer, Calli, Thomas, Emily, Abnizova, Irina, Bucciarelli, Pauline E., Jones, David, Teague, Jon W., Abedi-Ardekani, Behnoush, Serra, Stefano, Scoazec, Jean-Yves, Saffar, Hiva, Azmoudeh-Ardalan, Farid, Sotoudeh, Masoud, Nikmanesh, Arash, Poustchi, Hossein, Niavarani, Ahmadreza, Gharavi, Samad, Eden, Michael, Richman, Paul, Campos, Lia S., Fitzgerald, Rebecca C., Ribeiro, Luis Felipe, Soares-Lima, Sheila Coelho, Dzamalala, Charles, Mmbaga, Blandina Theophil, Shibata, Tatsuhiro, Menya, Diana, Goldstein, Alisa M., Hu, Nan, Malekzadeh, Reza, Fazel, Abdolreza, McCormack, Valerie, McKay, James, Perdomo, Sandra, Scelo, Ghislaine, Chanudet, Estelle, Humphreys, Laura, Alexandrov, Ludmil B., Brennan, Paul, and Stratton, Michael R.
- Published
- 2021
- Full Text
- View/download PDF
20. Convergent somatic mutations in metabolism genes in chronic liver disease
- Author
-
Ng, Stanley W. K., Rouhani, Foad J., Brunner, Simon F., Brzozowska, Natalia, Aitken, Sarah J., Yang, Ming, Abascal, Federico, Moore, Luiza, Nikitopoulou, Efterpi, Chappell, Lia, Leongamornlert, Daniel, Ivovic, Aleksandra, Robinson, Philip, Butler, Timothy, Sanders, Mathijs A., Williams, Nicholas, Coorens, Tim H. H., Teague, Jon, Raine, Keiran, Butler, Adam P., Hooks, Yvette, Wilson, Beverley, Birtchnell, Natalie, Naylor, Huw, Davies, Susan E., Stratton, Michael R., Martincorena, Iñigo, Rahbari, Raheleh, Frezza, Christian, Hoare, Matthew, and Campbell, Peter J.
- Published
- 2021
- Full Text
- View/download PDF
21. Increased somatic mutation burdens in normal human cells due to defective DNA polymerases
- Author
-
Robinson, Philip S., Coorens, Tim H. H., Palles, Claire, Mitchell, Emily, Abascal, Federico, Olafsson, Sigurgeir, Lee, Bernard C. H., Lawson, Andrew R. J., Lee-Six, Henry, Moore, Luiza, Sanders, Mathijs A., Hewinson, James, Martin, Lynn, Pinna, Claudia M. A., Galavotti, Sara, Rahbari, Raheleh, Campbell, Peter J., Martincorena, Iñigo, Tomlinson, Ian, and Stratton, Michael R.
- Published
- 2021
- Full Text
- View/download PDF
22. Extensive phylogenies of human development inferred from somatic mutations
- Author
-
Coorens, Tim H. H., Moore, Luiza, Robinson, Philip S., Sanghvi, Rashesh, Christopher, Joseph, Hewinson, James, Przybilla, Moritz J., Lawson, Andrew R. J., Spencer Chapman, Michael, Cagan, Alex, Oliver, Thomas R. W., Neville, Matthew D. C., Hooks, Yvette, Noorani, Ayesha, Mitchell, Thomas J., Fitzgerald, Rebecca C., Campbell, Peter J., Martincorena, Iñigo, Rahbari, Raheleh, and Stratton, Michael R.
- Published
- 2021
- Full Text
- View/download PDF
23. The mutational landscape of human somatic and germline cells
- Author
-
Moore, Luiza, Cagan, Alex, Coorens, Tim H. H., Neville, Matthew D. C., Sanghvi, Rashesh, Sanders, Mathijs A., Oliver, Thomas R. W., Leongamornlert, Daniel, Ellis, Peter, Noorani, Ayesha, Mitchell, Thomas J., Butler, Timothy M., Hooks, Yvette, Warren, Anne Y., Jorgensen, Mette, Dawson, Kevin J., Menzies, Andrew, O’Neill, Laura, Latimer, Calli, Teng, Mabel, van Boxtel, Ruben, Iacobuzio-Donahue, Christine A., Martincorena, Inigo, Heer, Rakesh, Campbell, Peter J., Fitzgerald, Rebecca C., Stratton, Michael R., and Rahbari, Raheleh
- Published
- 2021
- Full Text
- View/download PDF
24. The driver landscape of sporadic chordoma.
- Author
-
Tarpey, Patrick S, Behjati, Sam, Young, Matthew D, Martincorena, Inigo, Alexandrov, Ludmil B, Farndon, Sarah J, Guzzo, Charlotte, Hardy, Claire, Latimer, Calli, Butler, Adam P, Teague, Jon W, Shlien, Adam, Futreal, P Andrew, Shah, Sohrab, Bashashati, Ali, Jamshidi, Farzad, Nielsen, Torsten O, Huntsman, David, Baumhoer, Daniel, Brandner, Sebastian, Wunder, Jay, Dickson, Brendan, Cogswell, Patricia, Sommer, Josh, Phillips, Joanna J, Amary, M Fernanda, Tirabosco, Roberto, Pillay, Nischalan, Yip, Stephen, Stratton, Michael R, Flanagan, Adrienne M, and Campbell, Peter J
- Subjects
Cell Line ,Tumor ,Humans ,Chordoma ,Bone Neoplasms ,T-Box Domain Proteins ,Fetal Proteins ,Vesicular Transport Proteins ,Case-Control Studies ,Gene Duplication ,Mutation ,Polymorphism ,Single Nucleotide ,Phosphatidylinositol 3-Kinases ,Class I Phosphatidylinositol 3-Kinases ,Cell Line ,Tumor ,Polymorphism ,Single Nucleotide - Abstract
Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma.Chordoma is a rare often incurable malignant bone tumour. Here, the authors investigate driver mutations of sporadic chordoma in 104 cases, revealing duplications in notochordal transcription factor brachyury (T), PI3K signalling mutations, and mutations in LYST, a potential novel cancer gene in chordoma.
- Published
- 2017
25. Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.
- Author
-
Ju, Young Seok, Martincorena, Inigo, Gerstung, Moritz, Petljak, Mia, Alexandrov, Ludmil B, Rahbari, Raheleh, Wedge, David C, Davies, Helen R, Ramakrishna, Manasa, Fullam, Anthony, Martin, Sancha, Alder, Christopher, Patel, Nikita, Gamble, Steve, O'Meara, Sarah, Giri, Dilip D, Sauer, Torril, Pinder, Sarah E, Purdie, Colin A, Borg, Åke, Stunnenberg, Henk, van de Vijver, Marc, Tan, Benita KT, Caldas, Carlos, Tutt, Andrew, Ueno, Naoto T, van 't Veer, Laura J, Martens, John WM, Sotiriou, Christos, Knappskog, Stian, Span, Paul N, Lakhani, Sunil R, Eyfjörd, Jórunn Erla, Børresen-Dale, Anne-Lise, Richardson, Andrea, Thompson, Alastair M, Viari, Alain, Hurles, Matthew E, Nik-Zainal, Serena, Campbell, Peter J, and Stratton, Michael R
- Subjects
Blood Cells ,Humans ,Mutagenesis ,Cell Lineage ,Embryonic Development ,Mutation ,Mosaicism ,Germ-Line Mutation ,Genome ,Human ,Adult ,Embryo ,Mammalian ,Mutation Rate ,Embryo ,Mammalian ,Genome ,Human ,General Science & Technology - Abstract
Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues. Although it is known that gross chromosomal abnormalities are remarkably common in early human embryos, our understanding of early embryonic somatic mutations is very limited. Here we use whole-genome sequences of normal blood from 241 adults to identify 163 early embryonic mutations. We estimate that approximately three base substitution mutations occur per cell per cell-doubling event in early human embryogenesis and these are mainly attributable to two known mutational signatures. We used the mutations to reconstruct developmental lineages of adult cells and demonstrate that the two daughter cells of many early embryonic cell-doubling events contribute asymmetrically to adult blood at an approximately 2:1 ratio. This study therefore provides insights into the mutation rates, mutational processes and developmental outcomes of cell dynamics that operate during early human embryogenesis.
- Published
- 2017
26. Somatic mutation landscapes at single-molecule resolution
- Author
-
Abascal, Federico, Harvey, Luke M. R., Mitchell, Emily, Lawson, Andrew R. J., Lensing, Stefanie V., Ellis, Peter, Russell, Andrew J. C., Alcantara, Raul E., Baez-Ortega, Adrian, Wang, Yichen, Kwa, Eugene Jing, Lee-Six, Henry, Cagan, Alex, Coorens, Tim H. H., Chapman, Michael Spencer, Olafsson, Sigurgeir, Leonard, Steven, Jones, David, Machado, Heather E., Davies, Megan, Øbro, Nina F., Mahubani, Krishnaa T., Allinson, Kieren, Gerstung, Moritz, Saeb-Parsy, Kourosh, Kent, David G., Laurenti, Elisa, Stratton, Michael R., Rahbari, Raheleh, Campbell, Peter J., Osborne, Robert J., and Martincorena, Iñigo
- Published
- 2021
- Full Text
- View/download PDF
27. Author Correction: The repertoire of mutational signatures in human cancer
- Author
-
Alexandrov, Ludmil B., Kim, Jaegil, Haradhvala, Nicholas J., Huang, Mi Ni, Tian Ng, Alvin Wei, Wu, Yang, Boot, Arnoud, Covington, Kyle R., Gordenin, Dmitry A., Bergstrom, Erik N., Islam, S. M. Ashiqul, Lopez-Bigas, Nuria, Klimczak, Leszek J., McPherson, John R., Morganella, Sandro, Sabarinathan, Radhakrishnan, Wheeler, David A., Mustonen, Ville, Getz, Gad, Rozen, Steven G., and Stratton, Michael R.
- Published
- 2023
- Full Text
- View/download PDF
28. Author Correction: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
- Author
-
Garcia-Alonso, Luz, Handfield, Louis-François, Roberts, Kenny, Nikolakopoulou, Konstantina, Fernando, Ridma C., Gardner, Lucy, Woodhams, Benjamin, Arutyunyan, Anna, Polanski, Krzysztof, Hoo, Regina, Sancho-Serra, Carmen, Li, Tong, Kwakwa, Kwasi, Tuck, Elizabeth, Lorenzi, Valentina, Massalha, Hassan, Prete, Martin, Kleshchevnikov, Vitalii, Tarkowska, Aleksandra, Porter, Tarryn, Mazzeo, Cecilia Icoresi, van Dongen, Stijn, Dabrowska, Monika, Vaskivskyi, Vasyl, Mahbubani, Krishnaa T., Park, Jong-eun, Jimenez-Linan, Mercedes, Campos, Lia, Kiselev, Vladimir Yu., Lindskog, Cecilia, Ayuk, Paul, Prigmore, Elena, Stratton, Michael R., Saeb-Parsy, Kourosh, Moffett, Ashley, Moore, Luiza, Bayraktar, Omer A., Teichmann, Sarah A., Turco, Margherita Y., and Vento-Tormo, Roser
- Published
- 2023
- Full Text
- View/download PDF
29. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment
- Author
-
Díaz-Gay, Marcos, primary, Vangara, Raviteja, additional, Barnes, Mark, additional, Wang, Xi, additional, Islam, S M Ashiqul, additional, Vermes, Ian, additional, Duke, Stephen, additional, Narasimman, Nithish Bharadhwaj, additional, Yang, Ting, additional, Jiang, Zichen, additional, Moody, Sarah, additional, Senkin, Sergey, additional, Brennan, Paul, additional, Stratton, Michael R, additional, and Alexandrov, Ludmil B, additional
- Published
- 2023
- Full Text
- View/download PDF
30. Mutagenicity of acrylamide and glycidamide in human TP53 knock-in (Hupki) mouse embryo fibroblasts
- Author
-
Hölzl-Armstrong, Lisa, Kucab, Jill E., Moody, Sarah, Zwart, Edwin P., Loutkotová, Lucie, Duffy, Veronica, Luijten, Mirjam, Gamboa da Costa, Gonçalo, Stratton, Michael R., Phillips, David H., and Arlt, Volker M.
- Published
- 2020
- Full Text
- View/download PDF
31. The mutational landscape of normal human endometrial epithelium
- Author
-
Moore, Luiza, Leongamornlert, Daniel, Coorens, Tim H. H., Sanders, Mathijs A., Ellis, Peter, Dentro, Stefan C., Dawson, Kevin J., Butler, Tim, Rahbari, Raheleh, Mitchell, Thomas J., Maura, Francesco, Nangalia, Jyoti, Tarpey, Patrick S., Brunner, Simon F., Lee-Six, Henry, Hooks, Yvette, Moody, Sarah, Mahbubani, Krishnaa T., Jimenez-Linan, Mercedes, Brosens, Jan J., Iacobuzio-Donahue, Christine A., Martincorena, Inigo, Saeb-Parsy, Kourosh, Campbell, Peter J., and Stratton, Michael R.
- Published
- 2020
- Full Text
- View/download PDF
32. Tobacco smoking and somatic mutations in human bronchial epithelium
- Author
-
Yoshida, Kenichi, Gowers, Kate H. C., Lee-Six, Henry, Chandrasekharan, Deepak P., Coorens, Tim, Maughan, Elizabeth F., Beal, Kathryn, Menzies, Andrew, Millar, Fraser R., Anderson, Elizabeth, Clarke, Sarah E., Pennycuick, Adam, Thakrar, Ricky M., Butler, Colin R., Kakiuchi, Nobuyuki, Hirano, Tomonori, Hynds, Robert E., Stratton, Michael R., Martincorena, Iñigo, Janes, Sam M., and Campbell, Peter J.
- Published
- 2020
- Full Text
- View/download PDF
33. Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma
- Author
-
Noorani, Ayesha, Li, Xiaodun, Goddard, Martin, Crawte, Jason, Alexandrov, Ludmil B., Secrier, Maria, Eldridge, Matthew D., Bower, Lawrence, Weaver, Jamie, Lao-Sirieix, Pierre, Martincorena, Inigo, Debiram-Beecham, Irene, Grehan, Nicola, MacRae, Shona, Malhotra, Shalini, Miremadi, Ahmad, Thomas, Tabitha, Galbraith, Sarah, Petersen, Lorraine, Preston, Stephen D., Gilligan, David, Hindmarsh, Andrew, Hardwick, Richard H., Stratton, Michael R., Wedge, David C., and Fitzgerald, Rebecca C.
- Published
- 2020
- Full Text
- View/download PDF
34. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
- Author
-
Ju, Young Seok, Tubio, Jose MC, Mifsud, William, Fu, Beiyuan, Davies, Helen R, Ramakrishna, Manasa, Li, Yilong, Yates, Lucy, Gundem, Gunes, Tarpey, Patrick S, Behjati, Sam, Papaemmanuil, Elli, Martin, Sancha, Fullam, Anthony, Gerstung, Moritz, Group, ICGC Prostate Cancer Working, Group, ICGC Bone Cancer Working, Group, ICGC Breast Cancer Working, Nangalia, Jyoti, Green, Anthony R, Caldas, Carlos, Borg, Åke, Tutt, Andrew, Lee, Ming Ta Michael, Veer, Laura J van't, Tan, Benita KT, Aparicio, Samuel, Span, Paul N, Martens, John WM, Knappskog, Stian, Vincent-Salomon, Anne, Børresen-Dale, Anne-Lise, Eyfjörd, Jórunn Erla, Flanagan, Adrienne M, Foster, Christopher, Neal, David E, Cooper, Colin, Eeles, Rosalind, Lakhani, Sunil R, Desmedt, Christine, Thomas, Gilles, Richardson, Andrea L, Purdie, Colin A, Thompson, Alastair M, McDermott, Ultan, Yang, Fengtang, Nik-Zainal, Serena, Campbell, Peter J, and Stratton, Michael R
- Subjects
Biochemistry and Cell Biology ,Genetics ,Biological Sciences ,Stem Cell Research - Nonembryonic - Human ,Human Genome ,Stem Cell Research ,Cancer ,1.1 Normal biological development and functioning ,Underpinning research ,Aetiology ,2.1 Biological and endogenous factors ,Generic health relevance ,Amino Acid Sequence ,Cell Line ,Tumor ,Cell Nucleus ,Chromosomes ,DNA Copy Number Variations ,DNA End-Joining Repair ,DNA Replication ,DNA ,Mitochondrial ,Genome ,Human ,Genome ,Mitochondrial ,HeLa Cells ,Humans ,In Situ Hybridization ,Fluorescence ,Mitochondria ,Molecular Sequence Data ,Neoplasms ,Reproducibility of Results ,Sequence Analysis ,DNA ,ICGC Prostate Cancer Working Group ,ICGC Bone Cancer Working Group ,ICGC Breast Cancer Working Group ,Hela Cells ,Medical and Health Sciences ,Bioinformatics - Abstract
Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.
- Published
- 2015
35. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue
- Author
-
Cooper, Colin S, Eeles, Rosalind, Wedge, David C, Van Loo, Peter, Gundem, Gunes, Alexandrov, Ludmil B, Kremeyer, Barbara, Butler, Adam, Lynch, Andrew G, Camacho, Niedzica, Massie, Charlie E, Kay, Jonathan, Luxton, Hayley J, Edwards, Sandra, Kote-Jarai, Zsofia, Dennis, Nening, Merson, Sue, Leongamornlert, Daniel, Zamora, Jorge, Corbishley, Cathy, Thomas, Sarah, Nik-Zainal, Serena, Ramakrishna, Manasa, O'Meara, Sarah, Matthews, Lucy, Clark, Jeremy, Hurst, Rachel, Mithen, Richard, Bristow, Robert G, Boutros, Paul C, Fraser, Michael, Cooke, Susanna, Raine, Keiran, Jones, David, Menzies, Andrew, Stebbings, Lucy, Hinton, Jon, Teague, Jon, McLaren, Stuart, Mudie, Laura, Hardy, Claire, Anderson, Elizabeth, Joseph, Olivia, Goody, Victoria, Robinson, Ben, Maddison, Mark, Gamble, Stephen, Greenman, Christopher, Berney, Dan, Hazell, Steven, Livni, Naomi, Fisher, Cyril, Ogden, Christopher, Kumar, Pardeep, Thompson, Alan, Woodhouse, Christopher, Nicol, David, Mayer, Erik, Dudderidge, Tim, Shah, Nimish C, Gnanapragasam, Vincent, Voet, Thierry, Campbell, Peter, Futreal, Andrew, Easton, Douglas, Warren, Anne Y, Foster, Christopher S, Stratton, Michael R, Whitaker, Hayley C, McDermott, Ultan, Brewer, Daniel S, and Neal, David E
- Subjects
Human Genome ,Urologic Diseases ,Prevention ,Genetics ,Prostate Cancer ,Cancer ,Aging ,Case-Control Studies ,Cell Lineage ,Clonal Evolution ,Clone Cells ,DNA Mutational Analysis ,Humans ,Male ,Mutation ,Neoplasms ,Multiple Primary ,Phylogeny ,Prostate ,Prostatic Neoplasms ,ICGC Prostate Group ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.
- Published
- 2015
36. Somatic mutant clones colonize the human esophagus with age
- Author
-
Martincorena, Iñigo, Fowler, Joanna C., Wabik, Agnieszka, Lawson, Andrew R. J., Abascal, Federico, Hall, Michael W. J., Cagan, Alex, Murai, Kasumi, Mahbubani, Krishnaa, Stratton, Michael R., Fitzgerald, Rebecca C., Handford, Penny A., Campbell, Peter J., Saeb-Parsy, Kourosh, and Jones, Philip H.
- Published
- 2018
37. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver
- Author
-
Brunner, Simon F., Roberts, Nicola D., Wylie, Luke A., Moore, Luiza, Aitken, Sarah J., Davies, Susan E., Sanders, Mathijs A., Ellis, Pete, Alder, Chris, Hooks, Yvette, Abascal, Federico, Stratton, Michael R., Martincorena, Inigo, Hoare, Matthew, and Campbell, Peter J.
- Published
- 2019
- Full Text
- View/download PDF
38. The landscape of somatic mutation in normal colorectal epithelial cells
- Author
-
Lee-Six, Henry, Olafsson, Sigurgeir, Ellis, Peter, Osborne, Robert J., Sanders, Mathijs A., Moore, Luiza, Georgakopoulos, Nikitas, Torrente, Franco, Noorani, Ayesha, Goddard, Martin, Robinson, Philip, Coorens, Tim H. H., O’Neill, Laura, Alder, Christopher, Wang, Jingwei, Fitzgerald, Rebecca C., Zilbauer, Matthias, Coleman, Nicholas, Saeb-Parsy, Kourosh, Martincorena, Inigo, Campbell, Peter J., and Stratton, Michael R.
- Published
- 2019
- Full Text
- View/download PDF
39. A Survey of Homozygous Deletions in Human Cancer Genomes
- Author
-
Cox, Charles, Bignell, Graham, Greenman, Chris, Stabenau, Arne, Warren, William, Stephens, Philip, Davies, Helen, Watt, Stephen, Teague, Jon, Edkins, Sara, Birney, Ewan, Easton, Douglas F., Wooster, Richard, Futreal, P. Andrew, Stratton, Michael R., and Vogelstein, Bert
- Published
- 2005
40. 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
41. 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
42. Complex landscapes of somatic rearrangement in human breast cancer genomes
- Author
-
Stephens, Philip J, McBride, David J, Lin, Meng-Lay, Varela, Ignacio, Pleasance, Erin D, Simpson, Jared T, Stebbings, Lucy A, Leroy, Catherine, Edkins, Sarah, Mudie, Laura J, Greenman, Chris D, Jia, Mingming, Latimer, Calli, Teague, Jon W, Lau, King Wai, Burton, John, Quail, Michael A, Swerdlow, Harold, Churcher, Carol, Natrajan, Rachael, Sieuwerts, Anieta M, Martens, John WM, Silver, Daniel P, Langerød, Anita, Russnes, Hege EG, Foekens, John A, Reis-Filho, Jorge S, van ’t Veer, Laura, Richardson, Andrea L, Børresen-Dale, Anne-Lise, Campbell, Peter J, Futreal, P Andrew, and Stratton, Michael R
- Subjects
Cancer ,Human Genome ,Breast Cancer ,Genetics ,Aetiology ,2.1 Biological and endogenous factors ,Breast Neoplasms ,Cell Line ,Tumor ,Cells ,Cultured ,Chromosome Aberrations ,DNA Breaks ,Female ,Gene Rearrangement ,Genome ,Human ,Genomic Library ,Humans ,Sequence Analysis ,DNA ,General Science & Technology - Abstract
Multiple somatic rearrangements are often found in cancer genomes; however, the underlying processes of rearrangement and their contribution to cancer development are poorly characterized. Here we use a paired-end sequencing strategy to identify somatic rearrangements in breast cancer genomes. There are more rearrangements in some breast cancers than previously appreciated. Rearrangements are more frequent over gene footprints and most are intrachromosomal. Multiple rearrangement architectures are present, but tandem duplications are particularly common in some cancers, perhaps reflecting a specific defect in DNA maintenance. Short overlapping sequences at most rearrangement junctions indicate that these have been mediated by non-homologous end-joining DNA repair, although varying sequence patterns indicate that multiple processes of this type are operative. Several expressed in-frame fusion genes were identified but none was recurrent. The study provides a new perspective on cancer genomes, highlighting the diversity of somatic rearrangements and their potential contribution to cancer development.
- Published
- 2009
43. Evaluation of Linkage of Breast Cancer to the Putative BRCA3 Locus on Chromosome 13q21 in 128 Multiple Case Families from the Breast Cancer Linkage Consortium
- Author
-
Thompson, Deborah, Szabo, Csilla I., Mangion, Jon, Oldenburg, Rogier A., Odefrey, Fabrice, Seal, Sheila, Barfoot, Rita, Kroeze-Jansema, Karin, Teare, Dawn, Rahman, Nazneen, Renard, Hélène, Mann, Graham, Hopper, John L., Buys, Saundra S., Andrulis, Irene L., Senie, Ruby, Daly, Mary B., West, Dee, Ostrander, Elaine A., Offit, Ken, Peretz, Tamar, Osorio, Ana, Benitez, J., Nathanson, Katherine L., Sinilnikova, Olga M., Oláh, Edith, Bignon, Yves-Jean, Ruiz, Pablo, Badzioch, Michael D., Futreal, Andrew P., Phelan, Catherine M., Narod, Steven A., Lynch, Henry T., Eeles, Ros A., Meijers-Heijboer, Hanne, Stoppa-Lyonnet, Dominique, Couch, Fergus J., Eccles, Diana M., Evans, D. Gareth, Chang-Claude, Jenny, Lenoir, Gilbert, Weber, Barbara L., Devilee, Peter, Easton, Douglas F., Goldgar, David E., and Stratton, Michael R.
- Published
- 2002
44. Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors
- Author
-
Cheng, Jiqiu, Demeulemeester, Jonas, Wedge, David C., Vollan, Hans Kristian M., Pitt, Jason J., Russnes, Hege G., Pandey, Bina P., Nilsen, Gro, Nord, Silje, Bignell, Graham R., White, Kevin P., Børresen-Dale, Anne-Lise, Campbell, Peter J., Kristensen, Vessela N., Stratton, Michael R., Lingjærde, Ole Christian, Moreau, Yves, and Van Loo, Peter
- Published
- 2019
- Full Text
- View/download PDF
45. Population dynamics of normal human blood inferred from somatic mutations
- Author
-
Lee-Six, Henry, Øbro, Nina Friesgaard, Shepherd, Mairi S., Grossmann, Sebastian, Dawson, Kevin, Belmonte, Miriam, Osborne, Robert J., Huntly, Brian J. P., Martincorena, Inigo, Anderson, Elizabeth, O’Neill, Laura, Stratton, Michael R., Laurenti, Elisa, Green, Anthony R., Kent, David G., and Campbell, Peter J.
- Published
- 2018
- Full Text
- View/download PDF
46. Intra-tumour diversification in colorectal cancer at the single-cell level
- Author
-
Roerink, Sophie F., Sasaki, Nobuo, Lee-Six, Henry, Young, Matthew D., Alexandrov, Ludmil B., Behjati, Sam, Mitchell, Thomas J., Grossmann, Sebastian, Lightfoot, Howard, Egan, David A., Pronk, Apollo, Smakman, Niels, van Gorp, Joost, Anderson, Elizabeth, Gamble, Stephen J., Alder, Chris, van de Wetering, Marc, Campbell, Peter J., Stratton, Michael R., and Clevers, Hans
- Published
- 2018
- Full Text
- View/download PDF
47. The evolution of two transmissible cancers in Tasmanian devils
- Author
-
Stammnitz, Maximilian R., primary, Gori, Kevin, additional, Kwon, Young Mi, additional, Harry, Edward, additional, Martin, Fergal J., additional, Billis, Konstantinos, additional, Cheng, Yuanyuan, additional, Baez-Ortega, Adrian, additional, Chow, William, additional, Comte, Sebastien, additional, Eggertsson, Hannes, additional, Fox, Samantha, additional, Hamede, Rodrigo, additional, Jones, Menna, additional, Lazenby, Billie, additional, Peck, Sarah, additional, Pye, Ruth, additional, Quail, Michael A., additional, Swift, Kate, additional, Wang, Jinhong, additional, Wood, Jonathan, additional, Howe, Kerstin, additional, Stratton, Michael R., additional, Ning, Zemin, additional, and Murchison, Elizabeth P., additional
- Published
- 2023
- Full Text
- View/download PDF
48. Abstract 1168: Mutational processes in tumour-adjacent normal kidneys across countries with varying cancer incidence rates
- Author
-
Wang, Yichen, primary, Moody, Sarah, additional, Abedi-Ardekani, Behnoush, additional, Latimer, Calli, additional, Cheema, Saamin, additional, Wang, Jingwei, additional, Fitzgerald, Stephen, additional, Humphreys, Laura, additional, Brennan, Paul, additional, and Stratton, Michael R., additional
- Published
- 2023
- Full Text
- View/download PDF
49. Supplementary Information from Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency
- Author
-
Davies, Helen, primary, Morganella, Sandro, primary, Purdie, Colin A., primary, Jang, Se Jin, primary, Borgen, Elin, primary, Russnes, Hege, primary, Glodzik, Dominik, primary, Zou, Xueqing, primary, Viari, Alain, primary, Richardson, Andrea L., primary, Børresen-Dale, Anne-Lise, primary, Thompson, Alastair, primary, Eyfjord, Jorunn E., primary, Kong, Gu, primary, Stratton, Michael R., primary, and Nik-Zainal, Serena, primary
- Published
- 2023
- Full Text
- View/download PDF
50. Supplementary Table 2 from Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency
- Author
-
Davies, Helen, primary, Morganella, Sandro, primary, Purdie, Colin A., primary, Jang, Se Jin, primary, Borgen, Elin, primary, Russnes, Hege, primary, Glodzik, Dominik, primary, Zou, Xueqing, primary, Viari, Alain, primary, Richardson, Andrea L., primary, Børresen-Dale, Anne-Lise, primary, Thompson, Alastair, primary, Eyfjord, Jorunn E., primary, Kong, Gu, primary, Stratton, Michael R., primary, and Nik-Zainal, Serena, primary
- Published
- 2023
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.