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2. Author Correction: The evolution of lung cancer and impact of subclonal selection in TRACERx

Author

Frankell, Alexander M., Dietzen, Michelle, Al Bakir, Maise, Lim, Emilia L., Karasaki, Takahiro, Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Huebner, Ariana, Bunkum, Abigail, Hill, Mark S., Grigoriadis, Kristiana, Moore, David A., Black, James R. M., Liu, Wing Kin, Thol, Kerstin, Pich, Oriol, Watkins, Thomas B. K., Naceur-Lombardelli, Cristina, Cook, Daniel E., Salgado, Roberto, Wilson, Gareth A., Bailey, Chris, Angelova, Mihaela, Bentham, Robert, Martínez-Ruiz, Carlos, Abbosh, Christopher, Nicholson, Andrew G., Le Quesne, John, Biswas, Dhruva, Rosenthal, Rachel, Puttick, Clare, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Smith, Jon, Xing, Wei, Nicod, Jerome, Price, Gillian, Kerr, Keith M., Naidu, Babu, Middleton, Gary, Blyth, Kevin G., Fennell, Dean A., Forster, Martin D., Lee, Siow Ming, Falzon, Mary, Hewish, Madeleine, Shackcloth, Michael J., Lim, Eric, Benafif, Sarah, Russell, Peter, Boleti, Ekaterini, Krebs, Matthew G., Lester, Jason F., Papadatos-Pastos, Dionysis, Ahmad, Tanya, Thakrar, Ricky M., Lawrence, David, Navani, Neal, Janes, Sam M., Dive, Caroline, Blackhall, Fiona H., Summers, Yvonne, Cave, Judith, Marafioti, Teresa, Herrero, Javier, Quezada, Sergio A., Peggs, Karl S., Schwarz, Roland F., Van Loo, Peter, Miedema, Daniël M., Birkbak, Nicolai J., Hiley, Crispin T., Hackshaw, Allan, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, and Swanton, Charles

Published
2024
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4. Race- and Ethnicity-Related Differences in Heart Failure With Preserved Ejection Fraction Using Natural Language Processing

Author

Brown, Sam, Biswas, Dhruva, Wu, Jack, Ryan, Matthew, Bernstein, Brett S., Fairhurst, Natalie, Kaye, George, Baral, Ranu, Cannata, Antonio, Searle, Tom, Melikian, Narbeh, Sado, Daniel, Lüscher, Thomas F., Teo, James, Dobson, Richard, Bromage, Daniel I., McDonagh, Theresa A., Vazir, Ali, Shah, Ajay M., and O’Gallagher, Kevin

Published
2024
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5. The evolution of lung cancer and impact of subclonal selection in TRACERx

Author

Frankell, Alexander M., Dietzen, Michelle, Al Bakir, Maise, Lim, Emilia L., Karasaki, Takahiro, Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Huebner, Ariana, Bunkum, Abigail, Hill, Mark S., Grigoriadis, Kristiana, Moore, David A., Black, James R. M., Liu, Wing Kin, Thol, Kerstin, Pich, Oriol, Watkins, Thomas B. K., Naceur-Lombardelli, Cristina, Cook, Daniel E., Salgado, Roberto, Wilson, Gareth A., Bailey, Chris, Angelova, Mihaela, Bentham, Robert, Martínez-Ruiz, Carlos, Abbosh, Christopher, Nicholson, Andrew G., Le Quesne, John, Biswas, Dhruva, Rosenthal, Rachel, Puttick, Clare, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Smith, Jon, Xing, Wei, Nicod, Jerome, Price, Gillian, Kerr, Keith M., Naidu, Babu, Middleton, Gary, Blyth, Kevin G., Fennell, Dean A., Forster, Martin D., Lee, Siow Ming, Falzon, Mary, Hewish, Madeleine, Shackcloth, Michael J., Lim, Eric, Benafif, Sarah, Russell, Peter, Boleti, Ekaterini, Krebs, Matthew G., Lester, Jason F., Papadatos-Pastos, Dionysis, Ahmad, Tanya, Thakrar, Ricky M., Lawrence, David, Navani, Neal, Janes, Sam M., Dive, Caroline, Blackhall, Fiona H., Summers, Yvonne, Cave, Judith, Marafioti, Teresa, Herrero, Javier, Quezada, Sergio A., Peggs, Karl S., Schwarz, Roland F., Van Loo, Peter, Miedema, Daniël M., Birkbak, Nicolai J., Hiley, Crispin T., Hackshaw, Allan, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, and Swanton, Charles

Published
2023
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6. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA

Author

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

Published
2023
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7. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx

Author

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

Published
2023
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8. Molecular portraits of cancer evolution and ecology

Author

Biswas, Dhruva

Abstract

Research on the molecular lesions that drive cancers holds the translational promise of unmasking distinct disease subtypes in otherwise pathologically identical patients. Yet clinical adoption is hindered by the reproducibility crisis for cancer biomarkers. In this thesis, a novel metric uncovered transcriptional diversity within individual non-small cell lung cancers, driven by chromosomal instability. Existing prognostic biomarkers were confounded by tumour sampling bias, arising from this diversity, in ~50% of patients assessed. An atlas of consistently expressed genes was derived to address this diagnostic challenge, yielding a clonal biomarker robust to sampling bias. This diagnostic based on cancer evolutionary principles maintained prognostic value in a metaanalysis of >900 patients, and over known risk factors in stage I disease, motivating further development as a clinical assay. Next, in situ RNA profiles of immune, fibroblast and endothelial cell subsets were generated from cancerous and adjacent non-malignant lung tissue. The phenotypic adaptation of stromal cells in the tumour microenvironment undermined the performance of existing molecular signatures for cell-type enumeration. Transcriptome-wide analysis delineated ~10% of genes displaying cell-type-specific expression, paving the way for high-fidelity signatures for the accurate digital dissection of tumour ecology. Lastly, the impact of branching, Darwinian evolution on the detection of epistatic interactions was evaluated in a pan-cancer analysis. The clonal status of driver genes was associated with the proportion of significant epistatic findings in 44-78% of the cancer-types assessed. Integrating the clonal architecture of tumours in future analyses could help decipher evolutionary dependencies. This work provides pragmatic solutions for refining molecular portraits of cancer in the light of their evolutionary and ecological features, moving the needle for precision cancer diagnostics.

Published
2021

10. Pervasive chromosomal instability and karyotype order in tumour evolution

Author

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

Subjects
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.

Published
2020

11. 134 Race and ethnicity-related differences in the diagnosis of heart failure with preserved ejection fraction using natural language processing

Author

Brown, Sam, primary, Biswas, Dhruva, additional, Wu, Ho Chung, additional, Ryan, Matt, additional, Bernstein, Brett, additional, Fairhurst, Natalie, additional, Kaye, George, additional, Baral, Ranu, additional, Cannata, Antonio, additional, Searle, Thomas, additional, Melikian, Narbeh, additional, Sado, Daniel, additional, Lüscher, Thomas, additional, Teo, James, additional, Dobson, Richard, additional, Bromage, Daniel, additional, McDonagh, Theresa, additional, Vazir, Ali, additional, Shah, Ajay, additional, and O’Gallagher, Kevin, additional

Published
2024
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12. A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer

Author

Wu, Yin, Biswas, Dhruva, Usaite, Ieva, Angelova, Mihaela, Boeing, Stefan, Karasaki, Takahiro, Veeriah, Selvaraju, Czyzewska-Khan, Justyna, Morton, Cienne, Joseph, Magdalene, Hessey, Sonya, Reading, James, Georgiou, Andrew, Al-Bakir, Maise, McGranahan, Nicholas, Jamal-Hanjani, Mariam, Hackshaw, Allan, Quezada, Sergio A., Hayday, Adrian C., and Swanton, Charles

Published
2022
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14. Artificial intelligence methods for improved detection of undiagnosed heart failure with preserved ejection fraction

Author

Wu, Jack, primary, Biswas, Dhruva, additional, Ryan, Matthew, additional, Bernstein, Brett S., additional, Rizvi, Maleeha, additional, Fairhurst, Natalie, additional, Kaye, George, additional, Baral, Ranu, additional, Searle, Tom, additional, Melikian, Narbeh, additional, Sado, Daniel, additional, Lüscher, Thomas F., additional, Grocott‐Mason, Richard, additional, Carr‐White, Gerald, additional, Teo, James, additional, Dobson, Richard, additional, Bromage, Daniel I., additional, McDonagh, Theresa A., additional, Shah, Ajay M., additional, and O'Gallagher, Kevin, additional

Published
2024
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15. Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy

Author

Aitken, Jim, Allen, Zoe, Ambler, Rachel, Ambrose, Karen, Ashton, Emma, Avola, Alida, Balakrishnan, Samutheswari, Barns-Jenkins, Caitlin, Barr, Genevieve, Barrell, Sam, Basu, Souradeep, Beale, Rupert, Beesley, Clare, Bhardwaj, Nisha, Bibi, Shahnaz, Bineva-Todd, Ganka, Biswas, Dhruva, Blackman, Michael J., Bonnet, Dominique, Bowker, Faye, Broncel, Malgorzata, Brooks, Claire, Buck, Michael D., Buckton, Andrew, Budd, Timothy, Burrell, Alana, Busby, Louise, Bussi, Claudio, Butterworth, Simon, Byott, Matthew, Byrne, Fiona, Byrne, Richard, Caidan, Simon, Campbell, Joanna, Canton, Johnathan, Cardoso, Ana, Carter, Nick, Carvalho, Luiz, Carzaniga, Raffaella, Chandler, Natalie, Chen, Qu, Cherepanov, Peter, Churchward, Laura, Clark, Graham, Clayton, Bobbi, Cobolli Gigli, Clementina, Collins, Zena, Cottrell, Sally, Crawford, Margaret, Cubitt, Laura, Cullup, Tom, Davies, Heledd, Davis, Patrick, Davison, Dara, Dearing, Vicky, Debaisieux, Solene, Diaz-Romero, Monica, Dibbs, Alison, Diring, Jessica, Driscoll, Paul C., D'Avola, Annalisa, Earl, Christopher, Edwards, Amelia, Ekin, Chris, Evangelopoulos, Dimitrios, Faraway, Rupert, Fearns, Antony, Ferron, Aaron, Fidanis, Efthymios, Fitz, Dan, Fleming, James, Frampton, Daniel, Frederico, Bruno, Gaiba, Alessandra, Gait, Anthony, Gamblin, Steve, Gärtner, Kathleen, Gaul, Liam, Golding, Helen M., Goldman, Jacki, Goldstone, Robert, Gomez Dominguez, Belen, Gong, Hui, Grant, Paul R., Greco, Maria, Grobler, Mariana, Guedan, Anabel, Gutierrez, Maximiliano G., Hackett, Fiona, Hall, Ross, Halldorsson, Steinar, Harris, Suzanne, Hashim, Sugera, Hatipoglu, Emine, Healy, Lyn, Heaney, Judith, Herbst, Susanne, Hewitt, Graeme, Higgins, Theresa, Hindmarsh, Steve, Hirani, Rajnika, Hope, Joshua, Horton, Elizabeth, Hoskins, Beth, Howell, Michael, Howitt, Louise, Hoyle, Jacqueline, Htun, Mint R., Hubank, Michael, Huerga Encabo, Hector, Hughes, Deborah, Hughes, Jane, Huseynova, Almaz, Hwang, Ming-Shih, Instrell, Rachael, Jackson, Deborah, Jamal-Hanjani, Mariam, Jenkins, Lucy, Jiang, Ming, Johnson, Mark, Jones, Leigh, Kanu, Nnennaya, Kassiotis, George, Kelly, Gavin, Kiely, Louise, Teixeira, Anastacio King Spert, Kirk, Stuart, Kjaer, Svend, Knuepfer, Ellen, Komarov, Nikita, Kotzampaltiris, Paul, Kousis, Konstantinos, Krylova, Tammy, Kucharska, Ania, Labrum, Robyn, Lambe, Catherine, Lappin, Michelle, Lee, Stacey-Ann, Levett, Andrew, Levett, Lisa, Levi, Marcel, Liu, Hon Wing, Loughlin, Sam, Lu, Wei-Ting, MacRae, James I., Madoo, Akshay, Marczak, Julie A., Martensson, Mimmi, Martinez, Thomas, Marzook, Bishara, Matthews, John, Matz, Joachim M., McCall, Samuel, McCoy, Laura E., McKay, Fiona, McNamara, Edel C., Minutti, Carlos M., Mistry, Gita, Molina-Arcas, Miriam, Montaner, Beatriz, Montgomery, Kylie, Moore, Catherine, Moore, David, Moraiti, Anastasia, Moreira-Teixeira, Lucia, Mukherjee, Joyita, Naceur-Lombardelli, Cristina, Nelson, Aileen, Nicod, Jerome, Nightingale, Luke, Nofal, Stephanie, Nurse, Paul, Nutan, Savita, Oedekoven, Caroline, O'Garra, Anne, O'Leary, Jean D., Olsen, Jessica, O'Neill, Olga, O'Reilly, Nicola, Suarez, Paula Ordonez, Osborne, Neil, Pabari, Amar, Pajak, Aleksandra, Papayannopoulos, Venizelos, Paraskevopoulou, Stavroula M, Patel, Namita, Patel, Yogen, Paun, Oana, Peat, Nigel, Peces-Barba Castano, Laura, Caballero, Ana Perez, Perez-Lloret, Jimena, Perrault, Magali S., Perrin, Abigail, Poh, Roy, Poirier, Enzo Z., Polke, James M., Pollitt, Marc, Prieto-Godino, Lucia, Proust, Alize, Puvirajasinghe, Clinda, Queval, Christophe, Ramachandran, Vijaya, Ramaprasad, Abhinay, Ratcliffe, Peter, Reed, Laura, Reis e Sousa, Caetano, Richardson, Kayleigh, Ridewood, Sophie, Roberts, Fiona, Roberts, Rowenna, Rodgers, Angela, Romero Clavijo, Pablo, Rosa, Annachiara, Rossi, Alice, Roustan, Chloe, Rowan, Andrew, Sahai, Erik, Sait, Aaron, Sala, Katarzyna, Sanchez, Emilie, Sanderson, Theo, Santucci, Pierre, Sardar, Fatima, Sateriale, Adam, Saunders, Jill A., Sawyer, Chelsea, Schlott, Anja, Schweighoffer, Edina, Segura-Bayona, Sandra, Shah Punatar, Rajvee, Shahmanesh, Maryam, Shaw, Joe, Silva Dos Santos, Mariana, Silvestre, Margaux, Singer, Matthew, Snell, Daniel M., Song, Ok-Ryul, Spyer, Moira J., Steel, Louisa, Strange, Amy, Sullivan, Adrienne E., Tan, Michele S.Y., Tautz-Davis, Zoe H., Taylor, Effie, Taylor, Gunes, Taylor, Harriet B., Taylor-Beadling, Alison, Teixeira Subtil, Fernanda, Terré Torras, Berta, Toolan-Kerr, Patrick, Torelli, Francesca, Toteva, Tea, Treeck, Moritz, Trojer, Hadija, Tsai, Ming-Han C., Turner, James M.A., Turner, Melanie, Ule, Jernej, Ulferts, Rachel, Vanloo, Sharon P., Veeriah, Selvaraju, Venkatesan, Subramanian, Vousden, Karen, Wack, Andreas, Walder, Claire, Walker, Philip A., Wang, Yiran, Ward, Sophia, Wenman, Catharina, Williams, Luke, Williams, Matthew J., Keong Wong, Wai, Wright, Joshua, Wu, Mary, Wynne, Lauren, Xiang, Zheng, Yap, Melvyn, Zagalak, Julian A., Zecchin, Davide, Zillwood, Rachel, Carthiyaniamma, Santhakumari, DeTisi, Jane, Dick, Julie, Hill, Andrea, Kipper, Karin, Kullar, Birinder, Norris, Sarah, Rugg-Gunn, Fergus, Salvatierra, Rebecca, Shaya, Gabriel, Sloan, Astrid, Singh, Priyanka, Varley, James, Whatley, Ben, Balestrini, Simona, Koepp, Matthias J., Gandhi, Sonia, Rickman, Hannah M., Shin, Gee Yen, Houlihan, Catherine F., Anders-Cannon, Jonny, Silvennoinen, Katri, Xiao, Fenglai, Zagaglia, Sara, Hudgell, Kirsty, Ziomek, Mariusz, Haimes, Paul, Sampson, Adam, Parker, Annie, Helen Cross, J., Pardington, Rosemarie, Nastouli, Eleni, Swanton, Charles, Sander, Josemir W., and Sisodiya, Sanjay M.

Published
2021
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16. Natural Language Processing to Identify Racial and Ethnic Disparities in Aortic Stenosis

Author

Biswas, Dhruva, primary, Wu, Jack, additional, Bharucha, Apurva, additional, Fairhurst, Natalie, additional, Kaye, George, additional, Jones, Kate, additional, Copeland, Freya Parker, additional, O’Donnell, Bethan, additional, Kyle, Daniel, additional, Searle, Tom, additional, Pareek, Nilesh, additional, Dworakowski, Rafal, additional, Papachristidis, Alexandros, additional, Melikian, Narbeh, additional, Wendler, Olaf, additional, Deshpande, Ranjit, additional, Baghai, Max, additional, Galloway, James, additional, Teo, James T, additional, Dobson, Richard, additional, Byrne, Jonathan, additional, MacCarthy, Philip, additional, Shah, Ajay M, additional, Eskanderi, Mehdi, additional, and O’Gallagher, Kevin, additional

Published
2023
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17. Quantifying the impact of immunotherapy on RNA dynamics in cancer

Author

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

Published
2023
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18. TCT-766 Ethnicity and Aortic Stenosis: Presentation, Management, and Outcomes

Author

Biswas, Dhruva, primary, Wu, Jack, additional, Bharucha, Apurva, additional, Fairhurst, Natalie, additional, Kaye, George, additional, Baghai, Max, additional, Pareek, Nilesh, additional, Webb, Ian, additional, Melikian, Narbeh, additional, Dworakowski, Rafal, additional, Byrne, Jonathan, additional, MacCarthy, Philip, additional, Shah, Ajay, additional, Eskandari, Mehdi, additional, and O'Gallagher, Kevin, additional

Published
2023
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19. A clonal expression biomarker associates with lung cancer mortality

Author

Biswas, Dhruva, Birkbak, Nicolai J., Rosenthal, Rachel, Hiley, Crispin T., Lim, Emilia L., Papp, Krisztian, and Boeing, Stefan

Subjects
RNA sequencing -- Usage, Lung cancer -- Genetic aspects -- Care and treatment, Genetic transcription -- Research, Biological markers -- Research, Biological sciences, Health
Abstract

An aim of molecular biomarkers is to stratify patients with cancer into disease subtypes predictive of outcome, improving diagnostic precision beyond clinical descriptors such as tumor stage.sup.1. Transcriptomic intratumor heterogeneity (RNA-ITH) has been shown to confound existing expression-based biomarkers across multiple cancer types.sup.2-6. Here, we analyze multi-region whole-exome and RNA sequencing data for 156 tumor regions from 48 patients enrolled in the TRACERx study to explore and control for RNA-ITH in non-small cell lung cancer. We find that chromosomal instability is a major driver of RNA-ITH, and existing prognostic gene expression signatures are vulnerable to tumor sampling bias. To address this, we identify genes expressed homogeneously within individual tumors that encode expression modules of cancer cell proliferation and are often driven by DNA copy-number gains selected early in tumor evolution. Clonal transcriptomic biomarkers overcome tumor sampling bias, associate with survival independent of clinicopathological risk factors, and may provide a general strategy to refine biomarker design across cancer types. TRACERx Lung: Intratumoral transcriptional heterogeneity, which often hinders the development of clinically useful RNA-expression-biased biomarkers for cancer, can now be overcome with an approach for the identification of clonal expression biomarkers., Author(s): Dhruva Biswas [sup.1] [sup.2] [sup.3] , Nicolai J. Birkbak [sup.1] [sup.3] [sup.4] [sup.5] , Rachel Rosenthal [sup.1] [sup.2] [sup.3] , Crispin T. Hiley [sup.1] [sup.3] , Emilia L. Lim [...]

Published
2019
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20. The T cell differentiation landscape is shaped by tumour mutations in lung cancer

Author

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.

Published
2020
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21. Artificial Intelligence methods for Improved Detection of undiagnosed Heart Failure with Preserved Ejection Fraction (HFpEF)

Author

Wu, Jack, primary, Biswas, Dhruva, additional, Ryan, Matthew, additional, Bernstein, Brett, additional, Fairhurst, Natalie, additional, Kaye, George, additional, Baral, Ranu, additional, Searle, Tom, additional, Melikian, Narbeh, additional, Sado, Daniel, additional, Teo, James, additional, Dobson, Richard, additional, Bromage, Daniel I, additional, McDonagh, Theresa A, additional, Shah, Ajay M, additional, and O'Gallagher, Kevin, additional

Published
2023
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22. Cancer cell – fibroblast crosstalk via HB-EGF/EGFR/MEK signaling promotes macrophage recruitment in squamous cell carcinoma

Author

Giangreco, Giovanni, primary, Rullan, Antonio, additional, Naito, Yutaka, additional, Biswas, Dhruva, additional, Liu, Yun-Hsin, additional, Hooper, Steven, additional, Nenclares, Pablo, additional, Bhide, Shreerang, additional, Cheang, Maggie Chon U, additional, Chakravarty, Probir, additional, Hirata, Eishu, additional, Swanton, Charles, additional, Melcher, Alan, additional, Harrington, Kevin, additional, and Sahai, Erik, additional

Published
2023
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23. Abstract LB237: Functional characterisation of TRACERx reveals mechanisms of NSCLC evolution

Author

Lu, Wei-Ting, primary, Zalmas, Lykourgos-Panagiotis, additional, Bailey, Chris, additional, Pich, Oriol, additional, Ruiz, Carlos M., additional, Black, James, additional, Stavrou, Georgia, additional, Biswas, Dhruva, additional, Gimeno-Valiente, Francisco, additional, Litchfield, Kevin, additional, Bartek, Jiri, additional, McGranahan, Nicholas, additional, Kanu, Nnennaya, additional, and Swanton, Charles, additional

Published
2023
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24. Data from Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Author

Li, Jun, primary, Duran, Mercedes A., primary, Dhanota, Ninjit, primary, Chatila, Walid K., primary, Bettigole, Sarah E., primary, Kwon, John, primary, Sriram, Roshan K., primary, Humphries, Matthew P., primary, Salto-Tellez, Manuel, primary, James, Jacqueline A., primary, Hanna, Matthew G., primary, Melms, Johannes C., primary, Vallabhaneni, Sreeram, primary, Litchfield, Kevin, primary, Usaite, Ieva, primary, Biswas, Dhruva, primary, Bareja, Rohan, primary, Li, Hao Wei, primary, Martin, Maria Laura, primary, Dorsaint, Princesca, primary, Cavallo, Julie-Ann, primary, Li, Peng, primary, Pauli, Chantal, primary, Gottesdiener, Lee, primary, DiPardo, Benjamin J., primary, Hollmann, Travis J., primary, Merghoub, Taha, primary, Wen, Hannah Y., primary, Reis-Filho, Jorge S., primary, Riaz, Nadeem, primary, Su, Shin-San Michael, primary, Kalbasi, Anusha, primary, Vasan, Neil, primary, Powell, Simon N., primary, Wolchok, Jedd D., primary, Elemento, Olivier, primary, Swanton, Charles, primary, Shoushtari, Alexander N., primary, Parkes, Eileen E., primary, Izar, Benjamin, primary, and Bakhoum, Samuel F., primary

Published
2023
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25. Supplementary Data PDF from Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Author

Li, Jun, primary, Duran, Mercedes A., primary, Dhanota, Ninjit, primary, Chatila, Walid K., primary, Bettigole, Sarah E., primary, Kwon, John, primary, Sriram, Roshan K., primary, Humphries, Matthew P., primary, Salto-Tellez, Manuel, primary, James, Jacqueline A., primary, Hanna, Matthew G., primary, Melms, Johannes C., primary, Vallabhaneni, Sreeram, primary, Litchfield, Kevin, primary, Usaite, Ieva, primary, Biswas, Dhruva, primary, Bareja, Rohan, primary, Li, Hao Wei, primary, Martin, Maria Laura, primary, Dorsaint, Princesca, primary, Cavallo, Julie-Ann, primary, Li, Peng, primary, Pauli, Chantal, primary, Gottesdiener, Lee, primary, DiPardo, Benjamin J., primary, Hollmann, Travis J., primary, Merghoub, Taha, primary, Wen, Hannah Y., primary, Reis-Filho, Jorge S., primary, Riaz, Nadeem, primary, Su, Shin-San Michael, primary, Kalbasi, Anusha, primary, Vasan, Neil, primary, Powell, Simon N., primary, Wolchok, Jedd D., primary, Elemento, Olivier, primary, Swanton, Charles, primary, Shoushtari, Alexander N., primary, Parkes, Eileen E., primary, Izar, Benjamin, primary, and Bakhoum, Samuel F., primary

Published
2023
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26. Body composition and lung cancer-associated cachexia in TRACERx

Author

Al-Sawaf, Othman, Weiss, Jakob, Skrzypski, Marcin, Lam, Jie Min, Karasaki, Takahiro, Zambrana, Francisco, Kidd, Andrew C, Frankell, Alexander M, Watkins, Thomas BK, Martinez-Ruiz, Carlos, Puttick, Clare, Black, James RM, Huebner, Ariana, Al Bakir, Maise, Sokac, Mateo, Collins, Susie, Veeriah, Selvaraju, Magno, Neil, Naceur-Lombardelli, Cristina, Prymas, Paulina, Toncheva, Antonia, Ward, Sophia, Jayanth, Nick, Salgado, Roberto, Bridge, Christopher P, Christiani, David C, Mak, Raymond H, Bay, Camden, Rosenthal, Michael, Sattar, Naveed, Welsh, Paul, Liu, Ying, Perrimon, Norbert, Popuri, Karteek, Beg, Mirza Faisal, McGranahan, Nicholas, Hackshaw, Allan, Breen, Danna M, O'Rahilly, Stephen, Birkbak, Nicolai J, Aerts, Hugo JWL, Jamal-Hanjani, Mariam, Swanton, Charles, Lester, Jason F, Bajaj, Amrita, Nakas, Apostolos, Sodha-Ramdeen, Azmina, Ang, Keng, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Boyles, Rebecca, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Dulloo, Sean, Fennell, Dean A, Matharu, Gurdeep, Shaw, Jacqui A, Riley, Joan, Primrose, Lindsay, Boleti, Ekaterini, Cheyne, Heather, Khalil, Mohammed, Richardson, Shirley, Cruickshank, Tracey, Price, Gillian, Kerr, Keith M, Benafif, Sarah, Gilbert, Kayleigh, Naidu, Babu, Patel, Akshay J, Osman, Aya, Lacson, Christer, Langman, Gerald, Shackleford, Helen, Djearaman, Madava, Kadiri, Salma, Middleton, Gary, Leek, Angela, Hodgkinson, Jack Davies, Totten, Nicola, Montero, Angeles, Smith, Elaine, Fontaine, Eustace, Granato, Felice, Doran, Helen, Novasio, Juliette, Rammohan, Kendadai, Joseph, Leena, Bishop, Paul, Shah, Rajesh, Moss, Stuart, Joshi, Vijay, Crosbie, Philip, Gomes, Fabio, Brown, Kate, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Oliveira, Pedro, Lindsay, Colin R, Blackhall, Fiona H, Krebs, Matthew G, Summers, Yvonne, Clipson, Alexandra, Tugwood, Jonathan, Kerr, Alastair, Rothwell, Dominic G, Kilgour, Elaine, Dive, Caroline, Schwarz, Roland F, Kaufmann, Tom L, Wilson, Gareth A, Rosenthal, Rachel, Van Loo, Peter, Szallasi, Zoltan, Kisistok, Judit, Diossy, Miklos, Demeulemeester, Jonas, Bunkum, Abigail, Stewart, Aengus, Magness, Alastair, Rowan, Andrew, Karamani, Angeliki, Chain, Benny, Campbell, Brittany B, Castignani, Carla, Bailey, Chris, Abbosh, Christopher, Weeden, Clare E, Lee, Claudia, Richard, Corentin, Hiley, Crispin T, Moore, David A, Pearce, David R, Karagianni, Despoina, Biswas, Dhruva, Levi, Dina, Hoxha, Elena, Cadieux, Elizabeth Larose, Lim, Emilia L, Colliver, Emma, Nye, Emma, Gronroos, Eva, Galvez-Cancino, Felip, Athanasopoulou, Foteini, Gimeno-Valiente, Francisco, Kassiotis, George, Stavrou, Georgia, Mastrokalos, Gerasimos, Zhai, Haoran, Lowe, Helen L, Matos, Ignacio Garcia, Goldman, Jacki, Reading, James L, Herrero, Javier, Rane, Jayant K, Nicod, Jerome, Hartley, John A, Peggs, Karl S, Enfield, Katey SS, Selvaraju, Kayalvizhi, Thol, Kerstin, Litchfield, Kevin, Ng, Kevin W, Chen, Kezhong, Dijkstra, Krijn, Grigoriadis, Kristiana, Thakkar, Krupa, Ensell, Leah, Shah, Mansi, Duran, Marcos Vasquez, Litovchenko, Maria, Sunderland, Mariana Werner, Hill, Mark S, Dietzen, Michelle, Leung, Michelle, Escudero, Mickael, Angelova, Mihaela, Tanic, Miljana, Sivakumar, Monica, Kanu, Nnennaya, Chervova, Olga, Lucas, Olivia, Pich, Oriol, Hobson, Philip, Pawlik, Piotr, Stone, Richard Kevin, Bentham, Robert, Hynds, Robert E, Vendramin, Roberto, Saghafinia, Sadegh, Lopez, Saioa, Gamble, Samuel, Ung, Seng Kuong Anakin, Quezada, Sergio A, Vanloo, Sharon, Zaccaria, Simone, Hessey, Sonya, Boeing, Stefan, Beck, Stephan, Bola, Supreet Kaur, Denner, Tamara, Marafioti, Teresa, Mourikis, Thanos P, Spanswick, Victoria, Barbe, Vittorio, Lu, Wei-Ting, Hill, William, Liu, Wing Kin, Wu, Yin, Naito, Yutaka, Ramsden, Zoe, Veiga, Catarina, Royle, Gary, Collins-Fekete, Charles-Antoine, Fraioli, Francesco, Ashford, Paul, Clark, Tristan, Forster, Martin D, Lee, Siow Ming, Borg, Elaine, Falzon, Mary, Papadatos-Pastos, Dionysis, Wilson, James, Ahmad, Tanya, Procter, Alexander James, Ahmed, Asia, Taylor, Magali N, Nair, Arjun, Lawrence, David, Patrini, Davide, Navani, Neal, Thakrar, Ricky M, Janes, Sam M, Hoogenboom, Emilie Martinoni, Monk, Fleur, Holding, James W, Choudhary, Junaid, Bhakhri, Kunal, Scarci, Marco, Hayward, Martin, Panagiotopoulos, Nikolaos, Gorman, Pat, Khiroya, Reena, Stephens, Robert CM, Wong, Yien Ning Sophia, Bandula, Steve, Sharp, Abigail, Smith, Sean, Gower, Nicole, Dhanda, Harjot Kaur, Chan, Kitty, Pilotti, Camilla, Leslie, Rachel, Grapa, Anca, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Yuan, Yinyin, Chuter, David, MacKenzie, Mairead, Chee, Serena, Alzetani, Aiman, Cave, Judith, Scarlett, Lydia, Richards, Jennifer, Ingram, Papawadee, Austin, Silvia, Lim, Eric, De Sousa, Paulo, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Bhayani, Harshil, Ambrose, Lyn, Devaraj, Anand, Chavan, Hema, Begum, Sofina, Buderi, Silviu, Kaniu, Daniel, Malima, Mpho, Booth, Sarah, Nicholson, Andrew G, Fernandes, Nadia, Shah, Pratibha, Proli, Chiara, Hewish, Madeleine, Danson, Sarah, Shackcloth, Michael J, Robinson, Lily, Russell, Peter, Blyth, Kevin G, Dick, Craig, Le Quesne, John, Kirk, Alan, Asif, Mo, Bilancia, Rocco, Kostoulas, Nikos, and Thomas, Mathew

Subjects
Male, Proteomics, Cachexia, Lung Neoplasms, Antigens, Neoplasm, Carcinoma, Non-Small-Cell Lung, Body Weight, Body Composition, Humans, Neoplasm Recurrence, Local, Muscle, Skeletal, Neoplasm Proteins
Abstract

Cancer-associated cachexia (CAC) is a major contributor to morbidity and mortality in individuals with non-small cell lung cancer. Key features of CAC include alterations in body composition and body weight. Here, we explore the association between body composition and body weight with survival and delineate potential biological processes and mediators that contribute to the development of CAC. Computed tomography-based body composition analysis of 651 individuals in the TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy (Rx)) study suggested that individuals in the bottom 20th percentile of the distribution of skeletal muscle or adipose tissue area at the time of lung cancer diagnosis, had significantly shorter lung cancer-specific survival and overall survival. This finding was validated in 420 individuals in the independent Boston Lung Cancer Study. Individuals classified as having developed CAC according to one or more features at relapse encompassing loss of adipose or muscle tissue, or body mass index-adjusted weight loss were found to have distinct tumor genomic and transcriptomic profiles compared with individuals who did not develop such features. Primary non-small cell lung cancers from individuals who developed CAC were characterized by enrichment of inflammatory signaling and epithelial-mesenchymal transitional pathways, and differentially expressed genes upregulated in these tumors included cancer-testis antigen MAGEA6 and matrix metalloproteinases, such as ADAMTS3. In an exploratory proteomic analysis of circulating putative mediators of cachexia performed in a subset of 110 individuals from TRACERx, a significant association between circulating GDF15 and loss of body weight, skeletal muscle and adipose tissue was identified at relapse, supporting the potential therapeutic relevance of targeting GDF15 in the management of CAC. ispartof: NATURE MEDICINE vol:29 issue:4 ispartof: location:United States status: Published online

Published
2023

27. The evolution of non-small cell lung cancer metastases in TRACERx

Author

Al Bakir, Maise, Huebner, Ariana, Martinez-Ruiz, Carlos, Grigoriadis, Kristiana, Watkins, Thomas BK, Pich, Oriol, Moore, David A, Veeriah, Selvaraju, Ward, Sophia, Laycock, Joanne, Johnson, Diana, Rowan, Andrew, Razaq, Maryam, Akther, Mita, Naceur-Lombardelli, Cristina, Prymas, Paulina, Toncheva, Antonia, Hessey, Sonya, Dietzen, Michelle, Colliver, Emma, Frankell, Alexander, Bunkum, Abigail, Lim, Emilia L, Karasaki, Takahiro, Abbosh, Christopher, Hiley, Crispin T, Hill, Mark S, Cook, Daniel E, Wilson, Gareth A, Salgado, Roberto, Nye, Emma, Stone, Richard Kevin, Fennell, Dean A, Price, Gillian, Kerr, Keith M, Naidu, Babu, Middleton, Gary, Summers, Yvonne, Lindsay, Colin R, Blackhall, Fiona H, Cave, Judith, Blyth, Kevin G, Nair, Arjun, Ahmed, Asia, Taylor, Magali N, Procter, Alexander James, Falzon, Mary, Lawrence, David, Navani, Neal, Thakrar, Ricky M, Janes, Sam M, Papadatos-Pastos, Dionysis, Forster, Martin D, Lee, Siow Ming, Ahmad, Tanya, Quezada, Sergio, Peggs, Karl S, Van Loo, Peter, Dive, Caroline, Hackshaw, Allan, Birkbak, Nicolai J, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, Swanton, Charles, Lester, Jason F, Bajaj, Amrita, Nakas, Apostolos, Sodha-Ramdeen, Azmina, Ang, Keng, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Boyles, Rebecca, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Dulloo, Sean, Matharu, Gurdeep, Shaw, Jacqui A, Riley, Joan, Primrose, Lindsay, Boleti, Ekaterini, Cheyne, Heather, Khalil, Mohammed, Richardson, Shirley, Cruickshank, Tracey, Benafif, Sarah, Gilbert, Kayleigh, Patel, Akshay J, Osman, Aya, Lacson, Christer, Langman, Gerald, Shackleford, Helen, Djearaman, Madava, Kadiri, Salma, Leek, Angela, Hodgkinson, Jack Davies, Totten, Nicola, Montero, Angeles, Smith, Elaine, Fontaine, Eustace, Granato, Felice, Doran, Helen, Novasio, Juliette, Rammohan, Kendadai, Joseph, Leena, Bishop, Paul, Shah, Rajesh, Moss, Stuart, Joshi, Vijay, Crosbie, Philip, Gomes, Fabio, Brown, Kate, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Oliveira, Pedro, Krebs, Matthew G, Clipson, Alexandra, Tugwood, Jonathan, Kerr, Alastair, Rothwell, Dominic G, Kilgour, Elaine, Aerts, Hugo JWL, Schwarz, Roland F, Kaufmann, Tom L, Rosenthal, Rachel, Szallasi, Zoltan, Kisistok, Judit, Sokac, Mateo, Diossy, Miklos, Demeulemeester, Jonas, Stewart, Aengus, Magness, Alastair, Karamani, Angeliki, Chain, Benny, Campbell, Brittany B, Castignani, Carla, Bailey, Chris, Puttick, Clare, Weeden, Clare E, Lee, Claudia, Richard, Corentin, Pearce, David R, Karagianni, Despoina, Biswas, Dhruva, Levi, Dina, Hoxha, Elena, Larose Cadieux, Elizabeth, Gronroos, Eva, Galvez-Cancino, Felip, Athanasopoulou, Foteini, Gimeno-Valiente, Francisco, Kassiotis, George, Stavrou, Georgia, Mastrokalos, Gerasimos, Zhai, Haoran, Lowe, Helen L, Matos, Ignacio, Goldman, Jacki, Reading, James L, Black, James RM, Herrero, Javier, Rane, Jayant K, Nicod, Jerome, Lam, Jie Min, Hartley, John A, Enfield, Katey SS, Selvaraju, Kayalvizhi, Thol, Kerstin, Litchfield, Kevin, Ng, Kevin W, Chen, Kezhong, Dijkstra, Krijn, Thakkar, Krupa, Ensell, Leah, Shah, Mansi, Vasquez, Marcos, Litovchenko, Maria, Werner Sunderland, Mariana, Leung, Michelle, Escudero, Mickael, Angelova, Mihaela, Tanic, Miljana, Sivakumar, Monica, Kanu, Nnennaya, Chervova, Olga, Lucas, Olivia, Al-Sawaf, Othman, Hobson, Philip, Pawlik, Piotr, Bentham, Robert, Hynds, Robert E, Vendramin, Roberto, Saghafinia, Sadegh, Lopez, Saioa, Gamble, Samuel, Ung, Seng Kuong Anakin, Vanloo, Sharon, Boeing, Stefan, Beck, Stephan, Bola, Supreet Kaur, Denner, Tamara, Marafioti, Teresa, Mourikis, Thanos P, Spanswick, Victoria, Barbe, Vittorio, Lu, Wei-Ting, Hill, William, Liu, Wing Kin, Wu, Yin, Naito, Yutaka, Ramsden, Zoe, Veiga, Catarina, Royle, Gary, Collins-Fekete, Charles-Antoine, Fraioli, Francesco, Ashford, Paul, Clark, Tristan, Borg, Elaine, Wilson, James, Patrini, Davide, Martinoni Hoogenboom, Emilie, Monk, Fleur, Holding, James W, Choudhary, Junaid, Bhakhri, Kunal, Scarci, Marco, Hayward, Martin, Panagiotopoulos, Nikolaos, Gorman, Pat, Khiroya, Reena, Stephens, Robert CM, Wong, Yien Ning Sophia, Bandula, Steve, Sharp, Abigail, Smith, Sean, Gower, Nicole, Dhanda, Harjot Kaur, Chan, Kitty, Pilotti, Camilla, Leslie, Rachel, Grapa, Anca, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Yuan, Yinyin, Chuter, David, MacKenzie, Mairead, Chee, Serena, Alzetani, Aiman, Scarlett, Lydia, Richards, Jennifer, Ingram, Papawadee, Austin, Silvia, Lim, Eric, De Sousa, Paulo, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Bhayani, Harshil, Ambrose, Lyn, Devaraj, Anand, Chavan, Hema, Begum, Sofina, Buderi, Silviu, Kaniu, Daniel, Malima, Mpho, Booth, Sarah, Nicholson, Andrew G, Fernandes, Nadia, Shah, Pratibha, Proli, Chiara, Hewish, Madeleine, Danson, Sarah, Shackcloth, Michael J, Robinson, Lily, Russell, Peter, Dick, Craig, Le Quesne, John, Kirk, Alan, Asif, Mo, Bilancia, Rocco, Kostoulas, Nikos, and Thomas, Mathew

Subjects
Clonal Evolution, Cohort Studies, Evolution, Molecular, Lung Neoplasms, Carcinoma, Non-Small-Cell Lung, Disease Progression, Humans, Neoplasm Metastasis, Neoplasm Recurrence, Local, Clone Cells
Abstract

Metastatic disease is responsible for the majority of cancer-related deaths1. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse. ispartof: NATURE vol:616 issue:7957 ispartof: location:England status: Published online

Published
2023

28. The evolution of lung cancer and impact of subclonal selection in TRACERx

Author

Frankell, Alexander M, Dietzen, Michelle, Al Bakir, Maise, Lim, Emilia L, Karasaki, Takahiro, Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Huebner, Ariana, Bunkum, Abigail, Hill, Mark S, Grigoriadis, Kristiana, Moore, David A, Black, James RM, Liu, Wing Kin, Thol, Kerstin, Pich, Oriol, Watkins, Thomas BK, Naceur-Lombardelli, Cristina, Cook, Daniel E, Salgado, Roberto, Wilson, Gareth A, Bailey, Chris, Angelova, Mihaela, Bentham, Robert, Martinez-Ruiz, Carlos, Abbosh, Christopher, Nicholson, Andrew G, Le Quesne, John, Biswas, Dhruva, Rosenthal, Rachel, Puttick, Clare, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Smith, Jon, Xing, Wei, Nicod, Jerome, Price, Gillian, Kerr, Keith M, Naidu, Babu, Middleton, Gary, Blyth, Kevin G, Fennell, Dean A, Forster, Martin D, Lee, Siow Ming, Falzon, Mary, Hewish, Madeleine, Shackcloth, Michael J, Lim, Eric, Benafif, Sarah, Russell, Peter, Boleti, Ekaterini, Krebs, Matthew G, Lester, Jason F, Papadatos-Pastos, Dionysis, Ahmad, Tanya, Thakrar, Ricky M, Lawrence, David, Navani, Neal, Janes, Sam M, Dive, Caroline, Blackhall, Fiona H, Summers, Yvonne, Cave, Judith, Marafioti, Teresa, Herrero, Javier, Quezada, Sergio A, Peggs, Karl S, Schwarz, Roland F, Van Loo, Peter, Miedema, Daniel M, Birkbak, Nicolai J, Hiley, Crispin T, Hackshaw, Allan, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, Swanton, Charles, Bajaj, Amrita, Nakas, Apostolos, Sodha-Ramdeen, Azmina, Ang, Keng, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Boyles, Rebecca, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Dulloo, Sean, Matharu, Gurdeep, Shaw, Jacqui A, Riley, Joa, Primrose, Lindsay, Cheyne, Heather, Khalil, Mohammed, Richardson, Shirley, Cruickshank, Tracey, Gilbert, Kayleigh, Patel, Akshay J, Osman, Aya, Lacson, Christer, Langman, Gerald, Shackleford, Helen, Djearaman, Madava, Kadiri, Salma, Leek, Angela, Hodgkinson, Jack Davies, Totten, Nicola, Montero, Angeles, Smith, Elaine, Fontaine, Eustace, Granato, Felice, Doran, Helen, Novasio, Juliette, Rammohan, Kendadai, Joseph, Leena, Bishop, Paul, Shah, Rajesh, Moss, Stuart, Joshi, Vijay, Crosbie, Philip, Gomes, Fabio, Brown, Kate, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Oliveira, Pedro, Lindsay, Colin R, Clipson, Alexandra, Tugwood, Jonathan, Kerr, Alastair, Rothwell, Dominic G, Kilgour, Elaine, Aerts, Hugo JWL, Kaufmann, Tom L, Szallasi, Zoltan, Kisistok, Judit, Sokac, Mateo, Diossy, Miklos, Demeulemeester, Jonas, Stewart, Aengus, Magness, Alastair, Rowan, Andrew, Karamani, Angeliki, Chain, Benny, Campbell, Brittany B, Castignani, Carla, Weeden, Clare E, Richard, Corentin, Pearce, David R, Karagianni, Despoina, Levi, Dina, Hoxha, Elena, Larose Cadieux, Elizabeth, Nye, Emma, Gronroos, Eva, Galvez-Cancino, Felip, Athanasopoulou, Foteini, Gimeno-Valiente, Francisco, Kassiotis, George, Stavrou, Georgia, Mastrokalos, Gerasimos, Zhai, Haoran L, Lowe, Helen L, Matos, Ignacio, Goldman, Jacki, Reading, James L, Rane, Jayant K, Lam, Jie Min, Hartley, John A, Enfield, Katey SS, Selvaraju, Kayalvizhi, Litchfield, Kevin, Ng, Kevin W, Chen, Kezhong, Dijkstra, Krijn, Thakkar, Krupa, Ensell, Leah, Shah, Mansi, Vasquez, Marcos, Litovchenko, Maria, Werner Sunderland, Mariana, Leung, Michelle, Escudero, Mickael, Tanic, Miljana, Sivakumar, Monica, Kanu, Nnennaya, Chervova, Olga, Lucas, Olivia, Al-Sawaf, Othman, Hobson, Philip, Pawlik, Piotr, Stone, Richard Kevin, Hynds, Robert E, Vendramin, Roberto, Saghafinia, Sadegh, Lopez, Saioa, Gamble, Samuel, Ung, Seng Kuong Anakin, Vanloo, Sharon, Boeing, Stefan, Beck, Stephan, Bola, Supreet Kaur, Denner, Tamara, Mourikis, Thanos P, Spanswick, Victoria, Barbe, Vittorio, Lu, Wei-Ting, Hill, William, Wu, Yin, Naito, Yutaka, Ramsden, Zoe, Veiga, Catarina, Royle, Gary, Collins-Fekete, Charles-Antoine, Fraioli, Francesco, Ashford, Paul, Clark, Tristan, Borg, Elaine, Wilson, James, Procter, Alexander James, Ahmed, Asia, Taylor, Magali N, Nair, Arjun, Patrini, Davide, Martinoni Hoogenboom, Emilie, Monk, Fleur, Holding, James W, Choudhary, Junaid, Bhakhri, Kunal, Scarci, Marco, Hayward, Martin, Panagiotopoulos, Nikolaos, Gorman, Pat, Khiroya, Reena, Stephens, Robert CM, Wong, Yien Ning Sophia, Bandula, Steve, Sharp, Abigail, Smith, Sean, Gower, Nicole, Dhanda, Harjot Kaur, Chan, Kitty, Pilotti, Camilla, Leslie, Rachel, Grapa, Anca, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Yuan, Yinyin, Chuter, David, MacKenzie, Mairead, Chee, Serena, Alzetani, Aiman, Scarlett, Lydia, Richards, Jennifer, Ingram, Papawadee, Austin, Silvia, De Sousa, Paulo, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Bhayani, Harshil, Ambrose, Lyn, Devaraj, Anand, Chavan, Hema, Begum, Sofina, Buderi, Silviu, Kaniu, Daniel, Malima, Mpho, Booth, Sarah, Fernandes, Nadia, Shah, Pratibha, Proli, Chiara, Danson, Sarah, Robinson, Lily, Dick, Craig, Kirk, Alan, Asif, Mo, Bilancia, Rocco, Kostoulas, Nikos, and Thomas, Mathew

Subjects
Lung Neoplasms, Treatment Outcome, DNA Copy Number Variations, Mutagenesis, Carcinoma, Non-Small-Cell Lung, Mutation, Smoking, Humans, Adenocarcinoma of Lung, Neoplasm Recurrence, Local, Phylogeny
Abstract

Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource. ispartof: NATURE vol:616 issue:7957 ispartof: location:England status: Published online

Published
2023

30. Abstract 645: Heterogeneity of immunotherapy biomarkers in the TRACERx non-small cell lung cancer multi-region lung cancer cohort study

Author

Hiley, Crispin T., primary, Litchfield, Kevin, additional, Pich, Oriol, additional, Moore, David, additional, Naceur-Lombardelli, Cristina, additional, Veeriah, Selvaraju, additional, Bakir, Maise Al, additional, Summan, Simranpreet, additional, Grigoriadis, Kristiana, additional, Ruiz, Carlos Martinez, additional, Puttick, Clare, additional, Enfield, Katey, additional, Ward, Sophia, additional, Frankell, Alexander, additional, Biswas, Dhruva, additional, Rosenthal, Rachel, additional, Birkbak, Nicolai J., additional, Jamal-Hanjani, Mariam, additional, McGranahan, Nicholas, additional, Swanton, Charles, additional, and Consortium, TRACERx, additional

Published
2022
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31. Abstract 5636: V-delta-1 T cells are resident in the human lung and associate with survival in patients with non-small cell lung cancer in the TRACERx Study

Author

Wu, Yin, primary, Biswas, Dhruva, additional, Usaite, Ieva, additional, Mihaela, Angelova, additional, Boeing, Stefan, additional, Karasaki, Takahiro, additional, Veeriah, Selvaraju, additional, Czyzewska-Khan, Justyna, additional, Reading, James, additional, Georgiou, Andrew, additional, Al-Bakir, Maise, additional, McGranahan, Nicholas, additional, Jamal-Hanjani, Mariam, additional, Hackshaw, Allan, additional, Consortium, TRACERx, additional, Quezada, Sergio, additional, Hayday, Adrian, additional, and Swanton, Charles, additional

Published
2022
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33. Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay

Author

Orlando, Francesco, Romanel, Alessandro, Trujillo, Blanca, Sigouros, Michael, Wetterskog, Daniel, Quaini, Orsetta, Leone, Gianmarco, Xiang, Jenny Z, Wingate, Anna, Tagawa, Scott, Jayaram, Anuradha, Linch, Mark, Swanton, Charles, Jamal-Hanjani, Mariam, Abbosh, Chris, Zaccaria, Simone, Hessey, Sonya, Shiu, Kai-Keen, Bridgewater, John, Hochhauser, Daniel, Forster, Martin, Lee, Siow-Ming, Ahmad, Tanya, Papadatos-Pastos, Dionysis, Janes, Sam, Van Loo, Peter, Enfield, Katey, McGranahan, Nicholas, Huebner, Ariana, Quezada, Sergio, Beck, Stephan, Parker, Peter, Enver, Tariq, Hynds, Robert E, Dijkstra, Krijn, Pearce, David R, Falzon, Mary, Proctor, Ian, Sinclair, Ron, Lok, Chi-wah, Rhodes, Zoe, Moore, David, Marafioti, Teresa, Mitchison, Miriam, Ellery, Peter, Sivakumar, Monica, Brandner, Sebastian, Rowan, Andrew, Hiley, Crispin, Veeriah, Selvaraju, Shaw, Heather, Attard, Gert, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Prymas, Paulina, Watkins, Tom, Bailey, Chris, Ruiz, Carlos Martinez, Litchfield, Kevin, Al-Bakir, Maise, Kanu, Nnenna, Ward, Sophie, Lim, Emilia, Reading, James, Chain, Benny, Alba, Blanca Trujillo, Akay, Melek, Flanagan, Adrienne, Biswas, Dhruva, Pich, Oriol, Dietzen, Michelle, Puttick, Clare, Colliver, Emma, Magness, Alistair, Angelova, Mihaela, Black, James, Lucas, Olivia, Hill, William, Liu, Wing-Kin, Frankell, Alexander, Magno, Neil, Athanasopoulou, Foteini, Wilson, Gareth, Rosenthal, Rachel, Salgado, Roberto, Lee, Claudia, Grigoriadis, Kristiana, Al-Sawaf, Othman, Karasaki, Takahiro, Bunkum, Abigail, Noorani, Imran, Benafif, Sarah, Barbe, Vittorio, Bola, Supreet, Vainauskas, Osvaldas, Hasan, Mahedi, Lise, Stefano, Leone, GianMarco, Alifrangis, Constantine, McGovern, Ursula, Thol, Kerstin, Gamble, Samuel, Ung, Seng Kuong, Sahwangarrom, Teerapon, Marin, Claudia Peinador, Wong, Sophia, Pawlik, Piotr, Gishen, Faye, Tookman, Adrian, Stone, Paddy, Stirling, Caroline, Turajlic, Samra, Larkin, James, Pickering, Lisa, Furness, Andrew, Young, Kate, Drake, Will, Edmonds, Kim, Hunter, Nikki, Mangwende, Mary, Pearce, Karla, Grostate, Lauren, Au, Lewis, Spain, Lavinia, Shepherd, Scott, Yan, Haixi, Shum, Ben, Tippu, Zayd, Hanley, Brian, Spencer, Charlotte, Emmerich, Max, Gerard, Camille, Schmitt, Andreas Michael, Del Rosario, Lyra, Carlyle, Eleanor, Lewis, Charlotte, Holt, Lucy, Lucanas, Analyn, O'Flaherty, Molly, Hazell, Steve, Mudhar, Hardeep, Messiou, Christina, Latifoltojar, Arash, Fendler, Annika, Byrne, Fiona, Pallinkonda, Husayn, Lobon, Irene, Coulton, Alex, Cattin, Anne Laure, Deng, Daqi, Feng, Geoffrey Hugang, Rowan, Andew, Yousaf, Nadia, Popat, Sanjay, Curtis, Olivia, Milner-Watts, Charlotte, Stamp, Gordon, Nye, Emma, Murra, Aida, Korteweg, Justine, Kelly, Denise, Terry, Lauren, Biano, Jennifer, Peat, Kema, Kelly, Kayleigh, Hill, Peter, Josephs, Debra, Irshad, Sheeba, Chandra, Ashish, Spicer, James, Mahadeva, Ula, Green, Anna, Stewart, Ruby, Iredale, Lara-Rose, Mackay, Tina, Deakin, Ben, Enting, Debra, Rudman, Sarah, Ghosh, Sharmistha, Karapagniotou, Lena, Pintus, Elias, Tutt, Andrew, Howlett, Sarah, Michalarea, Vasiliki, Brenton, James, Caldas, Carlos, Fitzgerald, Rebecca, Jimenez-Linan, Merche, Provenzano, Elena, Cluroe, Alison, Paterson, Anna, Aitken, Sarah, Allinson, Kieren, Stewart, Grant, McDermott, Ultan, Beddowes, Emma, Maughan, Tim, Ansorge, Olaf, Campbell, Peter, Roxburgh, Patricia, Fraser, Sioban, Kidd, Andrew, Blyth, Kevin, Le Quesne, John, Krebs, Matthew, Blackhall, Fiona, Summers, Yvonne, Oliveira, Pedro, Ortega-Franco, Ana, Dive, Caroline, Gomes, Fabio, Carter, Mat, Dransfield, Jo, Thomas, Anne, Fennell, Dean, Shaw, Jacqui, Naidu, Babu, Baijal, Shobhit, Tanchel, Bruce, Langman, Gerald, Robinson, Andrew, Collard, Martin, Cockcroft, Peter, Ferris, Charlotte, Bancroft, Hollie, Kerr, Amy, Middleton, Gary, Webb, Joanne, Kadiri, Salma, Colloby, Peter, Olisemeke, Bernard, Wilson, Rodelaine, Tomlinson, Ian, McNeish, Iain, Jogai, Sanjay, Holden, Samantha, Fernandes, Tania, Hampton, Blanche, McKenzie, Mairead, Hackshaw, Allan, Sharp, Abby, Chan, Kitty, Farrelly, Laura, Bridger, Hayley, Leslie, Rachel, Consortium, PEACE, Rubin, Mark A, Wyatt, Alexander W, Beltran, Himisha, Attard, Gerhardt, and Demichelis, Francesca

Subjects
Chemical Biology & High Throughput, Signalling & Oncogenes, Human Biology & Physiology, Ecology,Evolution & Ethology, Genome Integrity & Repair, Tumour Biology, Genetics & Genomics, Computational & Systems Biology
Abstract

Sequencing of cell-free DNA (cfDNA) in cancer patients’ plasma offers a minimally-invasive solution to detect tumor cell genomic alterations to aid real-time clinical decision-making. The reliability of copy number detection decreases at lower cfDNA tumor fractions, limiting utility at earlier stages of the disease. To test a novel strategy for detection of allelic imbalance, we developed a prostate cancer bespoke assay, PCF_SELECT, that includes an innovative sequencing panel covering ∼25 000 high minor allele frequency SNPs and tailored analytical solutions to enable allele-informed evaluation. First, we assessed it on plasma samples from 50 advanced prostate cancer patients. We then confirmed improved detection of genomic alterations in samples with

Published
2022
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34. Impact of cancer evolution on immune surveillance and checkpoint inhibitor response

Author

Wu, Yin, Biswas, Dhruva, and Swanton, Charles

Subjects
Chemical Biology & High Throughput, Signalling & Oncogenes, Human Biology & Physiology, Ecology,Evolution & Ethology, Genome Integrity & Repair, bacteria, biochemical phenomena, metabolism, and nutrition, Tumour Biology, Genetics & Genomics, Computational & Systems Biology
Abstract

Intratumour heterogeneity (ITH) is pervasive across all cancers studied and may provide the evolving tumour multiple routes to escape immune surveillance. Immune checkpoint inhibitors (CPIs) are rapidly becoming standard of care for many cancers. Here, we discuss recent work investigating the influence of ITH on patient response to immune checkpoint inhibitor (CPI) therapy. At its simplest, ITH may confound the diagnostic accuracy of predictive biomarkers used to stratify patients for CPI therapy. Furthermore, ITH is fuelled by mechanisms of genetic instability that can both engage immune surveillance and drive immune evasion. A greater appreciation of the interplay between ITH and the immune system may hold the key to increasing the proportion of patients experiencing durable responses from CPI therapy.

Published
2022
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37. Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy

Author

Balestrini, Simona, primary, Koepp, Matthias J., additional, Gandhi, Sonia, additional, Rickman, Hannah M., additional, Shin, Gee Yen, additional, Houlihan, Catherine F., additional, Anders-Cannon, Jonny, additional, Silvennoinen, Katri, additional, Xiao, Fenglai, additional, Zagaglia, Sara, additional, Hudgell, Kirsty, additional, Ziomek, Mariusz, additional, Haimes, Paul, additional, Sampson, Adam, additional, Parker, Annie, additional, Helen Cross, J., additional, Pardington, Rosemarie, additional, Nastouli, Eleni, additional, Swanton, Charles, additional, Sander, Josemir W., additional, Sisodiya, Sanjay M., additional, Aitken, Jim, additional, Allen, Zoe, additional, Ambler, Rachel, additional, Ambrose, Karen, additional, Ashton, Emma, additional, Avola, Alida, additional, Balakrishnan, Samutheswari, additional, Barns-Jenkins, Caitlin, additional, Barr, Genevieve, additional, Barrell, Sam, additional, Basu, Souradeep, additional, Beale, Rupert, additional, Beesley, Clare, additional, Bhardwaj, Nisha, additional, Bibi, Shahnaz, additional, Bineva-Todd, Ganka, additional, Biswas, Dhruva, additional, Blackman, Michael J., additional, Bonnet, Dominique, additional, Bowker, Faye, additional, Broncel, Malgorzata, additional, Brooks, Claire, additional, Buck, Michael D., additional, Buckton, Andrew, additional, Budd, Timothy, additional, Burrell, Alana, additional, Busby, Louise, additional, Bussi, Claudio, additional, Butterworth, Simon, additional, Byott, Matthew, additional, Byrne, Fiona, additional, Byrne, Richard, additional, Caidan, Simon, additional, Campbell, Joanna, additional, Canton, Johnathan, additional, Cardoso, Ana, additional, Carter, Nick, additional, Carvalho, Luiz, additional, Carzaniga, Raffaella, additional, Chandler, Natalie, additional, Chen, Qu, additional, Cherepanov, Peter, additional, Churchward, Laura, additional, Clark, Graham, additional, Clayton, Bobbi, additional, Cobolli Gigli, Clementina, additional, Collins, Zena, additional, Cottrell, Sally, additional, Crawford, Margaret, additional, Cubitt, Laura, additional, Cullup, Tom, additional, Davies, Heledd, additional, Davis, Patrick, additional, Davison, Dara, additional, Dearing, Vicky, additional, Debaisieux, Solene, additional, Diaz-Romero, Monica, additional, Dibbs, Alison, additional, Diring, Jessica, additional, Driscoll, Paul C., additional, D'Avola, Annalisa, additional, Earl, Christopher, additional, Edwards, Amelia, additional, Ekin, Chris, additional, Evangelopoulos, Dimitrios, additional, Faraway, Rupert, additional, Fearns, Antony, additional, Ferron, Aaron, additional, Fidanis, Efthymios, additional, Fitz, Dan, additional, Fleming, James, additional, Frampton, Daniel, additional, Frederico, Bruno, additional, Gaiba, Alessandra, additional, Gait, Anthony, additional, Gamblin, Steve, additional, Gärtner, Kathleen, additional, Gaul, Liam, additional, Golding, Helen M., additional, Goldman, Jacki, additional, Goldstone, Robert, additional, Gomez Dominguez, Belen, additional, Gong, Hui, additional, Grant, Paul R., additional, Greco, Maria, additional, Grobler, Mariana, additional, Guedan, Anabel, additional, Gutierrez, Maximiliano G., additional, Hackett, Fiona, additional, Hall, Ross, additional, Halldorsson, Steinar, additional, Harris, Suzanne, additional, Hashim, Sugera, additional, Hatipoglu, Emine, additional, Healy, Lyn, additional, Heaney, Judith, additional, Herbst, Susanne, additional, Hewitt, Graeme, additional, Higgins, Theresa, additional, Hindmarsh, Steve, additional, Hirani, Rajnika, additional, Hope, Joshua, additional, Horton, Elizabeth, additional, Hoskins, Beth, additional, Howell, Michael, additional, Howitt, Louise, additional, Hoyle, Jacqueline, additional, Htun, Mint R., additional, Hubank, Michael, additional, Huerga Encabo, Hector, additional, Hughes, Deborah, additional, Hughes, Jane, additional, Huseynova, Almaz, additional, Hwang, Ming-Shih, additional, Instrell, Rachael, additional, Jackson, Deborah, additional, Jamal-Hanjani, Mariam, additional, Jenkins, Lucy, additional, Jiang, Ming, additional, Johnson, Mark, additional, Jones, Leigh, additional, Kanu, Nnennaya, additional, Kassiotis, George, additional, Kelly, Gavin, additional, Kiely, Louise, additional, Teixeira, Anastacio King Spert, additional, Kirk, Stuart, additional, Kjaer, Svend, additional, Knuepfer, Ellen, additional, Komarov, Nikita, additional, Kotzampaltiris, Paul, additional, Kousis, Konstantinos, additional, Krylova, Tammy, additional, Kucharska, Ania, additional, Labrum, Robyn, additional, Lambe, Catherine, additional, Lappin, Michelle, additional, Lee, Stacey-Ann, additional, Levett, Andrew, additional, Levett, Lisa, additional, Levi, Marcel, additional, Liu, Hon Wing, additional, Loughlin, Sam, additional, Lu, Wei-Ting, additional, MacRae, James I., additional, Madoo, Akshay, additional, Marczak, Julie A., additional, Martensson, Mimmi, additional, Martinez, Thomas, additional, Marzook, Bishara, additional, Matthews, John, additional, Matz, Joachim M., additional, McCall, Samuel, additional, McCoy, Laura E., additional, McKay, Fiona, additional, McNamara, Edel C., additional, Minutti, Carlos M., additional, Mistry, Gita, additional, Molina-Arcas, Miriam, additional, Montaner, Beatriz, additional, Montgomery, Kylie, additional, Moore, Catherine, additional, Moore, David, additional, Moraiti, Anastasia, additional, Moreira-Teixeira, Lucia, additional, Mukherjee, Joyita, additional, Naceur-Lombardelli, Cristina, additional, Nelson, Aileen, additional, Nicod, Jerome, additional, Nightingale, Luke, additional, Nofal, Stephanie, additional, Nurse, Paul, additional, Nutan, Savita, additional, Oedekoven, Caroline, additional, O'Garra, Anne, additional, O'Leary, Jean D., additional, Olsen, Jessica, additional, O'Neill, Olga, additional, O'Reilly, Nicola, additional, Suarez, Paula Ordonez, additional, Osborne, Neil, additional, Pabari, Amar, additional, Pajak, Aleksandra, additional, Papayannopoulos, Venizelos, additional, Paraskevopoulou, Stavroula M, additional, Patel, Namita, additional, Patel, Yogen, additional, Paun, Oana, additional, Peat, Nigel, additional, Peces-Barba Castano, Laura, additional, Caballero, Ana Perez, additional, Perez-Lloret, Jimena, additional, Perrault, Magali S., additional, Perrin, Abigail, additional, Poh, Roy, additional, Poirier, Enzo Z., additional, Polke, James M., additional, Pollitt, Marc, additional, Prieto-Godino, Lucia, additional, Proust, Alize, additional, Puvirajasinghe, Clinda, additional, Queval, Christophe, additional, Ramachandran, Vijaya, additional, Ramaprasad, Abhinay, additional, Ratcliffe, Peter, additional, Reed, Laura, additional, Reis e Sousa, Caetano, additional, Richardson, Kayleigh, additional, Ridewood, Sophie, additional, Roberts, Fiona, additional, Roberts, Rowenna, additional, Rodgers, Angela, additional, Romero Clavijo, Pablo, additional, Rosa, Annachiara, additional, Rossi, Alice, additional, Roustan, Chloe, additional, Rowan, Andrew, additional, Sahai, Erik, additional, Sait, Aaron, additional, Sala, Katarzyna, additional, Sanchez, Emilie, additional, Sanderson, Theo, additional, Santucci, Pierre, additional, Sardar, Fatima, additional, Sateriale, Adam, additional, Saunders, Jill A., additional, Sawyer, Chelsea, additional, Schlott, Anja, additional, Schweighoffer, Edina, additional, Segura-Bayona, Sandra, additional, Shah Punatar, Rajvee, additional, Shahmanesh, Maryam, additional, Shaw, Joe, additional, Silva Dos Santos, Mariana, additional, Silvestre, Margaux, additional, Singer, Matthew, additional, Snell, Daniel M., additional, Song, Ok-Ryul, additional, Spyer, Moira J., additional, Steel, Louisa, additional, Strange, Amy, additional, Sullivan, Adrienne E., additional, Tan, Michele S.Y., additional, Tautz-Davis, Zoe H., additional, Taylor, Effie, additional, Taylor, Gunes, additional, Taylor, Harriet B., additional, Taylor-Beadling, Alison, additional, Teixeira Subtil, Fernanda, additional, Terré Torras, Berta, additional, Toolan-Kerr, Patrick, additional, Torelli, Francesca, additional, Toteva, Tea, additional, Treeck, Moritz, additional, Trojer, Hadija, additional, Tsai, Ming-Han C., additional, Turner, James M.A., additional, Turner, Melanie, additional, Ule, Jernej, additional, Ulferts, Rachel, additional, Vanloo, Sharon P., additional, Veeriah, Selvaraju, additional, Venkatesan, Subramanian, additional, Vousden, Karen, additional, Wack, Andreas, additional, Walder, Claire, additional, Walker, Philip A., additional, Wang, Yiran, additional, Ward, Sophia, additional, Wenman, Catharina, additional, Williams, Luke, additional, Williams, Matthew J., additional, Keong Wong, Wai, additional, Wright, Joshua, additional, Wu, Mary, additional, Wynne, Lauren, additional, Xiang, Zheng, additional, Yap, Melvyn, additional, Zagalak, Julian A., additional, Zecchin, Davide, additional, Zillwood, Rachel, additional, Carthiyaniamma, Santhakumari, additional, DeTisi, Jane, additional, Dick, Julie, additional, Hill, Andrea, additional, Kipper, Karin, additional, Kullar, Birinder, additional, Norris, Sarah, additional, Rugg-Gunn, Fergus, additional, Salvatierra, Rebecca, additional, Shaya, Gabriel, additional, Sloan, Astrid, additional, Singh, Priyanka, additional, Varley, James, additional, and Whatley, Ben, additional

Published
2021
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38. Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

Author

Litchfield, Kevin, primary, Reading, James L., additional, Puttick, Clare, additional, Thakkar, Krupa, additional, Abbosh, Chris, additional, Bentham, Robert, additional, Watkins, Thomas B.K., additional, Rosenthal, Rachel, additional, Biswas, Dhruva, additional, Rowan, Andrew, additional, Lim, Emilia, additional, Al Bakir, Maise, additional, Turati, Virginia, additional, Guerra-Assunção, José Afonso, additional, Conde, Lucia, additional, Furness, Andrew J.S., additional, Saini, Sunil Kumar, additional, Hadrup, Sine R., additional, Herrero, Javier, additional, Lee, Se-Hoon, additional, Van Loo, Peter, additional, Enver, Tariq, additional, Larkin, James, additional, Hellmann, Matthew D., additional, Turajlic, Samra, additional, Quezada, Sergio A., additional, McGranahan, Nicholas, additional, and Swanton, Charles, additional

Published
2021
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39. Scalable and robust SARS-CoV-2 testing in an academic center

Author

Aitken, Jim, Ambrose, Karen, Barrell, Sam, Beale, Rupert, Bineva-Todd, Ganka, Biswas, Dhruva, Byrne, Richard, Caidan, Simon, Cherepanov, Peter, Churchward, Laura, Clark, Graham, Crawford, Margaret, Cubitt, Laura, Dearing, Vicky, Earl, Christopher, Edwards, Amelia, Ekin, Chris, Fidanis, Efthymios, Gaiba, Alessandra, Gamblin, Steve, Gandhi, Sonia, Goldman, Jacki, Goldstone, Robert, Grant, Paul R., Greco, Maria, Heaney, Judith, Hindmarsh, Steve, Houlihan, Catherine F., Howell, Michael, Hubank, Michael, Hughes, Deborah, Instrell, Rachael, Jackson, Deborah, Jamal-Hanjani, Mariam, Jiang, Ming, Johnson, Mark, Jones, Leigh, Kanu, Nnennaya, Kassiotis, George, Kirk, Stuart, Kjaer, Svend, Levett, Andrew, Levett, Lisa, Levi, Marcel, Lu, Wei-Ting, MacRae, James I., Matthews, John, McCoy, Laura E., Moore, Catherine, Moore, David, Nastouli, Eleni, Nicod, Jerome, Nightingale, Luke, Olsen, Jessica, O’Reilly, Nicola, Pabari, Amar, Papayannopoulos, Venizelos, Patel, Namita, Peat, Nigel, Pollitt, Marc, Ratcliffe, Peter, Reis e Sousa, Caetano, Rosa, Annachiara, Rosenthal, Rachel, Roustan, Chloe, Rowan, Andrew, Shin, Gee Yen, Snell, Daniel M., Song, Ok-Ryul, Spyer, Moira J., Strange, Amy, Swanton, Charles, Turner, James M. A., Turner, Melanie, Wack, Andreas, Walker, Philip A., Ward, Sophia, Wong, Wai Keong, Wright, Joshua, Wu, Mary, Allen, Zoe, Ambler, Rachel, Ashton, Emma, Avola, Alida, Balakrishnan, Samutheswari, Barns-Jenkins, Caitlin, Barr, Genevieve, Basu, Souradeep, Beesley, Clare, Bhardwaj, Nisha, Bibi, Shahnaz, Blackman, Michael J., Bonnet, Dominique, Bowker, Faye, Broncel, Malgorzata, Brooks, Claire, Buck, Michael D., Buckton, Andrew, Budd, Timothy, Burrell, Alana, Busby, Louise, Bussi, Claudio, Butterworth, Simon, Byrne, Fiona, Campbell, Joanna, Canton, Johnathan, Cardoso, Ana, Carter, Nick, Carvalho, Luiz, Carzaniga, Raffaella, Chandler, Natalie, Chen, Qu, Clayton, Bobbi, Gigli, Clementina Cobolli, Collins, Zena, Cottrell, Sally, Cullup, Tom, Davies, Heledd, Davis, Patrick, Davison, Dara, Debaisieux, Solene, Diaz-Romero, Monica, Dibbs, Alison, Diring, Jessica, Driscoll, Paul C., D’Avola, Annalisa, Evangelopoulos, Dimitrios, Faraway, Rupert, Fearns, Antony, Ferron, Aaron, Dan Fitz, Fleming, James, Frederico, Bruno, Gait, Anthony, Gaul, Liam, Golding, Helen M., Gomez Dominguez, Belen, Gong, Hui, Grobler, Mariana, Guedan, Anabel, Gutierrez, Maximiliano G., Hackett, Fiona, Hall, Ross, Halldorsson, Steinar, Harris, Suzanne, Hashim, Sugera, Healy, Lyn, Herbst, Susanne, Hewitt, Graeme, Higgins, Theresa, Hirani, Rajnika, Hope, Joshua, Horton, Elizabeth, Hoskins, Beth, Howitt, Louise, Hoyle, Jacqueline, Htun, Mint R., Huerga Encabo, Hector, Hughes, Jane, Huseynova, Almaz, Hwang, Ming-Shih, Jenkins, Lucy, Kiely, Louise, King Spert Teixeira, Anastacio, Knuepfer, Ellen, Komarov, Nikita, Kotzampaltiris, Paul, Kousis, Konstantinos, Krylova, Tammy, Kucharska, Ania, Labrum, Robyn, Lambe, Catherine, Lappin, Michelle, Lee, Stacey-Ann, Liu, Hon Wing, Loughlin, Sam, Madoo, Akshay, Marczak, Julie A., Martensson, Mimmi, Martinez, Thomas, Marzook, Bishara, Matz, Joachim M., McCall, Samuel, McKay, Fiona, McNamara, Edel C., Minutti, Carlos M., Mistry, Gita, Molina-Arcas, Miriam, Montaner, Beatriz, Montgomery, Kylie, Moraiti, Anastasia, Moreira-Teixeira, Lucia, Mukherjee, Joyita, Naceur-Lombardelli, Cristina, Nelson, Aileen, Nofal, Stephanie, Nurse, Paul, Nutan, Savita, Oedekoven, Caroline, O’Garra, Anne, O’Leary, Jean D., O’Neill, Olga, Suarez, Paula Ordonez, Osborne, Neil, Pajak, Aleksandra, Patel, Yogen, Paun, Oana, Peces-Barba Castano, Laura, Perez Caballero, Ana, Perez-Lloret, Jimena, Perrault, Magali S., Perrin, Abigail, Poh, Roy, Poirier, Enzo Z., Polke, James M., Prieto-Godino, Lucia, Proust, Alize, Puvirajasinghe, Clinda, Queval, Christophe, Ramachandran, Vijaya, Ramaprasad, Abhinay, Reed, Laura, Richardson, Kayleigh, Ridewood, Sophie, Roberts, Fiona, Roberts, Rowenna, Rodgers, Angela, Clavijo, Pablo Romero, Rossi, Alice, Sahai, Erik, Sait, Aaron, Sala, Katarzyna, Sanderson, Theo, Santucci, Pierre, Sardar, Fatima, Sateriale, Adam, Saunders, Jill A., Sawyer, Chelsea, Schlott, Anja, Schweighoffer, Edina, Segura-Bayona, Sandra, Shah Punatar, Rajvee, Shaw, Joe, Silva Dos Santos, Mariana, Silvestre, Margaux, Singer, Matthew, Steel, Louisa, Sullivan, Adrienne E., Tan, Michele S. Y., Tautz-Davis, Zoe H., Taylor, Effie, Taylor, Gunes, Taylor, Harriet B., Taylor-Beadling, Alison, Teixeira Subtil, Fernanda, Terré Torras, Berta, Toolan-Kerr, Patrick, Torelli, Francesca, Toteva, Tea, Treeck, Moritz, Trojer, Hadija, Tsai, Ming-Han C., Ule, Jernej, Ulferts, Rachel, Vanloo, Sharon P., Veeriah, Selvaraju, Venkatesan, Subramanian, Vousden, Karen, Walder, Claire, Wang, Yiran, Wenman, Catharina, Williams, Luke, Williams, Matthew J., Wynne, Lauren, Xiang, Zheng, Yap, Melvyn, Zagalak, Julian A., Zecchin, Davide, and Zillwood, Rachel

Subjects
2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Crick COVID-19 Consortium, Biomedical Engineering, Bioengineering, CORONAVIRUS, medicine.disease_cause, Applied Microbiology and Biotechnology, medicine, Medical Laboratory Science, Humans, Royaume uni, Coronavirus, Reino unido, Science & Technology, business.industry, Clinical Laboratory Techniques, Reverse Transcriptase Polymerase Chain Reaction, Academies and Institutes, Virology, United Kingdom, Europe, Biotechnology & Applied Microbiology, Molecular Medicine, business, Coronavirus Infections, Life Sciences & Biomedicine, Biotechnology, PNEUMONIA OUTBREAK
Published
2020

40. Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Author

Li, Jun, primary, Duran, Mercedes A., additional, Dhanota, Ninjit, additional, Chatila, Walid K., additional, Bettigole, Sarah E., additional, Kwon, John, additional, Sriram, Roshan K., additional, Humphries, Matthew P., additional, Salto-Tellez, Manuel, additional, James, Jacqueline A., additional, Hanna, Matthew G., additional, Melms, Johannes C., additional, Vallabhaneni, Sreeram, additional, Litchfield, Kevin, additional, Usaite, Ieva, additional, Biswas, Dhruva, additional, Bareja, Rohan, additional, Li, Hao Wei, additional, Martin, Maria Laura, additional, Dorsaint, Princesca, additional, Cavallo, Julie-Ann, additional, Li, Peng, additional, Pauli, Chantal, additional, Gottesdiener, Lee, additional, DiPardo, Benjamin J., additional, Hollmann, Travis J., additional, Merghoub, Taha, additional, Wen, Hannah Y., additional, Reis-Filho, Jorge S., additional, Riaz, Nadeem, additional, Su, Shin-San Michael, additional, Kalbasi, Anusha, additional, Vasan, Neil, additional, Powell, Simon N., additional, Wolchok, Jedd D., additional, Elemento, Olivier, additional, Swanton, Charles, additional, Shoushtari, Alexander N., additional, Parkes, Eileen E., additional, Izar, Benjamin, additional, and Bakhoum, Samuel F., additional

Published
2020
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42. Publisher Correction: A clonal expression biomarker associates with lung cancer mortality

Author

Biswas, Dhruva, Birkbak, Nicolai J., Rosenthal, Rachel, Hiley, Crispin T., Lim, Emilia L., Papp, Krisztian, and Boeing, Stefan

Subjects
Biological sciences, Health
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper., Author(s): Dhruva Biswas [sup.1] [sup.2] [sup.3] , Nicolai J. Birkbak [sup.1] [sup.3] [sup.4] [sup.5] , Rachel Rosenthal [sup.1] [sup.2] [sup.3] , Crispin T. Hiley [sup.1] [sup.3] , Emilia L. Lim [...]

Published
2020
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43. Meta-analysis of tumor and T cell intrinsic mechanisms of sensitization to checkpoint inhibition

Author

Litchfield, Kevin, primary, Reading, James L., additional, Puttick, Clare, additional, Abbosh, Chris, additional, Bentham, Robert, additional, Watkins, Thomas B. K., additional, Rosenthal, Rachel, additional, Biswas, Dhruva, additional, Lim, Emilia, additional, AL-Bakir, Maise, additional, Turati, Virginia, additional, Guerra-Assunção, José Afonso, additional, Conde, Lucia, additional, Furness, Andrew J.S., additional, Saini, Sunil Kumar, additional, Hadrup, Sine R, additional, Herrero, Javier, additional, Rowan, Andrew, additional, Enver, Tariq, additional, Hellmann, Matthew D., additional, Larkin, James, additional, Turajlic, Samra, additional, Quezada, Sergio, additional, McGranahan, Nicholas, additional, and Swanton, Charles, additional

Published
2020
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44. Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers

Author

Houlihan, Catherine F, primary, Vora, Nina, additional, Byrne, Thomas, additional, Lewer, Dan, additional, Kelly, Gavin, additional, Heaney, Judith, additional, Gandhi, Sonia, additional, Spyer, Moira J, additional, Beale, Rupert, additional, Cherepanov, Peter, additional, Moore, David, additional, Gilson, Richard, additional, Gamblin, Steve, additional, Kassiotis, George, additional, McCoy, Laura E, additional, Swanton, Charles, additional, Hayward, Andrew, additional, Nastouli, Eleni, additional, Aitken, Jim, additional, Allen, Zoe, additional, Ambler, Rachel, additional, Ambrose, Karen, additional, Ashton, Emma, additional, Avola, Alida, additional, Balakrishnan, Samutheswari, additional, Barns-Jenkins, Caitlin, additional, Barr, Genevieve, additional, Barrell, Sam, additional, Basu, Souradeep, additional, Beesley, Clare, additional, Bhardwaj, Nisha, additional, Bibi, Shahnaz, additional, Bineva-Todd, Ganka, additional, Biswas, Dhruva, additional, Blackman, Michael J, additional, Bonnet, Dominique, additional, Bowker, Faye, additional, Broncel, Malgorzata, additional, Brooks, Claire, additional, Buck, Michael D, additional, Buckton, Andrew, additional, Budd, Timothy, additional, Burrell, Alana, additional, Busby, Louise, additional, Bussi, Claudio, additional, Butterworth, Simon, additional, Byrne, Fiona, additional, Byrne, Richard, additional, Caidan, Simon, additional, Campbell, Joanna, additional, Canton, Johnathan, additional, Cardoso, Ana, additional, Carter, Nick, additional, Carvalho, Luiz, additional, Carzaniga, Raffaella, additional, Chandler, Natalie, additional, Chen, Qu, additional, Churchward, Laura, additional, Clark, Graham, additional, Clayton, Bobbi, additional, Cobolli Gigli, Clementina, additional, Collins, Zena, additional, Cottrell, Sally, additional, Crawford, Margaret, additional, Cubitt, Laura, additional, Cullup, Tom, additional, Davies, Heledd, additional, Davis, Patrick, additional, Davison, Dara, additional, D'Avola, Annalisa, additional, Dearing, Vicky, additional, Debaisieux, Solene, additional, Diaz-Romero, Monica, additional, Dibbs, Alison, additional, Diring, Jessica, additional, Driscoll, Paul C, additional, Earl, Christopher, additional, Edwards, Amelia, additional, Ekin, Chris, additional, Evangelopoulos, Dimitrios, additional, Faraway, Rupert, additional, Fearns, Antony, additional, Ferron, Aaron, additional, Fidanis, Efthymios, additional, Fitz, Dan, additional, Fleming, James, additional, Frederico, Bruno, additional, Gaiba, Alessandra, additional, Gait, Anthony, additional, Gaul, Liam, additional, Golding, Helen M, additional, Goldman, Jacki, additional, Goldstone, Robert, additional, Gomez Dominguez, Belen, additional, Gong, Hui, additional, Grant, Paul R, additional, Greco, Maria, additional, Grobler, Mariana, additional, Guedan, Anabel, additional, Gutierrez, Maximiliano G, additional, Hackett, Fiona, additional, Hall, Ross, additional, Halldorsson, Steinar, additional, Harris, Suzanne, additional, Hashim, Sugera, additional, Healy, Lyn, additional, Herbst, Susanne, additional, Hewitt, Graeme, additional, Higgins, Theresa, additional, Hindmarsh, Steve, additional, Hirani, Rajnika, additional, Hope, Joshua, additional, Horton, Elizabeth, additional, Hoskins, Beth, additional, Houlihan, Catherine F, additional, Howell, Michael, additional, Howitt, Louise, additional, Hoyle, Jacqueline, additional, Htun, Mint R, additional, Hubank, Michael, additional, Huerga Encabo, Hector, additional, Hughes, Deborah, additional, Hughes, Jane, additional, Huseynova, Almaz, additional, Hwang, Ming-Shih, additional, Instrell, Rachael, additional, Jackson, Deborah, additional, Jamal-Hanjani, Mariam, additional, Jenkins, Lucy, additional, Jiang, Ming, additional, Johnson, Mark, additional, Jones, Leigh, additional, Kanu, Nnennaya, additional, Kiely, Louise, additional, King Spert Teixeira, Anastacio, additional, Kirk, Stuart, additional, Kjaer, Svend, additional, Knuepfer, Ellen, additional, Komarov, Nikita, additional, Kotzampaltiris, Paul, additional, Kousis, Konstantinos, additional, Krylova, Tammy, additional, Kucharska, Ania, additional, Labrum, Robyn, additional, Lambe, Catherine, additional, Lappin, Michelle, additional, Lee, Stacey-Ann, additional, Levett, Andrew, additional, Levett, Lisa, additional, Levi, Marcel, additional, Liu, Hon-Wing, additional, Loughlin, Sam, additional, Lu, Wei-Ting, additional, MacRae, James I, additional, Madoo, Akshay, additional, Marczak, Julie A, additional, Martensson, Mimmi, additional, Martinez, Thomas, additional, Marzook, Bishara, additional, Matthews, John, additional, Matz, Joachim M, additional, McCall, Samuel, additional, McKay, Fiona, additional, McNamara, Edel C, additional, Minutti, Carlos M, additional, Mistry, Gita, additional, Molina-Arcas, Miriam, additional, Montaner, Beatriz, additional, Montgomery, Kylie, additional, Moore, Catherine, additional, Moraiti, Anastasia, additional, Moreira-Teixeira, Lucia, additional, Mukherjee, Joyita, additional, Naceur-Lombardelli, Cristina, additional, Nelson, Aileen, additional, Nicod, Jerome, additional, Nightingale, Luke, additional, Nofal, Stephanie, additional, Nurse, Paul, additional, Nutan, Savita, additional, Oedekoven, Caroline, additional, O'Garra, Anne, additional, O'Leary, Jean D, additional, Olsen, Jessica, additional, O'Neill, Olga, additional, Ordonez Suarez, Paula, additional, O'Reilly, Nicola, additional, Osborne, Neil, additional, Pabari, Amar, additional, Pajak, Aleksandra, additional, Papayannopoulos, Venizelos, additional, Patel, Namita, additional, Patel, Yogen, additional, Paun, Oana, additional, Peat, Nigel, additional, Peces-Barba Castano, Laura, additional, Perez Caballero, Ana, additional, Perez-Lloret, Jimena, additional, Perrault, Magali S, additional, Perrin, Abigail, additional, Poh, Roy, additional, Poirier, Enzo Z, additional, Polke, James M, additional, Pollitt, Marc, additional, Prieto-Godino, Lucia, additional, Proust, Alize, additional, Shah Punatar, Rajvee, additional, Puvirajasinghe, Clinda, additional, Queval, Christophe, additional, Ramachandran, Vijaya, additional, Ramaprasad, Abhinay, additional, Ratcliffe, Peter, additional, Reed, Laura, additional, Reis e Sousa, Caetano, additional, Richardson, Kayleigh, additional, Ridewood, Sophie, additional, Roberts, Rowenna, additional, Rodgers, Angela, additional, Romero Clavijo, Pablo, additional, Rosa, Annachiara, additional, Rossi, Alice, additional, Roustan, Chloe, additional, Rowan, Andrew, additional, Sahai, Erik, additional, Sait, Aaron, additional, Sala, Katarzyna, additional, Sanderson, Theo, additional, Santucci, Pierre, additional, Sardar, Fatima, additional, Sateriale, Adam, additional, Saunders, Jill A, additional, Sawyer, Chelsea, additional, Schlott, Anja, additional, Schweighoffer, Edina, additional, Segura-Bayona, Sandra, additional, Shaw, Joe, additional, Shin, Gee Yen, additional, Silva Dos Santos, Mariana, additional, Silvestre, Margaux, additional, Singer, Matthew, additional, Snell, Daniel M, additional, Song, Ok-Ryul, additional, Steel, Louisa, additional, Strange, Amy, additional, Sullivan, Adrienne E, additional, Tan, Michele SY, additional, Tautz-Davis, Zoe H, additional, Taylor, Effie, additional, Taylor, Gunes, additional, Taylor, Harriet B, additional, Taylor-Beadling, Alison, additional, Teixeira Subtil, Fernanda, additional, Terré Torras, Berta, additional, Toolan-Kerr, Patrick, additional, Torelli, Francesca, additional, Toteva, Tea, additional, Treeck, Moritz, additional, Trojer, Hadija, additional, Tsai, Ming-Han C, additional, Turner, James MA, additional, Turner, Melanie, additional, Ule, Jernej, additional, Ulferts, Rachel, additional, Vanloo, Sharon P, additional, Veeriah, Selvaraju, additional, Venkatesan, Subramanian, additional, Vousden, Karen, additional, Wack, Andreas, additional, Walder, Claire, additional, Walker, Philip A, additional, Wang, Yiran, additional, Ward, Sophia, additional, Wenman, Catharina, additional, Wiliams, Luke, additional, Williams, Matthew J, additional, Wong, Wai Keong, additional, Wright, Joshua, additional, Wu, Mary, additional, Wynne, Lauren, additional, Xiang, Zheng, additional, Yap, Melvyn, additional, Zagalak, Julian A, additional, Zecchin, Davide, additional, Zillwood, Rachel, additional, Matthews, Rebecca, additional, Severn, Abigail, additional, Adam, Sajida, additional, Enfield, Louise, additional, McBride, Angela, additional, Gärtner, Kathleen, additional, Edwards, Sarah, additional, Lorencatto, Fabiana, additional, Michie, Susan, additional, Manley, Ed, additional, Shahmanesh, Maryam, additional, Lukha, Hinal, additional, Prymas, Paulina, additional, McBain, Hazel, additional, Shortman, Robert, additional, Wood, Leigh, additional, Davies, Claudia, additional, Williams, Bethany, additional, Ng, Kevin W, additional, Cornish, Georgina H, additional, Faulkner, Nikhil, additional, Riddell, Andrew, additional, Hobson, Philip, additional, Agua-Doce, Ana, additional, Bartolovic, Kerol, additional, Russell, Emma, additional, Carr, Lotte, additional, Sanchez, Emilie, additional, Frampton, Daniel, additional, Byott, Matthew, additional, Paraskevopoulou, Stavroula M, additional, Crayton, Elise, additional, Meyer, Carly, additional, Gkouleli, Triantafylia, additional, Stoltenberg, Andrea, additional, Ranieri, Veronica, additional, Byrne, Tom, additional, Roberts, Fiona, additional, and Hatipoglu, Emine, additional

Published
2020
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45. An innate-like Vδ1 + γδ T cell compartment in the human breast is associated with remission in triple-negative breast cancer

Author

Wu, Yin, primary, Kyle-Cezar, Fernanda, additional, Woolf, Richard T., additional, Naceur-Lombardelli, Cristina, additional, Owen, Julie, additional, Biswas, Dhruva, additional, Lorenc, Anna, additional, Vantourout, Pierre, additional, Gazinska, Patrycja, additional, Grigoriadis, Anita, additional, Tutt, Andrew, additional, and Hayday, Adrian, additional

Published
2019
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46. Abstract 2678: A clonal expression biomarker improves prognostic accuracy: TRACERx lung

Author

Biswas, Dhruva, primary, Birkbak, Nicolai J., additional, Rosenthal, Rachel, additional, Hiley, Crispin T., additional, Lim, Emilia L., additional, Papp, Krisztian, additional, Krzystanek, Marcin, additional, Djureinovic, Dijana, additional, Wu, Yin, additional, Moore, David A., additional, Skrypski, Marcin, additional, Abbosh, Christopher, additional, Bakir, Maise Al, additional, Watkins, Thomas B., additional, Veeriah, Selvaraju, additional, Wilson, Gareth A., additional, Jamal-Hanjani, Mariam, additional, Chinnaiyan, Arul M., additional, Micke, Patrick, additional, Bartek, Jiri, additional, Csabai, Istvan, additional, Szallasi, Zoltan, additional, Herrero, Javier, additional, McGranahan, Nicholas, additional, and Swanton, Charles, additional

Published
2019
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47. An innate-like Vδ1+ γδ T cell compartment in the human breast is associated with remission in triple-negative breast cancer.

Author

Wu, Yin, Kyle-Cezar, Fernanda, Woolf, Richard T., Naceur-Lombardelli, Cristina, Owen, Julie, Biswas, Dhruva, Lorenc, Anna, Vantourout, Pierre, Gazinska, Patrycja, Grigoriadis, Anita, Tutt, Andrew, and Hayday, Adrian

Subjects
TRIPLE-negative breast cancer, T cells, HUMAN T cells, T cell receptors, BREAST cancer, CELL populations
Abstract

γδ T cells: Guarding and defending tissues Specific γδ T cell subsets are known to populate tissues such as the skin and gut. To ascertain γδ T cell participation in breast cancer surveillance, Wu et al. isolated cells from grid cultures of human breast tissue. They observed cytolytic innate-like Vδ1+ T cells in healthy human breast tissue as well as tumor tissue. Analysis of a small cohort of women with triple-negative breast cancer revealed that these Vδ1+ T cells were associated with remission and overall survival. These results demonstrate that human tissue-resident γδ T cells may affect breast cancer progression; these cells could be key to existing or future immunotherapy interventions. Innate-like tissue-resident γδ T cell compartments capable of protecting against carcinogenesis are well established in mice. Conversely, the degree to which they exist in humans, their potential properties, and their contributions to host benefit are mostly unresolved. Here, we demonstrate that healthy human breast harbors a distinct γδ T cell compartment, primarily expressing T cell receptor (TCR) Vδ1 chains, by comparison to Vδ2 chains that predominate in peripheral blood. Breast-resident Vδ1+ cells were functionally skewed toward cytolysis and IFN-γ production, but not IL-17, which has been linked with inflammatory pathologies. Breast-resident Vδ1+ cells could be activated innately via the NKG2D receptor, whereas neighboring CD8+ αβ T cells required TCR signaling. A comparable population of Vδ1+ cells was found in human breast tumors, and when paired tumor and nonmalignant samples from 11 patients with triple-negative breast cancer were analyzed, progression-free and overall survival correlated with Vδ1+ cell representation, but not with either total γδ T cells or Vδ2+ T cells. As expected, progression-free survival also correlated with αβ TCRs. However, whereas in most cases TCRαβ repertoires focused, typical of antigen-specific responses, this was not observed for Vδ1+ cells, consistent with their innate-like responsiveness. Thus, maximal patient benefit may accrue from the collaboration of innate-like responses mounted by tissue-resident Vδ1+ compartments and adaptive responses mounted by αβ T cells. [ABSTRACT FROM AUTHOR]

Published
2019
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48. Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse

Author

Chemi, Francesca, Rothwell, Dominic G., McGranahan, Nicholas, Gulati, Sakshi, Abbosh, Chris, Pearce, Simon P., Zhou, Cong, Wilson, Gareth A., Jamal-Hanjani, Mariam, Birkbak, Nicolai, Pierce, Jackie, Kim, Chang Sik, Ferdous, Saba, Burt, Deborah J., Slane-Tan, Daniel, Gomes, Fabio, Moore, David, Shah, Rajesh, Al Bakir, Maise, Hiley, Crispin, Veeriah, Selvaraju, Summers, Yvonne, Crosbie, Philip, Ward, Sophia, Mesquita, Barbara, Dynowski, Marek, Biswas, Dhruva, Tugwood, Jonathan, Blackhall, Fiona, Miller, Crispin, Hackshaw, Allan, Brady, Ged, Swanton, Charles, and Dive, Caroline

Abstract

Approximately 50% of patients with early-stage non-small-cell lung cancer (NSCLC) who undergo surgery with curative intent will relapse within 5 years1,2. Detection of circulating tumor cells (CTCs) at the time of surgery may represent a tool to identify patients at higher risk of recurrence for whom more frequent monitoring is advised. Here we asked whether CellSearch-detected pulmonary venous CTCs (PV-CTCs) at surgical resection of early-stage NSCLC represent subclones responsible for subsequent disease relapse. PV-CTCs were detected in 48% of 100 patients enrolled into the TRACERx study3, were associated with lung-cancer-specific relapse and remained an independent predictor of relapse in multivariate analysis adjusted for tumor stage. In a case study, genomic profiling of single PV-CTCs collected at surgery revealed higher mutation overlap with metastasis detected 10 months later (91%) than with the primary tumor (79%), suggesting that early-disseminating PV-CTCs were responsible for disease relapse. Together, PV-CTC enumeration and genomic profiling highlight the potential of PV-CTCs as early predictors of NSCLC recurrence after surgery. However, the limited sensitivity of PV-CTCs in predicting relapse suggests that further studies using a larger, independent cohort are warranted to confirm and better define the potential clinical utility of PV-CTCs in early-stage NSCLC.

Published
2019
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49. Author Correction: Scalable and robust SARS-CoV-2 testing in an academic center.

Author

Aitken, Jim, Ambrose, Karen, Barrell, Sam, Beale, Rupert, Bineva-Todd, Ganka, Biswas, Dhruva, Byrne, Richard, Caidan, Simon, Cherepanov, Peter, Churchward, Laura, Clark, Graham, Crawford, Margaret, Cubitt, Laura, Dearing, Vicky, Earl, Christopher, Edwards, Amelia, Ekin, Chris, Fidanis, Efthymios, Gaiba, Alessandra, and Gamblin, Steve

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

Published
2020
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50. Publisher Correction: Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse

Author

Chemi, Francesca, Rothwell, Dominic G., McGranahan, Nicholas, Gulati, Sakshi, Abbosh, Chris, Pearce, Simon P., Zhou, Cong, Wilson, Gareth A., Jamal-Hanjani, Mariam, Birkbak, Nicolai, Pierce, Jackie, Kim, Chang Sik, Ferdous, Saba, Burt, Deborah J., Slane-Tan, Daniel, Gomes, Fabio, Moore, David, Shah, Rajesh, Al Bakir, Maise, Hiley, Crispin, Veeriah, Selvaraju, Summers, Yvonne, Crosbie, Philip, Ward, Sophia, Mesquita, Barbara, Dynowski, Marek, Biswas, Dhruva, Tugwood, Jonathan, Blackhall, Fiona, Miller, Crispin, Hackshaw, Allan, Brady, Ged, Swanton, Charles, and Dive, Caroline

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020
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