377 results on '"Litchfield, Kevin"'
Search Results
2. Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer
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Kayhanian, Hamzeh, Cross, William, van der Horst, Suzanne E. M., Barmpoutis, Panagiotis, Lakatos, Eszter, Caravagna, Giulio, Zapata, Luis, Van Hoeck, Arne, Middelkamp, Sjors, Litchfield, Kevin, Steele, Christopher, Waddingham, William, Patel, Dominic, Milite, Salvatore, Jin, Chen, Baker, Ann-Marie, Alexander, Daniel C., Khan, Khurum, Hochhauser, Daniel, Novelli, Marco, Werner, Benjamin, van Boxtel, Ruben, Hageman, Joris H., Buissant des Amorie, Julian R., Linares, Josep, Ligtenberg, Marjolijn J. L., Nagtegaal, Iris D., Laclé, Miangela M., Moons, Leon M. G., Brosens, Lodewijk A. A., Pillay, Nischalan, Sottoriva, Andrea, Graham, Trevor A., Rodriguez-Justo, Manuel, Shiu, Kai-Keen, Snippert, Hugo J. G., and Jansen, Marnix
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- 2024
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3. Genomic and immune heterogeneity of multiple synchronous lung adenocarcinoma at different developmental stages
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Zhao, Yue, Gao, Jian, Wang, Jun, Fan, Fanfan, Cheng, Chao, Qian, Danwen, Guo, Ran, Zhang, Yang, Ye, Ting, Augustine, Marcellus, Lin, Yicong, Shang, Jun, Li, Hang, Pan, Yunjian, Huang, Qingyuan, Chen, Haiqing, Han, Han, Gao, Zhendong, Wang, Qiming, Zhang, Shiyue, Zhang, Mou, Fu, Fangqiu, Yan, Yueren, Fernandez Patel, Shanila, Vendramin, Roberto, Yuan, Hui, Zhang, Yawei, Xiang, Jiaqing, Hu, Hong, Sun, Yihua, Li, Yuan, Litchfield, Kevin, Cao, Zhiwei, and Chen, Haiquan
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- 2024
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4. Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma
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Culliford, Richard, Lawrence, Samuel E. D., Mills, Charlie, Tippu, Zayd, Chubb, Daniel, Cornish, Alex J., Browning, Lisa, Kinnersley, Ben, Bentham, Robert, Sud, Amit, Pallikonda, Husayn, Frangou, Anna, Gruber, Andreas J., Litchfield, Kevin, Wedge, David, Larkin, James, Turajlic, Samra, and Houlston, Richard S.
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- 2024
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5. Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response
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Coulton, Alexander, Murai, Jun, Qian, Danwen, Thakkar, Krupa, Lewis, Claire E., and Litchfield, Kevin
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- 2024
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6. Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling
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Hobor, Sebastijan, Al Bakir, Maise, Hiley, Crispin T., Skrzypski, Marcin, Frankell, Alexander M., Bakker, Bjorn, Watkins, Thomas B. K., Markovets, Aleksandra, Dry, Jonathan R., Brown, Andrew P., van der Aart, Jasper, van den Bos, Hilda, Spierings, Diana, Oukrif, Dahmane, Novelli, Marco, Chakrabarti, Turja, Rabinowitz, Adam H., Ait Hassou, Laila, Litière, Saskia, Kerr, D. Lucas, Tan, Lisa, Kelly, Gavin, Moore, David A., Renshaw, Matthew J., Venkatesan, Subramanian, Hill, William, Huebner, Ariana, Martínez-Ruiz, Carlos, Black, James R. M., Wu, Wei, Angelova, Mihaela, McGranahan, Nicholas, Downward, Julian, Chmielecki, Juliann, Barrett, Carl, Litchfield, Kevin, Chew, Su Kit, Blakely, Collin M., de Bruin, Elza C., Foijer, Floris, Vousden, Karen H., Bivona, Trever G., Hynds, Robert E., Kanu, Nnennaya, Zaccaria, Simone, Grönroos, Eva, and Swanton, Charles
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- 2024
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7. Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models
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Hynds, Robert E., Huebner, Ariana, Pearce, David R., Hill, Mark S., Akarca, Ayse U., Moore, David A., Ward, Sophia, Gowers, Kate H. C., Karasaki, Takahiro, Al Bakir, Maise, Wilson, Gareth A., Pich, Oriol, Martínez-Ruiz, Carlos, Hossain, A. S. Md Mukarram, Pearce, Simon P., Sivakumar, Monica, Ben Aissa, Assma, Grönroos, Eva, Chandrasekharan, Deepak, Kolluri, Krishna K., Towns, Rebecca, Wang, Kaiwen, Cook, Daniel E., Bosshard-Carter, Leticia, Naceur-Lombardelli, Cristina, Rowan, Andrew J., Veeriah, Selvaraju, Litchfield, Kevin, Crosbie, Philip A. J., Dive, Caroline, Quezada, Sergio A., Janes, Sam M., Jamal-Hanjani, Mariam, Marafioti, Teresa, McGranahan, Nicholas, and Swanton, Charles
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- 2024
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8. Fcγ receptors and immunomodulatory antibodies in cancer
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Galvez-Cancino, Felipe, Simpson, Alexander P., Costoya, Cristobal, Matos, Ignacio, Qian, Danwen, Peggs, Karl S., Litchfield, Kevin, and Quezada, Sergio A.
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- 2024
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9. Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology
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Ziff, Oliver J., Neeves, Jacob, Mitchell, Jamie, Tyzack, Giulia, Martinez-Ruiz, Carlos, Luisier, Raphaelle, Chakrabarti, Anob M., McGranahan, Nicholas, Litchfield, Kevin, Boulton, Simon J., Al-Chalabi, Ammar, Kelly, Gavin, Humphrey, Jack, and Patani, Rickie
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- 2023
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10. Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer
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Perelli, Luigi, Carbone, Federica, Zhang, Li, Huang, Justin K., Le, Courtney, Khan, Hania, Citron, Francesca, Del Poggetto, Edoardo, Gutschner, Tony, Tomihara, Hideo, Soeung, Melinda, Minelli, Rosalba, Srinivasan, Sanjana, Peoples, Michael, Lam, Truong Nguyen Anh, Lundgren, Sebastian, Xia, Ruohan, Zhu, Cihui, Mohamed, Alaa M. T., Zhang, Jianhua, Sircar, Kanishka, Sgambato, Alessandro, Gao, JianJun, Jonasch, Eric, Draetta, Giulio F., Futreal, Andrew, Bakouny, Ziad, Van Allen, Eliezer M., Choueiri, Toni, Signoretti, Sabina, Msaouel, Pavlos, Litchfield, Kevin, Turajlic, Samra, Wang, Linghua, Chen, Ying Bei, Di Natale, Renzo G., Hakimi, A. Ari, Giuliani, Virginia, Heffernan, Timothy P., Viale, Andrea, Bristow, Christopher A., Tannir, Nizar M., Carugo, Alessandro, and Genovese, Giannicola
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- 2023
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11. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance
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Chu, Yanshuo, Dai, Enyu, Li, Yating, Han, Guangchun, Pei, Guangsheng, Ingram, Davis R., Thakkar, Krupa, Qin, Jiang-Jiang, Dang, Minghao, Le, Xiuning, Hu, Can, Deng, Qing, Sinjab, Ansam, Gupta, Pravesh, Wang, Ruiping, Hao, Dapeng, Peng, Fuduan, Yan, Xinmiao, Liu, Yunhe, Song, Shumei, Zhang, Shaojun, Heymach, John V., Reuben, Alexandre, Elamin, Yasir Y., Pizzi, Melissa P., Lu, Yang, Lazcano, Rossana, Hu, Jian, Li, Mingyao, Curran, Michael, Futreal, Andrew, Maitra, Anirban, Jazaeri, Amir A., Ajani, Jaffer A., Swanton, Charles, Cheng, Xiang-Dong, Abbas, Hussein A., Gillison, Maura, Bhat, Krishna, Lazar, Alexander J., Green, Michael, Litchfield, Kevin, Kadara, Humam, Yee, Cassian, and Wang, Linghua
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- 2023
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12. The proteasome regulator PSME4 modulates proteasome activity and antigen diversity to abrogate antitumor immunity in NSCLC
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Javitt, Aaron, Shmueli, Merav D., Kramer, Matthias P., Kolodziejczyk, Aleksandra A., Cohen, Ivan J., Radomir, Lihi, Sheban, Daoud, Kamer, Iris, Litchfield, Kevin, Bab-Dinitz, Elizabeta, Zadok, Oranit, Neiens, Vanessa, Ulman, Adi, Wolf-Levy, Hila, Eisenberg-Lerner, Avital, Kacen, Assaf, Alon, Michal, Rêgo, Ana Toste, Stacher-Priehse, Elvira, Lindner, Michael, Koch, Ina, Bar, Jair, Swanton, Charles, Samuels, Yardena, Levin, Yishai, da Fonseca, Paula C. A., Elinav, Eran, Friedman, Nir, Meiners, Silke, and Merbl, Yifat
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- 2023
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13. Antibodies against endogenous retroviruses promote lung cancer immunotherapy
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Ng, Kevin W., Boumelha, Jesse, Enfield, Katey S. S., Almagro, Jorge, Cha, Hongui, Pich, Oriol, Karasaki, Takahiro, Moore, David A., Salgado, Roberto, Sivakumar, Monica, Young, George, Molina-Arcas, Miriam, de Carné Trécesson, Sophie, Anastasiou, Panayiotis, Fendler, Annika, Au, Lewis, Shepherd, Scott T. C., Martínez-Ruiz, Carlos, Puttick, Clare, Black, James R. M., Watkins, Thomas B. K., Kim, Hyemin, Shim, Seohee, Faulkner, Nikhil, Attig, Jan, Veeriah, Selvaraju, Magno, Neil, Ward, Sophia, Frankell, Alexander M., Al Bakir, Maise, Lim, Emilia L., Hill, Mark S., Wilson, Gareth A., Cook, Daniel E., Birkbak, Nicolai J., Behrens, Axel, Yousaf, Nadia, Popat, Sanjay, Hackshaw, Allan, Hiley, Crispin T., Litchfield, Kevin, McGranahan, Nicholas, Jamal-Hanjani, Mariam, Larkin, James, Lee, Se-Hoon, Turajlic, Samra, Swanton, Charles, Downward, Julian, and Kassiotis, George
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- 2023
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14. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA
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Abbosh, Christopher, Frankell, Alexander M., Harrison, Thomas, Kisistok, Judit, Garnett, Aaron, Johnson, Laura, Veeriah, Selvaraju, Moreau, Mike, Chesh, Adrian, Chaunzwa, Tafadzwa L., Weiss, Jakob, Schroeder, Morgan R., Ward, Sophia, Grigoriadis, Kristiana, Shahpurwalla, Aamir, Litchfield, Kevin, Puttick, Clare, Biswas, Dhruva, Karasaki, Takahiro, Black, James R. M., Martínez-Ruiz, Carlos, Bakir, Maise Al, Pich, Oriol, Watkins, Thomas B. K., Lim, Emilia L., Huebner, Ariana, Moore, David A., Godin-Heymann, Nadia, L’Hernault, Anne, Bye, Hannah, Odell, Aaron, Roberts, Paula, Gomes, Fabio, Patel, Akshay J., Manzano, Elizabeth, Hiley, Crispin T., Carey, Nicolas, Riley, Joan, Cook, Daniel E., Hodgson, Darren, Stetson, Daniel, Barrett, J. Carl, Kortlever, Roderik M., Evan, Gerard I., Hackshaw, Allan, Daber, Robert D., Shaw, Jacqui A., Aerts, Hugo J. W. L., Licon, Abel, Stahl, Josh, Jamal-Hanjani, Mariam, Birkbak, Nicolai J., McGranahan, Nicholas, and Swanton, Charles
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- 2023
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15. Genomic–transcriptomic evolution in lung cancer and metastasis
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Martínez-Ruiz, Carlos, Black, James R. M., Puttick, Clare, Hill, Mark S., Demeulemeester, Jonas, Larose Cadieux, Elizabeth, Thol, Kerstin, Jones, Thomas P., Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Prymas, Paulina, Rowan, Andrew, Ward, Sophia, Cubitt, Laura, Athanasopoulou, Foteini, Pich, Oriol, Karasaki, Takahiro, Moore, David A., Salgado, Roberto, Colliver, Emma, Castignani, Carla, Dietzen, Michelle, Huebner, Ariana, Al Bakir, Maise, Tanić, Miljana, Watkins, Thomas B. K., Lim, Emilia L., Al-Rashed, Ali M., Lang, Danny, Clements, James, Cook, Daniel E., Rosenthal, Rachel, Wilson, Gareth A., Frankell, Alexander M., de Carné Trécesson, Sophie, East, Philip, Kanu, Nnennaya, Litchfield, Kevin, Birkbak, Nicolai J., Hackshaw, Allan, Beck, Stephan, Van Loo, Peter, Jamal-Hanjani, Mariam, Swanton, Charles, and McGranahan, Nicholas
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- 2023
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16. Lung adenocarcinoma promotion by air pollutants
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Hill, William, Lim, Emilia L., Weeden, Clare E., Lee, Claudia, Augustine, Marcellus, Chen, Kezhong, Kuan, Feng-Che, Marongiu, Fabio, Evans, Jr, Edward J., Moore, David A., Rodrigues, Felipe S., Pich, Oriol, Bakker, Bjorn, Cha, Hongui, Myers, Renelle, van Maldegem, Febe, Boumelha, Jesse, Veeriah, Selvaraju, Rowan, Andrew, Naceur-Lombardelli, Cristina, Karasaki, Takahiro, Sivakumar, Monica, De, Swapnanil, Caswell, Deborah R., Nagano, Ai, Black, James R. M., Martínez-Ruiz, Carlos, Ryu, Min Hyung, Huff, Ryan D., Li, Shijia, Favé, Marie-Julie, Magness, Alastair, Suárez-Bonnet, Alejandro, Priestnall, Simon L., Lüchtenborg, Margreet, Lavelle, Katrina, Pethick, Joanna, Hardy, Steven, McRonald, Fiona E., Lin, Meng-Hung, Troccoli, Clara I., Ghosh, Moumita, Miller, York E., Merrick, Daniel T., Keith, Robert L., Al Bakir, Maise, Bailey, Chris, Hill, Mark S., Saal, Lao H., Chen, Yilun, George, Anthony M., Abbosh, Christopher, Kanu, Nnennaya, Lee, Se-Hoon, McGranahan, Nicholas, Berg, Christine D., Sasieni, Peter, Houlston, Richard, Turnbull, Clare, Lam, Stephen, Awadalla, Philip, Grönroos, Eva, Downward, Julian, Jacks, Tyler, Carlsten, Christopher, Malanchi, Ilaria, Hackshaw, Allan, Litchfield, Kevin, DeGregori, James, Jamal-Hanjani, Mariam, and Swanton, Charles
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- 2023
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17. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx
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Karasaki, Takahiro, Moore, David A., Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Magno, Neil, Ward, Sophia, Bakir, Maise Al, Watkins, Thomas B. K., Grigoriadis, Kristiana, Huebner, Ariana, Hill, Mark S., Frankell, Alexander M., Abbosh, Christopher, Puttick, Clare, Zhai, Haoran, Gimeno-Valiente, Francisco, Saghafinia, Sadegh, Kanu, Nnennaya, Dietzen, Michelle, Pich, Oriol, Lim, Emilia L., Martínez-Ruiz, Carlos, Black, James R. M., Biswas, Dhruva, Campbell, Brittany B., Lee, Claudia, Colliver, Emma, Enfield, Katey S. S., Hessey, Sonya, Hiley, Crispin T., Zaccaria, Simone, Litchfield, Kevin, Birkbak, Nicolai J., Cadieux, Elizabeth Larose, Demeulemeester, Jonas, Van Loo, Peter, Adusumilli, Prasad S., Tan, Kay See, Cheema, Waseem, Sanchez-Vega, Francisco, Jones, David R., Rekhtman, Natasha, Travis, William D., Hackshaw, Allan, Marafioti, Teresa, Salgado, Roberto, Le Quesne, John, Nicholson, Andrew G., McGranahan, Nicholas, Swanton, Charles, and Jamal-Hanjani, Mariam
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- 2023
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18. Melanoma dedifferentiation induced by interferon-gamma epigenetic remodeling in response to anti-PD-1 therapy
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Kim, Yeon Joo, Sheu, Katherine M, Tsoi, Jennifer, Abril-Rodriguez, Gabriel, Medina, Egmidio, Grasso, Catherine S, Torrejon, Davis Y, Champhekar, Ameya S, Litchfield, Kevin, Swanton, Charles, Speiser, Daniel E, Scumpia, Philip O, Hoffmann, Alexander, Graeber, Thomas G, Puig-Saus, Cristina, and Ribas, Antoni
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Human Genome ,Cancer ,Genetics ,Biomarkers ,Tumor ,Cell Dedifferentiation ,Cell Line ,Tumor ,Epigenesis ,Genetic ,Gene Expression Regulation ,Neoplastic ,Humans ,Immune Checkpoint Inhibitors ,Interferon-gamma ,Melanocytes ,Melanoma ,Neoplasm Proteins ,Programmed Cell Death 1 Receptor ,Cancer immunotherapy ,Cytokines ,Oncology ,Medical and Health Sciences ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Melanoma dedifferentiation has been reported to be a state of cellular resistance to targeted therapies and immunotherapies as cancer cells revert to a more primitive cellular phenotype. Here, we show that, counterintuitively, the biopsies of patient tumors that responded to anti-programmed cell death 1 (anti-PD-1) therapy had decreased expression of melanocytic markers and increased neural crest markers, suggesting treatment-induced dedifferentiation. When modeling the effects in vitro, we documented that melanoma cell lines that were originally differentiated underwent a process of neural crest dedifferentiation when continuously exposed to IFN-γ, through global chromatin landscape changes that led to enrichment in specific hyperaccessible chromatin regions. The IFN-γ-induced dedifferentiation signature corresponded with improved outcomes in patients with melanoma, challenging the notion that neural crest dedifferentiation is entirely an adverse phenotype.
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- 2021
19. Melanoma dedifferentiation induced by IFN-γ epigenetic remodeling in response to anti-PD-1 therapy.
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Kim, Yeon Joo, Sheu, Katherine M, Tsoi, Jennifer, Abril-Rodriguez, Gabriel, Medina, Egmidio, Grasso, Catherine S, Torrejon, Davis Y, Champhekar, Ameya S, Litchfield, Kevin, Swanton, Charles, Speiser, Daniel E, Scumpia, Philip O, Hoffmann, Alexander, Graeber, Thomas G, Puig-Saus, Cristina, and Ribas, Antoni
- Subjects
Cancer immunotherapy ,Cytokines ,Oncology ,Immunology ,Medical and Health Sciences - Abstract
Melanoma dedifferentiation has been reported to be a state of cellular resistance to targeted therapies and immunotherapies as cancer cells revert to a more primitive cellular phenotype. Here, we show that, counterintuitively, the biopsies of patient tumors that responded to anti-programmed cell death 1 (anti-PD-1) therapy had decreased expression of melanocytic markers and increased neural crest markers, suggesting treatment-induced dedifferentiation. When modeling the effects in vitro, we documented that melanoma cell lines that were originally differentiated underwent a process of neural crest dedifferentiation when continuously exposed to IFN-γ, through global chromatin landscape changes that led to enrichment in specific hyperaccessible chromatin regions. The IFN-γ-induced dedifferentiation signature corresponded with improved outcomes in patients with melanoma, challenging the notion that neural crest dedifferentiation is entirely an adverse phenotype.
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- 2021
20. Pervasive chromosomal instability and karyotype order in tumour evolution
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Watkins, Thomas BK, Lim, Emilia L, Petkovic, Marina, Elizalde, Sergi, Birkbak, Nicolai J, Wilson, Gareth A, Moore, David A, Grönroos, Eva, Rowan, Andrew, Dewhurst, Sally M, Demeulemeester, Jonas, Dentro, Stefan C, Horswell, Stuart, Au, Lewis, Haase, Kerstin, Escudero, Mickael, Rosenthal, Rachel, Bakir, Maise Al, Xu, Hang, Litchfield, Kevin, Lu, Wei Ting, Mourikis, Thanos P, Dietzen, Michelle, Spain, Lavinia, Cresswell, George D, Biswas, Dhruva, Lamy, Philippe, Nordentoft, Iver, Harbst, Katja, Castro-Giner, Francesc, Yates, Lucy R, Caramia, Franco, Jaulin, Fanny, Vicier, Cécile, Tomlinson, Ian PM, Brastianos, Priscilla K, Cho, Raymond J, Bastian, Boris C, Dyrskjøt, Lars, Jönsson, Göran B, Savas, Peter, Loi, Sherene, Campbell, Peter J, Andre, Fabrice, Luscombe, Nicholas M, Steeghs, Neeltje, Tjan-Heijnen, Vivianne CG, Szallasi, Zoltan, Turajlic, Samra, Jamal-Hanjani, Mariam, Van Loo, Peter, Bakhoum, Samuel F, Schwarz, Roland F, McGranahan, Nicholas, and Swanton, Charles
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Oncology and Carcinogenesis ,Cancer ,Human Genome ,Chromosomal Instability ,Chromosomes ,Human ,Pair 11 ,Chromosomes ,Human ,Pair 8 ,Clone Cells ,Cyclin E ,DNA Copy Number Variations ,Evolution ,Molecular ,Female ,Humans ,Karyotype ,Loss of Heterozygosity ,Male ,Mutagenesis ,Neoplasm Metastasis ,Neoplasms ,Oncogene Proteins ,General Science & Technology - Abstract
Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.
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- 2020
21. Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer
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Martins, Filipe Correia, Couturier, Dominique-Laurent, de Santiago, Ines, Sauer, Carolin Margarethe, Vias, Maria, Angelova, Mihaela, Sanders, Deborah, Piskorz, Anna, Hall, James, Hosking, Karen, Amirthanayagam, Anumithra, Cosulich, Sabina, Carnevalli, Larissa, Davies, Barry, Watkins, Thomas B. K., Funingana, Ionut G., Bolton, Helen, Haldar, Krishnayan, Latimer, John, Baldwin, Peter, Crawford, Robin, Eldridge, Matthew, Basu, Bristi, Jimenez-Linan, Mercedes, Mcpherson, Andrew W., McGranahan, Nicholas, Litchfield, Kevin, Shah, Sohrab P., McNeish, Iain, Caldas, Carlos, Evan, Gerard, Swanton, Charles, and Brenton, James D.
- Published
- 2022
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22. Spatial patterns of tumour growth impact clonal diversification in a computational model and the TRACERx Renal study
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Fu, Xiao, Zhao, Yue, Lopez, Jose I., Rowan, Andrew, Au, Lewis, Fendler, Annika, Hazell, Steve, Xu, Hang, Horswell, Stuart, Shepherd, Scott T. C., Spencer, Charlotte E., Spain, Lavinia, Byrne, Fiona, Stamp, Gordon, O’Brien, Tim, Nicol, David, Augustine, Marcellus, Chandra, Ashish, Rudman, Sarah, Toncheva, Antonia, Furness, Andrew J. S., Pickering, Lisa, Kumar, Santosh, Koh, Dow-Mu, Messiou, Christina, Dafydd, Derfel ap, Orton, Matthew R., Doran, Simon J., Larkin, James, Swanton, Charles, Sahai, Erik, Litchfield, Kevin, Turajlic, Samra, and Bates, Paul A.
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- 2022
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23. Vitamin D regulates microbiome-dependent cancer immunity
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Giampazolias, Evangelos, primary, Pereira da Costa, Mariana, additional, Lam, Khiem C., additional, Lim, Kok Haw Jonathan, additional, Cardoso, Ana, additional, Piot, Cécile, additional, Chakravarty, Probir, additional, Blasche, Sonja, additional, Patel, Swara, additional, Biram, Adi, additional, Castro-Dopico, Tomas, additional, Buck, Michael D., additional, Rodrigues, Richard R., additional, Poulsen, Gry Juul, additional, Palma-Duran, Susana A., additional, Rogers, Neil C., additional, Koufaki, Maria A., additional, Minutti, Carlos M., additional, Wang, Pengbo, additional, Vdovin, Alexander, additional, Frederico, Bruno, additional, Childs, Eleanor, additional, Lee, Sonia, additional, Simpson, Ben, additional, Iseppon, Andrea, additional, Omenetti, Sara, additional, Kelly, Gavin, additional, Goldstone, Robert, additional, Nye, Emma, additional, Suárez-Bonnet, Alejandro, additional, Priestnall, Simon L., additional, MacRae, James I., additional, Zelenay, Santiago, additional, Patil, Kiran Raosaheb, additional, Litchfield, Kevin, additional, Lee, James C., additional, Jess, Tine, additional, Goldszmid, Romina S., additional, and Reis e Sousa, Caetano, additional
- Published
- 2024
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24. Untranslated regions (UTRs) are a potential novel source of neoantigens for personalised immunotherapy
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Sng, Christopher C. T., primary, Kallor, Ashwin Adrian, additional, Simpson, Benjamin S., additional, Bedran, Georges, additional, Alfaro, Javier, additional, and Litchfield, Kevin, additional
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- 2024
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25. Using DNA sequencing data to quantify T cell fraction and therapy response
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Bentham, Robert, Litchfield, Kevin, Watkins, Thomas B. K., Lim, Emilia L., Rosenthal, Rachel, Martínez-Ruiz, Carlos, Hiley, Crispin T., Bakir, Maise Al, Salgado, Roberto, Moore, David A., Jamal-Hanjani, Mariam, Birkbak, Nicolai J., Escudero, Mickael, Stewart, Aengus, Rowan, Andrew, and Goldman, Jacki
- Subjects
Nucleotide sequencing -- Methods ,T cells -- Physiological aspects -- Genetic aspects ,Cellular therapy -- Methods ,DNA sequencing -- Methods ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy.sup.1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-[alpha] gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31-32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes. A robust, cost-effective technique based on whole-exome sequencing data can be used to characterize immune infiltrates, relate the extent of these infiltrates to somatic changes in tumours, and enables prediction of tumour responses to immune checkpoint inhibition therapy., Author(s): Robert Bentham [sup.1] [sup.2] , Kevin Litchfield [sup.2] [sup.3] , Thomas B. K. Watkins [sup.4] , Emilia L. Lim [sup.2] [sup.4] , Rachel Rosenthal [sup.4] , Carlos Martínez-Ruiz [sup.1] [...]
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- 2021
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26. E3 ubiquitin ligase HECTD2 mediates melanoma progression and immune evasion
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Ottina, Eleonora, Panova, Veera, Doglio, Laura, Kazachenka, Anastasiya, Cornish, Georgina, Kirkpatrick, Joanna, Attig, Jan, Young, George R., Litchfield, Kevin, Lesluyes, Tom, Van Loo, Peter, Swanton, Charles, MacRae, James, Tüting, Thomas, and Kassiotis, George
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- 2021
- Full Text
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27. Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases: A Mendelian Randomization Study
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Haycock, Philip C, Burgess, Stephen, Nounu, Aayah, Zheng, Jie, Okoli, George N, Bowden, Jack, Wade, Kaitlin Hazel, Timpson, Nicholas J, Evans, David M, Willeit, Peter, Aviv, Abraham, Gaunt, Tom R, Hemani, Gibran, Mangino, Massimo, Ellis, Hayley Patricia, Kurian, Kathreena M, Pooley, Karen A, Eeles, Rosalind A, Lee, Jeffrey E, Fang, Shenying, Chen, Wei V, Law, Matthew H, Bowdler, Lisa M, Iles, Mark M, Yang, Qiong, Worrall, Bradford B, Markus, Hugh Stephen, Hung, Rayjean J, Amos, Chris I, Spurdle, Amanda B, Thompson, Deborah J, O’Mara, Tracy A, Wolpin, Brian, Amundadottir, Laufey, Stolzenberg-Solomon, Rachael, Trichopoulou, Antonia, Onland-Moret, N Charlotte, Lund, Eiliv, Duell, Eric J, Canzian, Federico, Severi, Gianluca, Overvad, Kim, Gunter, Marc J, Tumino, Rosario, Svenson, Ulrika, van Rij, Andre, Baas, Annette F, Bown, Matthew J, Samani, Nilesh J, van t’Hof, Femke NG, Tromp, Gerard, Jones, Gregory T, Kuivaniemi, Helena, Elmore, James R, Johansson, Mattias, Mckay, James, Scelo, Ghislaine, Carreras-Torres, Robert, Gaborieau, Valerie, Brennan, Paul, Bracci, Paige M, Neale, Rachel E, Olson, Sara H, Gallinger, Steven, Li, Donghui, Petersen, Gloria M, Risch, Harvey A, Klein, Alison P, Han, Jiali, Abnet, Christian C, Freedman, Neal D, Taylor, Philip R, Maris, John M, Aben, Katja K, Kiemeney, Lambertus A, Vermeulen, Sita H, Wiencke, John K, Walsh, Kyle M, Wrensch, Margaret, Rice, Terri, Turnbull, Clare, Litchfield, Kevin, Paternoster, Lavinia, Standl, Marie, Abecasis, Gonçalo R, SanGiovanni, John Paul, Li, Yong, Mijatovic, Vladan, Sapkota, Yadav, Low, Siew-Kee, Zondervan, Krina T, Montgomery, Grant W, Nyholt, Dale R, van Heel, David A, Hunt, Karen, Arking, Dan E, Ashar, Foram N, Sotoodehnia, Nona, Woo, Daniel, and Rosand, Jonathan
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Rare Diseases ,Clinical Research ,Cancer ,Prevention ,Genetics ,Aetiology ,2.1 Biological and endogenous factors ,Adult ,Aged ,Aged ,80 and over ,Cardiovascular Diseases ,Female ,Genetic Predisposition to Disease ,Genome-Wide Association Study ,Germ-Line Mutation ,Humans ,Male ,Mendelian Randomization Analysis ,Middle Aged ,Neoplasms ,Polymorphism ,Single Nucleotide ,Risk Assessment ,Telomere ,Telomere Homeostasis ,Telomeres Mendelian Randomization Collaboration ,Public Health and Health Services ,Oncology and carcinogenesis - Abstract
ImportanceThe causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation.ObjectiveTo conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases.Data sourcesGenomewide association studies (GWAS) published up to January 15, 2015.Study selectionGWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available.Data extraction and synthesisSummary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population.Main outcomes and measuresOdds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation.ResultsSummary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [95% CI, 0.05-0.15]).Conclusions and relevanceIt is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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- 2017
28. Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases: A Mendelian Randomization Study.
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Telomeres Mendelian Randomization Collaboration, Haycock, Philip C, Burgess, Stephen, Nounu, Aayah, Zheng, Jie, Okoli, George N, Bowden, Jack, Wade, Kaitlin Hazel, Timpson, Nicholas J, Evans, David M, Willeit, Peter, Aviv, Abraham, Gaunt, Tom R, Hemani, Gibran, Mangino, Massimo, Ellis, Hayley Patricia, Kurian, Kathreena M, Pooley, Karen A, Eeles, Rosalind A, Lee, Jeffrey E, Fang, Shenying, Chen, Wei V, Law, Matthew H, Bowdler, Lisa M, Iles, Mark M, Yang, Qiong, Worrall, Bradford B, Markus, Hugh Stephen, Hung, Rayjean J, Amos, Chris I, Spurdle, Amanda B, Thompson, Deborah J, O'Mara, Tracy A, Wolpin, Brian, Amundadottir, Laufey, Stolzenberg-Solomon, Rachael, Trichopoulou, Antonia, Onland-Moret, N Charlotte, Lund, Eiliv, Duell, Eric J, Canzian, Federico, Severi, Gianluca, Overvad, Kim, Gunter, Marc J, Tumino, Rosario, Svenson, Ulrika, van Rij, Andre, Baas, Annette F, Bown, Matthew J, Samani, Nilesh J, van t'Hof, Femke NG, Tromp, Gerard, Jones, Gregory T, Kuivaniemi, Helena, Elmore, James R, Johansson, Mattias, Mckay, James, Scelo, Ghislaine, Carreras-Torres, Robert, Gaborieau, Valerie, Brennan, Paul, Bracci, Paige M, Neale, Rachel E, Olson, Sara H, Gallinger, Steven, Li, Donghui, Petersen, Gloria M, Risch, Harvey A, Klein, Alison P, Han, Jiali, Abnet, Christian C, Freedman, Neal D, Taylor, Philip R, Maris, John M, Aben, Katja K, Kiemeney, Lambertus A, Vermeulen, Sita H, Wiencke, John K, Walsh, Kyle M, Wrensch, Margaret, Rice, Terri, Turnbull, Clare, Litchfield, Kevin, Paternoster, Lavinia, Standl, Marie, Abecasis, Gonçalo R, SanGiovanni, John Paul, Li, Yong, Mijatovic, Vladan, Sapkota, Yadav, Low, Siew-Kee, Zondervan, Krina T, Montgomery, Grant W, Nyholt, Dale R, van Heel, David A, Hunt, Karen, Arking, Dan E, Ashar, Foram N, Sotoodehnia, Nona, and Woo, Daniel
- Subjects
Telomeres Mendelian Randomization Collaboration ,Telomere ,Humans ,Neoplasms ,Cardiovascular Diseases ,Genetic Predisposition to Disease ,Risk Assessment ,Germ-Line Mutation ,Polymorphism ,Single Nucleotide ,Adult ,Aged ,Aged ,80 and over ,Middle Aged ,Female ,Male ,Genome-Wide Association Study ,Mendelian Randomization Analysis ,Telomere Homeostasis ,Polymorphism ,Single Nucleotide ,and over ,Prevention ,Clinical Research ,Cancer ,Genetics ,Rare Diseases ,2.1 Biological and endogenous factors ,Oncology and Carcinogenesis ,Public Health and Health Services - Abstract
ImportanceThe causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation.ObjectiveTo conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases.Data sourcesGenomewide association studies (GWAS) published up to January 15, 2015.Study selectionGWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available.Data extraction and synthesisSummary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population.Main outcomes and measuresOdds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation.ResultsSummary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [95% CI, 0.05-0.15]).Conclusions and relevanceIt is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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- 2017
29. Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer
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CMM Groep Snippert, CMM Groep Cuppen, Cancer, Pathologie Pathologen staf, MS MDL 1, Kayhanian, Hamzeh, Cross, William, van der Horst, Suzanne E M, Barmpoutis, Panagiotis, Lakatos, Eszter, Caravagna, Giulio, Zapata, Luis, Van Hoeck, Arne, Middelkamp, Sjors, Litchfield, Kevin, Steele, Christopher, Waddingham, William, Patel, Dominic, Milite, Salvatore, Jin, Chen, Baker, Ann-Marie, Alexander, Daniel C, Khan, Khurum, Hochhauser, Daniel, Novelli, Marco, Werner, Benjamin, van Boxtel, Ruben, Hageman, Joris H, Buissant des Amorie, Julian R, Linares, Josep, Ligtenberg, Marjolijn J L, Nagtegaal, Iris D, Laclé, Miangela M, Moons, Leon M G, Brosens, Lodewijk A A, Pillay, Nischalan, Sottoriva, Andrea, Graham, Trevor A, Rodriguez-Justo, Manuel, Shiu, Kai-Keen, Snippert, Hugo J G, Jansen, Marnix, CMM Groep Snippert, CMM Groep Cuppen, Cancer, Pathologie Pathologen staf, MS MDL 1, Kayhanian, Hamzeh, Cross, William, van der Horst, Suzanne E M, Barmpoutis, Panagiotis, Lakatos, Eszter, Caravagna, Giulio, Zapata, Luis, Van Hoeck, Arne, Middelkamp, Sjors, Litchfield, Kevin, Steele, Christopher, Waddingham, William, Patel, Dominic, Milite, Salvatore, Jin, Chen, Baker, Ann-Marie, Alexander, Daniel C, Khan, Khurum, Hochhauser, Daniel, Novelli, Marco, Werner, Benjamin, van Boxtel, Ruben, Hageman, Joris H, Buissant des Amorie, Julian R, Linares, Josep, Ligtenberg, Marjolijn J L, Nagtegaal, Iris D, Laclé, Miangela M, Moons, Leon M G, Brosens, Lodewijk A A, Pillay, Nischalan, Sottoriva, Andrea, Graham, Trevor A, Rodriguez-Justo, Manuel, Shiu, Kai-Keen, Snippert, Hugo J G, and Jansen, Marnix
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- 2024
30. Cancer Associated Bacteria in Primary and Metastatic Non-Small Cell Lung Cancer
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Thakkar, Krupa, primary, Richard, Corentin, additional, Fu, Hongchang, additional, Simpson, Benjamin S., additional, Cha, Hongui, additional, Augustine, Marcellus, additional, Coulton, Alexander, additional, Castro, Andrea, additional, Veerian, Selvaraju, additional, AbdulJabbar, Khalid, additional, Zhang, Hanyun, additional, Hardas, Alexandros, additional, Al-Sawaf, Othman, additional, Huebner, Arianna, additional, Al-Bakir, Maise, additional, Karasaki, Takahiro, additional, Pich, Oriol, additional, Bailey, Chris, additional, Seo, Yongwoo David, additional, Damania, Ashish, additional, Chelvanambi, Manoj, additional, Ajami, Nadim J., additional, Moore, David, additional, Sivakumar, Monika, additional, Hill, Mark, additional, Frankell, Alexander, additional, Ward, Sophie, additional, Naceur-Lombardelli, Cristina, additional, Salgado, Roberto, additional, Akarca, Ayse, additional, Marafioti, Teresa, additional, McGranahan, Nicholas, additional, Jamal-Hanjani, Mariam, additional, Wargo, Jennifer, additional, Santini, Joanne, additional, Swanton, Charles, additional, and Litchfield, Kevin, additional
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- 2024
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31. Pharmacologic Inhibition of Nonsense-Mediated Decay Induces Anti-Tumour Immunogenicity in Ex Vivo Patient Tumours
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Vendramin, Roberto, primary, Fu, Hongchang, additional, Zhao, Yue, additional, Fernandez Patel, Shanila, additional, Qian, Danwen, additional, Ligammari, Lorena, additional, Levy, Ronen, additional, Greenberg, Polina, additional, Castro, Andrea, additional, Thakkar, Krupa, additional, Nguyen, Lisa, additional, Beattie, Gordon, additional, Murai, Jun, additional, Karagianni, Despoina, additional, Shah, Mansi, additional, Vlckova, Petra, additional, Rodriguez-Justo, Manuel, additional, Sng, Christopher C.T., additional, Simpson, Benjamin S., additional, Djikstra, Krijn K., additional, Bartok, Osnat, additional, Galvez-Cancino, Felipe, additional, Consortium, The TRACERx, additional, Gronroos, Eva, additional, Dann, Stephen, additional, Quezada, Sergio A., additional, Reading, James, additional, Samuels, Yardena, additional, Swanton, Charles, additional, and Litchfield, Kevin, additional
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- 2024
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32. Fcγ receptors and immunomodulatory antibodies in cancer
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Galvez-Cancino, Felipe, primary, Simpson, Alexander P., additional, Costoya, Cristobal, additional, Matos, Ignacio, additional, Qian, Danwen, additional, Peggs, Karl S., additional, Litchfield, Kevin, additional, and Quezada, Sergio A., additional
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- 2023
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33. Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma
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Houlston, Richard, primary, Culliford, Richard, additional, Lawrence, Sam, additional, Mills, Charlie, additional, Tippu, Zayd, additional, Chubb, Daniel, additional, Cornish, Alex, additional, Browining, Lisa, additional, Kinnersley, Ben, additional, Bentham, Robert, additional, Sud, Amit, additional, Pallikonda, Husayn, additional, Frangou, Anna, additional, Gruber, Andreas, additional, Litchfield, Kevin, additional, Wedge, David, additional, Larkin, James, additional, and Turajlic, Samra, additional
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- 2023
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34. 9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy
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Han, Guangchun, Yang, Guoliang, Hao, Dapeng, Lu, Yang, Thein, Kyaw, Simpson, Benjamin S., Chen, Jianfeng, Sun, Ryan, Alhalabi, Omar, Wang, Ruiping, Dang, Minghao, Dai, Enyu, Zhang, Shaojun, Nie, Fengqi, Zhao, Shuangtao, Guo, Charles, Hamza, Ameer, Czerniak, Bogdan, Cheng, Chao, Siefker-Radtke, Arlene, Bhat, Krishna, Futreal, Andrew, Peng, Guang, Wargo, Jennifer, Peng, Weiyi, Kadara, Humam, Ajani, Jaffer, Swanton, Charles, Litchfield, Kevin, Ahnert, Jordi Rodon, Gao, Jianjun, and Wang, Linghua
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- 2021
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35. Tumour mutational burden: primary versus metastatic tissue creates systematic bias
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Schnidrig, Desiree, Turajlic, Samra, and Litchfield, Kevin
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- 2019
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36. The T cell differentiation landscape is shaped by tumour mutations in lung cancer
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Ghorani, Ehsan, Reading, James L., Henry, Jake Y., Massy, Marc Robert de, Rosenthal, Rachel, Turati, Virginia, Joshi, Kroopa, Furness, Andrew J. S., Ben Aissa, Assma, Saini, Sunil Kumar, Ramskov, Sofie, Georgiou, Andrew, Sunderland, Mariana Werner, Wong, Yien Ning Sophia, Mucha, Maria Vila De, Day, William, Galvez-Cancino, Felipe, Becker, Pablo D., Uddin, Imran, Oakes, Theres, Ismail, Mazlina, Ronel, Tahel, Woolston, Annemarie, Jamal-Hanjani, Mariam, Veeriah, Selvaraju, Birkbak, Nicolai J., Wilson, Gareth A., Litchfield, Kevin, Conde, Lucia, Guerra-Assunção, José Afonso, Blighe, Kevin, Biswas, Dhruva, Salgado, Roberto, Lund, Tom, Bakir, Maise Al, Moore, David A., Hiley, Crispin T., Loi, Sherene, Sun, Yuxin, Yuan, Yinyin, AbdulJabbar, Khalid, Turajilic, Samra, Herrero, Javier, Enver, Tariq, Hadrup, Sine R., Hackshaw, Allan, Peggs, Karl S., McGranahan, Nicholas, Chain, Benny, Swanton, Charles, and Quezada, Sergio A.
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- 2020
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37. Cancer evolution: Darwin and beyond
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Vendramin, Roberto, Litchfield, Kevin, and Swanton, Charles
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- 2021
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38. Quantifying the impact of immunotherapy on RNA dynamics in cancer
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Usaite, Ieva, primary, Biswas, Dhruva, additional, Dijkstra, Krijn, additional, Watkins, Thomas BK, additional, Pich, Oriol, additional, Puttick, Clare, additional, Angelova, Mihaela, additional, Thakkar, Krupa, additional, Hiley, Crispin, additional, Birkbak, Nicolai, additional, Kok, Marleen, additional, Zaccaria, Simone, additional, Wu, Yin, additional, Litchfield, Kevin, additional, Swanton, Charles, additional, and Kanu, Nnennaya, additional
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- 2023
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39. Genomic and immune heterogeneity of multiple synchronous lung adenocarcinoma at different developmental stages
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Chen, Haiquan, primary, Zhao, Yue, additional, Gao, Jian, additional, Wang, Jun, additional, Fan, Fanfan, additional, Cheng, Chao, additional, Qian, Danwen, additional, Guo, Ran, additional, Zhang, Yang, additional, Ye, Ting, additional, Augustine, Marcellus, additional, Li, Hang, additional, Pan, Yunjian, additional, Huang, Qingyuan, additional, Chen, Haiqing, additional, Han, Han, additional, Gao, Zhendong, additional, Fu, Fangqiu, additional, Yan, Yueren, additional, Patel, Shanila, additional, Vendramin, Roberto, additional, Yuan, Hui, additional, Zhang, Yawei, additional, Xiang, Jiaqing, additional, Hu, Hong, additional, Sun, Yihua, additional, Li, Yuan, additional, Litchfield, Kevin, additional, and Cao, Zhiwei, additional
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- 2023
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40. Whole-genome sequencing uncovers the genomic determinants of therapeutic resistance to immune checkpoint blockade
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Litchfield, Kevin, primary, Simpson, Benjamin, additional, Cha, Hongui, additional, Castro, Andrea, additional, Bentham, Robert, additional, Ryan, Lucy, additional, Dietzen, Michelle, additional, Thol, Kerstin, additional, Kinnersley, Ben, additional, Martin, Alice, additional, Chubb, Daniel, additional, Cornish, Alex, additional, Coulton, Alex, additional, Thakkar, Krupa, additional, Bailey, Chris, additional, Jennings, Charlotte, additional, Kaye, Danny, additional, Bansal, Daljeet, additional, Humphries, Matthew, additional, Wright, Alexander, additional, Colquhoun, Catherine, additional, Stankeviciute, Gaby, additional, Helliwell, Jacob, additional, Arumugam, Prabhu, additional, Treanor, Darren, additional, McGranahan, Nicholas, additional, Larkin, James, additional, Turajlic, Samra, additional, Swanton, Charles, additional, Greenig, Juliane, additional, Hiley, Crispin, additional, and Consortium, GEL Genomics England Research, additional
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- 2023
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41. Supplementary Table 3 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
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Bedran, Georges, primary, Gasser, Hans-Christof, primary, Weke, Kenneth, primary, Wang, Tongjie, primary, Bedran, Dominika, primary, Laird, Alexander, primary, Battail, Christophe, primary, Zanzotto, Fabio Massimo, primary, Pesquita, Catia, primary, Axelson, Håkan, primary, Rajan, Ajitha, primary, Harrison, David J., primary, Palkowski, Aleksander, primary, Pawlik, Maciej, primary, Parys, Maciej, primary, O'Neill, J. Robert, primary, Brennan, Paul M., primary, Symeonides, Stefan N., primary, Goodlett, David R., primary, Litchfield, Kevin, primary, Fahraeus, Robin, primary, Hupp, Ted R., primary, Kote, Sachin, primary, and Alfaro, Javier A., primary
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- 2023
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42. Figure 3 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
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Bedran, Georges, primary, Gasser, Hans-Christof, primary, Weke, Kenneth, primary, Wang, Tongjie, primary, Bedran, Dominika, primary, Laird, Alexander, primary, Battail, Christophe, primary, Zanzotto, Fabio Massimo, primary, Pesquita, Catia, primary, Axelson, Håkan, primary, Rajan, Ajitha, primary, Harrison, David J., primary, Palkowski, Aleksander, primary, Pawlik, Maciej, primary, Parys, Maciej, primary, O'Neill, J. Robert, primary, Brennan, Paul M., primary, Symeonides, Stefan N., primary, Goodlett, David R., primary, Litchfield, Kevin, primary, Fahraeus, Robin, primary, Hupp, Ted R., primary, Kote, Sachin, primary, and Alfaro, Javier A., primary
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- 2023
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43. Figure 4 from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
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Bedran, Georges, primary, Gasser, Hans-Christof, primary, Weke, Kenneth, primary, Wang, Tongjie, primary, Bedran, Dominika, primary, Laird, Alexander, primary, Battail, Christophe, primary, Zanzotto, Fabio Massimo, primary, Pesquita, Catia, primary, Axelson, Håkan, primary, Rajan, Ajitha, primary, Harrison, David J., primary, Palkowski, Aleksander, primary, Pawlik, Maciej, primary, Parys, Maciej, primary, O'Neill, J. Robert, primary, Brennan, Paul M., primary, Symeonides, Stefan N., primary, Goodlett, David R., primary, Litchfield, Kevin, primary, Fahraeus, Robin, primary, Hupp, Ted R., primary, Kote, Sachin, primary, and Alfaro, Javier A., primary
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- 2023
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44. Escape from nonsense-mediated decay associates with anti-tumor immunogenicity
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Litchfield, Kevin, Reading, James L., Lim, Emilia L., Xu, Hang, Liu, Po, Al-Bakir, Maise, Wong, Yien Ning Sophia, Rowan, Andrew, Funt, Samuel A., Merghoub, Taha, Perkins, David, Lauss, Martin, Svane, Inge Marie, Jönsson, Göran, Herrero, Javier, Larkin, James, Quezada, Sergio A., Hellmann, Matthew D., Turajlic, Samra, and Swanton, Charles
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- 2020
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45. Genomic landscape of platinum resistant and sensitive testicular cancers
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Loveday, Chey, Litchfield, Kevin, Proszek, Paula Z., Cornish, Alex J., Santo, Flavia, Levy, Max, Macintyre, Geoff, Holryod, Amy, Broderick, Peter, Dudakia, Darshna, Benton, Barbara, Bakir, Maise Al, Hiley, Crispin, Grist, Emily, Swanton, Charles, Huddart, Robert, Powles, Tom, Chowdhury, Simon, Shipley, Janet, O’Connor, Simon, Brenton, James D., Reid, Alison, de Castro, David Gonzalez, Houlston, Richard S., and Turnbull, Clare
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- 2020
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46. Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
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Orlando, Giulia, Law, Philip J., Cornish, Alex J., Dobbins, Sara E., Chubb, Daniel, Broderick, Peter, Litchfield, Kevin, Hariri, Fadi, Pastinen, Tomi, Osborne, Cameron S., Taipale, Jussi, and Houlston, Richard S.
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- 2018
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47. Data from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
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Spain, Lavinia, primary, Coulton, Alexander, primary, Lobon, Irene, primary, Rowan, Andrew, primary, Schnidrig, Desiree, primary, Shepherd, Scott T.C., primary, Shum, Benjamin, primary, Byrne, Fiona, primary, Goicoechea, Maria, primary, Piperni, Elisa, primary, Au, Lewis, primary, Edmonds, Kim, primary, Carlyle, Eleanor, primary, Hunter, Nikki, primary, Renn, Alexandra, primary, Messiou, Christina, primary, Hughes, Peta, primary, Nobbs, Jaime, primary, Foijer, Floris, primary, van den Bos, Hilda, primary, Wardenaar, Rene, primary, Spierings, Diana C.J., primary, Spencer, Charlotte, primary, Schmitt, Andreas M., primary, Tippu, Zayd, primary, Lingard, Karla, primary, Grostate, Lauren, primary, Peat, Kema, primary, Kelly, Kayleigh, primary, Sarker, Sarah, primary, Vaughan, Sarah, primary, Mangwende, Mary, primary, Terry, Lauren, primary, Kelly, Denise, primary, Biano, Jennifer, primary, Murra, Aida, primary, Korteweg, Justine, primary, Lewis, Charlotte, primary, O'Flaherty, Molly, primary, Cattin, Anne-Laure, primary, Emmerich, Max, primary, Gerard, Camille L., primary, Pallikonda, Husayn Ahmed, primary, Lynch, Joanna, primary, Mason, Robert, primary, Rogiers, Aljosja, primary, Xu, Hang, primary, Huebner, Ariana, primary, McGranahan, Nicholas, primary, Al Bakir, Maise, primary, Murai, Jun, primary, Naceur-Lombardelli, Cristina, primary, Borg, Elaine, primary, Mitchison, Miriam, primary, Moore, David A., primary, Falzon, Mary, primary, Proctor, Ian, primary, Stamp, Gordon W.H., primary, Nye, Emma L., primary, Young, Kate, primary, Furness, Andrew J.S., primary, Pickering, Lisa, primary, Stewart, Ruby, primary, Mahadeva, Ula, primary, Green, Anna, primary, Larkin, James, primary, Litchfield, Kevin, primary, Swanton, Charles, primary, Jamal-Hanjani, Mariam, primary, and Turajlic, Samra, primary
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- 2023
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48. Supplementary Tables S1-S8 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
- Author
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Spain, Lavinia, primary, Coulton, Alexander, primary, Lobon, Irene, primary, Rowan, Andrew, primary, Schnidrig, Desiree, primary, Shepherd, Scott T.C., primary, Shum, Benjamin, primary, Byrne, Fiona, primary, Goicoechea, Maria, primary, Piperni, Elisa, primary, Au, Lewis, primary, Edmonds, Kim, primary, Carlyle, Eleanor, primary, Hunter, Nikki, primary, Renn, Alexandra, primary, Messiou, Christina, primary, Hughes, Peta, primary, Nobbs, Jaime, primary, Foijer, Floris, primary, van den Bos, Hilda, primary, Wardenaar, Rene, primary, Spierings, Diana C.J., primary, Spencer, Charlotte, primary, Schmitt, Andreas M., primary, Tippu, Zayd, primary, Lingard, Karla, primary, Grostate, Lauren, primary, Peat, Kema, primary, Kelly, Kayleigh, primary, Sarker, Sarah, primary, Vaughan, Sarah, primary, Mangwende, Mary, primary, Terry, Lauren, primary, Kelly, Denise, primary, Biano, Jennifer, primary, Murra, Aida, primary, Korteweg, Justine, primary, Lewis, Charlotte, primary, O'Flaherty, Molly, primary, Cattin, Anne-Laure, primary, Emmerich, Max, primary, Gerard, Camille L., primary, Pallikonda, Husayn Ahmed, primary, Lynch, Joanna, primary, Mason, Robert, primary, Rogiers, Aljosja, primary, Xu, Hang, primary, Huebner, Ariana, primary, McGranahan, Nicholas, primary, Al Bakir, Maise, primary, Murai, Jun, primary, Naceur-Lombardelli, Cristina, primary, Borg, Elaine, primary, Mitchison, Miriam, primary, Moore, David A., primary, Falzon, Mary, primary, Proctor, Ian, primary, Stamp, Gordon W.H., primary, Nye, Emma L., primary, Young, Kate, primary, Furness, Andrew J.S., primary, Pickering, Lisa, primary, Stewart, Ruby, primary, Mahadeva, Ula, primary, Green, Anna, primary, Larkin, James, primary, Litchfield, Kevin, primary, Swanton, Charles, primary, Jamal-Hanjani, Mariam, primary, and Turajlic, Samra, primary
- Published
- 2023
- Full Text
- View/download PDF
49. Supplementary Figures S1-S25 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
- Author
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Spain, Lavinia, primary, Coulton, Alexander, primary, Lobon, Irene, primary, Rowan, Andrew, primary, Schnidrig, Desiree, primary, Shepherd, Scott T.C., primary, Shum, Benjamin, primary, Byrne, Fiona, primary, Goicoechea, Maria, primary, Piperni, Elisa, primary, Au, Lewis, primary, Edmonds, Kim, primary, Carlyle, Eleanor, primary, Hunter, Nikki, primary, Renn, Alexandra, primary, Messiou, Christina, primary, Hughes, Peta, primary, Nobbs, Jaime, primary, Foijer, Floris, primary, van den Bos, Hilda, primary, Wardenaar, Rene, primary, Spierings, Diana C.J., primary, Spencer, Charlotte, primary, Schmitt, Andreas M., primary, Tippu, Zayd, primary, Lingard, Karla, primary, Grostate, Lauren, primary, Peat, Kema, primary, Kelly, Kayleigh, primary, Sarker, Sarah, primary, Vaughan, Sarah, primary, Mangwende, Mary, primary, Terry, Lauren, primary, Kelly, Denise, primary, Biano, Jennifer, primary, Murra, Aida, primary, Korteweg, Justine, primary, Lewis, Charlotte, primary, O'Flaherty, Molly, primary, Cattin, Anne-Laure, primary, Emmerich, Max, primary, Gerard, Camille L., primary, Pallikonda, Husayn Ahmed, primary, Lynch, Joanna, primary, Mason, Robert, primary, Rogiers, Aljosja, primary, Xu, Hang, primary, Huebner, Ariana, primary, McGranahan, Nicholas, primary, Al Bakir, Maise, primary, Murai, Jun, primary, Naceur-Lombardelli, Cristina, primary, Borg, Elaine, primary, Mitchison, Miriam, primary, Moore, David A., primary, Falzon, Mary, primary, Proctor, Ian, primary, Stamp, Gordon W.H., primary, Nye, Emma L., primary, Young, Kate, primary, Furness, Andrew J.S., primary, Pickering, Lisa, primary, Stewart, Ruby, primary, Mahadeva, Ula, primary, Green, Anna, primary, Larkin, James, primary, Litchfield, Kevin, primary, Swanton, Charles, primary, Jamal-Hanjani, Mariam, primary, and Turajlic, Samra, primary
- Published
- 2023
- Full Text
- View/download PDF
50. Supplementary figures from The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
- Author
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Bedran, Georges, primary, Gasser, Hans-Christof, primary, Weke, Kenneth, primary, Wang, Tongjie, primary, Bedran, Dominika, primary, Laird, Alexander, primary, Battail, Christophe, primary, Zanzotto, Fabio Massimo, primary, Pesquita, Catia, primary, Axelson, Håkan, primary, Rajan, Ajitha, primary, Harrison, David J., primary, Palkowski, Aleksander, primary, Pawlik, Maciej, primary, Parys, Maciej, primary, O'Neill, J. Robert, primary, Brennan, Paul M., primary, Symeonides, Stefan N., primary, Goodlett, David R., primary, Litchfield, Kevin, primary, Fahraeus, Robin, primary, Hupp, Ted R., primary, Kote, Sachin, primary, and Alfaro, Javier A., primary
- Published
- 2023
- Full Text
- View/download PDF
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