342 results on '"Cahill, Declan"'
Search Results
2. Does Radical Local Treatment in Oligometastatic Prostate Cancer Improve Overall Survival: A Systematic Review and Meta-analysis
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Madhavan, Kumar, Jena, Rahul, Marathi, Viswas Raghavendra, Kaushal, Devashish, Deen, Shameer, Rustagi, Sanchit, Cahill, Declan, and Sooriakumaran, Prasanna
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- 2023
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3. Prostate Cancer Survivorship and Physical Health
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Goonewardene, Sanchia S., Young, Annie, Cahill, Declan, Persad, Raj, Goonewardene, Sanchia S., editor, Brunckhorst, Oliver, editor, Albala, David, editor, and Ahmed, Kamran, editor
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- 2022
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4. Prostate Cancer Malignancy
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Goonewardene, Sanchia S., Motiwala, Hanif, Persad, Raj, Cahill, Declan, Goonewardene, Sanchia S., editor, Brunckhorst, Oliver, editor, Albala, David, editor, and Ahmed, Kamran, editor
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- 2022
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5. The Role of PET in Salvage Therapy for Prostate Cancer
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Goonewardene, Sanchia S., Persad, Raj, Albala, David, Cahill, Declan, Goonewardene, Sanchia S., editor, Persad, Raj, editor, Ventii, Karen, editor, Albala, David, editor, and Cahill, Declan, editor
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- 2021
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6. Salvage Therapy in Prostate Cancer: Predictors of Recurrence
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Goonewardene, Sanchia S., Persad, Raj, Albala, David, Cahill, Declan, Goonewardene, Sanchia S., editor, Persad, Raj, editor, Ventii, Karen, editor, Albala, David, editor, and Cahill, Declan, editor
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- 2021
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7. Salvage Brachytherapy—Outcomes from Low- and High-Dose Brachytherapy in Prostate Cancer
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Goonewardene, Sanchia S., Persad, Raj, Albala, David, Cahill, Declan, Goonewardene, Sanchia S., editor, Persad, Raj, editor, Ventii, Karen, editor, Albala, David, editor, and Cahill, Declan, editor
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- 2021
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8. Salvage Brachytherapy after Primary Brachytherapy in Recurrent Prostate Cancer
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Goonewardene, Sanchia S., Persad, Raj, Albala, David, Cahill, Declan, Goonewardene, Sanchia S., editor, Persad, Raj, editor, Ventii, Karen, editor, Albala, David, editor, and Cahill, Declan, editor
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- 2021
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9. Salvage Re-Irradiation After Locoregional Failure with Primary Radiotherapy for Prostate Cancer
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Goonewardene, Sanchia S., Persad, Raj, Albala, David, Cahill, Declan, Goonewardene, Sanchia S., editor, Persad, Raj, editor, Ventii, Karen, editor, Albala, David, editor, and Cahill, Declan, editor
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- 2021
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10. Salvage Cryotherapy in Prostate Cancer
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Goonewardene, Sanchia S., Persad, Raj, Albala, David, Cahill, Declan, Goonewardene, Sanchia S., editor, Persad, Raj, editor, Ventii, Karen, editor, Albala, David, editor, and Cahill, Declan, editor
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- 2021
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11. PD62-08 THE MAN VAN PROJECT: SECOND PHASE INTERIM RESULTS
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Moghul, Masood, primary, Croft, Fionnuala, additional, Mutch, Fiona, additional, Westaway, Elisabeth, additional, Kinsella, Netty, additional, Cahill, Declan, additional, and James, Nicholas D., additional
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- 2024
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12. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets
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Wedge, David C, Gundem, Gunes, Mitchell, Thomas, Woodcock, Dan J, Martincorena, Inigo, Ghori, Mohammed, Zamora, Jorge, Butler, Adam, Whitaker, Hayley, Kote-Jarai, Zsofia, Alexandrov, Ludmil B, Van Loo, Peter, Massie, Charlie E, Dentro, Stefan, Warren, Anne Y, Verrill, Clare, Berney, Dan M, Dennis, Nening, Merson, Sue, Hawkins, Steve, Howat, William, Lu, Yong-Jie, Lambert, Adam, Kay, Jonathan, Kremeyer, Barbara, Karaszi, Katalin, Luxton, Hayley, Camacho, Niedzica, Marsden, Luke, Edwards, Sandra, Matthews, Lucy, Bo, Valeria, Leongamornlert, Daniel, McLaren, Stuart, Ng, Anthony, Yu, Yongwei, Zhang, Hongwei, Dadaev, Tokhir, Thomas, Sarah, Easton, Douglas F, Ahmed, Mahbubl, Bancroft, Elizabeth, Fisher, Cyril, Livni, Naomi, Nicol, David, Tavaré, Simon, Gill, Pelvender, Greenman, Christopher, Khoo, Vincent, Van As, Nicholas, Kumar, Pardeep, Ogden, Christopher, Cahill, Declan, Thompson, Alan, Mayer, Erik, Rowe, Edward, Dudderidge, Tim, Gnanapragasam, Vincent, Shah, Nimish C, Raine, Keiran, Jones, David, Menzies, Andrew, Stebbings, Lucy, Teague, Jon, Hazell, Steven, Corbishley, Cathy, CAMCAP Study Group, de Bono, Johann, Attard, Gerhardt, Isaacs, William, Visakorpi, Tapio, Fraser, Michael, Boutros, Paul C, Bristow, Robert G, Workman, Paul, Sander, Chris, The TCGA Consortium, Hamdy, Freddie C, Futreal, Andrew, McDermott, Ultan, Al-Lazikani, Bissan, Lynch, Andrew G, Bova, G Steven, Foster, Christopher S, Brewer, Daniel S, Neal, David E, Cooper, Colin S, and Eeles, Rosalind A
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Genetics ,Human Genome ,Aging ,Cancer ,Urologic Diseases ,Biotechnology ,Prostate Cancer ,Aetiology ,5.1 Pharmaceuticals ,2.1 Biological and endogenous factors ,Development of treatments and therapeutic interventions ,Adult ,Aged ,Aged ,80 and over ,BRCA2 Protein ,Disease Progression ,Hepatocyte Nuclear Factor 3-alpha ,High-Throughput Nucleotide Sequencing ,Humans ,Male ,Middle Aged ,Mutation ,Oncogenes ,Prostatic Neoplasms ,CAMCAP Study Group ,TCGA Consortium ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.
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- 2018
13. A prospective prostate cancer screening programme for men with pathogenic variants in mismatch repair genes (IMPACT): initial results from an international prospective study
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Adams, Lisa, Adlard, Julian, Alfonso, Rosa, Ali, Saira, Andrew, Angela, Araújo, Luís, Azam, Nazya, Ball, Darran, Barker, Queenstone, Basevitch, Alon, Benton, Barbara, Berlin, Cheryl, Bermingham, Nicola, Biller, Leah, Bloss, Angela, Bradford, Matilda, Bradshaw, Nicola, Branson, Amy, Brendler, Charles, Brennan, Maria, Bulman, Barbara, Burgess, Lucy, Cahill, Declan, Callard, Alice, Calvo Verges, Nuria, Cardoso, Marta, Carter, Vanda, Catanzaro, Mario, Chamberlain, Anthony, Chapman, Cyril, Chong, Michael, Clark, Caroline, Clowes, Virginia, Cogley, Lyn, Cole, Trevor, Compton, Cecilia, Conner, Tom, Cookson, Sandra, Cornford, Philip, Costello, Philandra, Coulier, Laura, Davies, Michaela, Dechet, Christopher, DeSouza, Bianca, Devlin, Gemma, Douglas, Fiona, Douglas, Emma, Dudakia, Darshna, Duncan, Alexis, Ellery, Natalie, Everest, Sarah, Freemantle, Sue, Frydenberg, Mark, Fuller, Debbie, Gabriel, Camila, Gale, Madeline, Garcia, Lynda, Gay, Simona, Genova, Elena, George, Angela, Georgiou, Demetra, Gisbert, Alexandra, Gleeson, Margaret, Glover, Wayne, Gnanapragasam, Vincent, Goff, Sally, Goldgar, David, Gonçalves, Nuno, Goodman, Selina, Gorrie, Jennifer, Gott, Hannah, Grant, Anna, Gray, Catherine, Griffiths, Julie, Gupwell, Karin, Gurasashvili, Jana, Hanslien, Eldbjørg, Haraldsdottir, Sigurdis, Hart, Rachel, Hartigan, Catherine, Hawkes, Lara, Heaton, Tricia, Henderson, Alex, Henrique, Rui, Hilario, Kathrine, Hill, Kathryn, Hulick, Peter, Hunt, Clare, Hutchings, Melanie, Ibitoye, Rita, Inglehearn, Thomas, Ireland, Joanna, Islam, Farah, Ismail, Siti, Jacobs, Chris, James, Denzil, Jenkins, Sharon, Jobson, Irene, Johnstone, Anne, Jones, Oliver, Josefsberg Ben-Yehoshua, Sagi, Kaemba, Beckie, Kaul, Karen, Kemp, Zoe, Kinsella, Netty, Klehm, Margaret, Kockelbergh, Roger, Kohut, Kelly, Kosicka-Slawinska, Monika, Kulkarni, Anjana, Kumar, Pardeep, Lam, Jimmy, LeButt, Mandy, Leibovici, Dan, Lim, Ramona, Limb, Lauren, Lomas, Claire, Longmuir, Mark, López, Consol, Magnani, Tiziana, Maia, Sofia, Maiden, Jessica, Male, Alison, Manalo, Merrie, Martin, Phoebe, McBride, Donna, McGuire, Michael, McMahon, Romayne, McNally, Claire, McVeigh, Terri, Melzer, Ehud, Mencias, Mark, Mercer, Catherine, Mitchell, Gillian, Mora, Josefina, Morton, Catherine, Moss, Cathryn, Murphy, Morgan, Murphy, Declan, Mzazi, Shumi, Nadolski, Maria, Newlin, Anna, Nogueira, Pedro, O'Keefe, Rachael, O'Toole, Karen, O'Connell, Shona, Ogden, Chris, Okoth, Linda, Oliveira, Jorge, Paez, Edgar, Palou, Joan, Park, Linda, Patel, Nafisa, Paulo Souto, João, Pearce, Allison, Peixoto, Ana, Perez, Kimberley, Petelin, Lara, Pichert, Gabriella, Poile, Charlotte, Potter, Alison, Preitner, Nadia, Purnell, Helen, Quinn, Ellen, Radice, Paolo, Rankin, Brigette, Rees, Katie, Renton, Caroline, Richardson, Kate, Risby, Peter, Rogers, Jason, Ruderman, Maggie, Ruiz, April, Sajoo, Anaar, Salvatore, Natale, Sands, Victoria, Sanguedolce, Francesco, Sattar, Ayisha, Saunders, Kathryn, Schofield, Lyn, Scott, Rodney, Searle, Anne, Sehra, Ravinder, Selkirk, Christina, Shackleton, Kylie, Shanley, Sue, Shaw, Adam, Shevrin, Daniel, Shipman, Hannah, Sidat, Zahirah, Siguake, Kas, Simon, Kate, Smyth, Courtney, Snadden, Lesley, Solanky, Nita, Solomons, Joyce, Sorrentino, Margherita, Stayner, Barbara, Stephenson, Robert, Stoffel, Elena, Thomas, Maggie, Thompson, Alan, Tidey, Lizzie, Tischkowitz, Marc, Torokwa, Audrey, Townshend, Sharron, Treherne, Katy, Tricker, Karen, Trinh, Quoc-Dien, Tripathi, Vishakha, Turnbull, Clare, Valdagni, Riccardo, Van As, Nicholas, Venne, Vickie, Verdon, Lizzie, Vitellaro, Marco, Vogel, Kristen, Walker, Lisa, Watford, Amy, Watt, Cathy, Weintroub, Ilana, Weiss, Shelly, Weissman, Scott, Weston, Michelle, Wiggins, Jennifer, Wise, Gillian, Woodhouse, Christopher, Yesildag, Pembe, Youngs, Alice, Yurgelun, Matthew, Zollo, Fabiana, Bancroft, Elizabeth K, Page, Elizabeth C, Brook, Mark N, Thomas, Sarah, Taylor, Natalie, Pope, Jennifer, McHugh, Jana, Jones, Ann-Britt, Karlsson, Questa, Merson, Susan, Ong, Kai Ren, Hoffman, Jonathan, Huber, Camilla, Maehle, Lovise, Grindedal, Eli Marie, Stormorken, Astrid, Evans, D Gareth, Rothwell, Jeanette, Lalloo, Fiona, Brady, Angela F, Bartlett, Marion, Snape, Katie, Hanson, Helen, James, Paul, McKinley, Joanne, Mascarenhas, Lyon, Syngal, Sapna, Ukaegbu, Chinedu, Side, Lucy, Thomas, Tessy, Barwell, Julian, Teixeira, Manuel R, Izatt, Louise, Suri, Mohnish, Macrae, Finlay A, Poplawski, Nicola, Chen-Shtoyerman, Rakefet, Ahmed, Munaza, Musgrave, Hannah, Nicolai, Nicola, Greenhalgh, Lynn, Brewer, Carole, Pachter, Nicholas, Spigelman, Allan D, Azzabi, Ashraf, Helfand, Brian T, Halliday, Dorothy, Buys, Saundra, Ramon y Cajal, Teresa, Donaldson, Alan, Cooney, Kathleen A, Harris, Marion, McGrath, John, Davidson, Rosemarie, Taylor, Amy, Cooke, Peter, Myhill, Kathryn, Hogben, Matthew, Aaronson, Neil K, Ardern-Jones, Audrey, Bangma, Chris H, Castro, Elena, Dearnaley, David, Dias, Alexander, Dudderidge, Tim, Eccles, Diana M, Green, Kate, Eyfjord, Jorunn, Falconer, Alison, Foster, Christopher S, Gronberg, Henrik, Hamdy, Freddie C, Johannsson, Oskar, Khoo, Vincent, Lilja, Hans, Lindeman, Geoffrey J, Lubinski, Jan, Axcrona, Karol, Mikropoulos, Christos, Mitra, Anita V, Moynihan, Clare, Ni Raghallaigh, Holly, Rennert, Gad, Collier, Rebecca, Offman, Judith, Kote-Jarai, Zsofia, and Eeles, Rosalind A
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- 2021
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14. Association Between Preoperative Magnetic Resonance Imaging–based Urethral Parameters and Continence Recovery Following Robot-assisted Radical Prostatectomy
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Kim, Lawrence H.C., Patel, Amit, Kinsella, Netty, Sharabiani, Mansour T.A., Ap Dafydd, Derfel, and Cahill, Declan
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- 2020
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15. Sexual and Continence Rehabilitation after Radical Prostatectomy
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Aggarwal, Amit, primary, Cahill, Declan, additional, and Jena, Rahul, additional
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- 2024
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16. Effect of a brief physical activity-based presentation by a former patient for men treated with radical prostatectomy for prostate cancer: a mixed methods pilot study
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Fox, Louis, Wiseman, Theresa, Cahill, Declan, Fleure, Louisa, Kinsella, Janette, Curtis, Emily, Peat, Nicola, and Van Hemelrijck, Mieke
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- 2021
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17. A Single Educational Seminar Increases Confidence and Decreases Dropout from Active Surveillance by 5 Years After Diagnosis of Prostate Cancer
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Kinsella, Netty, Beckmann, Kerri, Cahill, Declan, Elhage, Oussama, Popert, Rick, Cathcart, Paul, Challacombe, Ben, Brown, Christian, and Van Hemelrijck, Mieke
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- 2019
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18. Salvage Brachytherapy—Outcomes from Low- and High-Dose Brachytherapy in Prostate Cancer
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Goonewardene, Sanchia S., primary, Persad, Raj, additional, Albala, David, additional, and Cahill, Declan, additional
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- 2020
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- View/download PDF
19. The Role of PET in Salvage Therapy for Prostate Cancer
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Goonewardene, Sanchia S., primary, Persad, Raj, additional, Albala, David, additional, and Cahill, Declan, additional
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- 2020
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20. Salvage Re-Irradiation After Locoregional Failure with Primary Radiotherapy for Prostate Cancer
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Goonewardene, Sanchia S., primary, Persad, Raj, additional, Albala, David, additional, and Cahill, Declan, additional
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- 2020
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21. Salvage Therapy in Prostate Cancer: Predictors of Recurrence
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Goonewardene, Sanchia S., primary, Persad, Raj, additional, Albala, David, additional, and Cahill, Declan, additional
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- 2020
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22. Salvage Brachytherapy after Primary Brachytherapy in Recurrent Prostate Cancer
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Goonewardene, Sanchia S., primary, Persad, Raj, additional, Albala, David, additional, and Cahill, Declan, additional
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- 2020
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23. Salvage Cryotherapy in Prostate Cancer
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Goonewardene, Sanchia S., primary, Persad, Raj, additional, Albala, David, additional, and Cahill, Declan, additional
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- 2020
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24. COmparing Urolift andStandardTransurethral resection of prostateAhead ofRadiotherapy in men with urinary symptoms secondary to prostate enlargement in Southwest London and North Cumbria (CO-STAR): a study protocol for a randomised feasibility study
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Wong, Kathie, primary, Kinsella, Netty, additional, Seth, Jai, additional, Nicol, David, additional, Cahill, Declan, additional, Kasivisvanathan, Ramanathan, additional, Withington, John, additional, Moghul, Masood, additional, Moss, Charlotte Louise, additional, Van Hemelrijck, Mieke, additional, Giorgakoudi, Kyriaki, additional, Cottrell, Chris, additional, Yates, Emma, additional, Khoo, Vincent, additional, and James, Nicholas D, additional
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- 2023
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25. 2911: Localised prostate cancer, time to rethink RT volumes-MRI & pathological correlation in 375 patients
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Kalra, Babusha, Singh, Akanksha, Hazell, Steve, Cahill, Declan, Mayer, Erik, Withey, Sam, Sohaib, Aslam, Pathmanathan, Angela, and Tree, Alison
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- 2024
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26. Can Nurse-Led Shared Medical Appointments Replace One-to-One Consultations for Erectile Dysfunction Post-Robotic-Assisted Laparoscopic Prostatectomy? A Quality Improvement Study in Survivorship
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Allchorne, Paula, Briggs, Karen, Fleure, Louise, Kinsella, Netty, Cahill, Declan, and Green, James S.A.
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Laparoscopy ,Robotic surgery ,Laparoscopic surgery ,Prostate cancer ,Impotence ,Cancer -- Care and treatment ,Self-care, Health ,Nursing ,Nurses -- Appointments, resignations and dismissals ,Health ,Health care industry - Abstract
Many men report unmet needs in erectile dysfunction self-care management following treatment of prostate cancer. While it is important to ensure timely access to survivorship care, increasing patient volume challenges current survivorship pathways and resources. This quality improvement project implemented and evaluated a new prostate cancer survivorship pathway for men post-robotic assisted laparoscopic prostatectomy to better address their needs in a timely manner. Key Words Group consultation, shared appointments, seminars, erectile dysfunction, survivorship pathway., Instructions for cNE contact Hours UNJ 2003 Continuing nursing education (CNE) contact hours can be earned for completing the learning activity associated with this article. Instructions are available at suna.org/library [...]
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- 2020
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27. Robot-assisted laparoscopic pyeloplasty: a single-centre experience
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Wood, Thomas Charles, Raison, Nicholas, El-Hage, Oussama, Ahmed, Kamran, Cahill, Declan, Challacombe, Benjamin J., Khan, Muhammad Shamim, and Dasgupta, Prokar
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- 2018
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28. MP12-09 THE MAN VAN: COMMUNITY BASED TARGETED CASE FINDING FOR PROSTATE CANCER
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Moghul, Masood, primary, Croft, Fionnuala, additional, Kaur, Kaljit, additional, Kinsella, Netty, additional, Cahill, Declan, additional, and James, Nicholas, additional
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- 2023
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29. Mobile Health Solutions for Prostate Cancer Diagnostics—A Systematic Review.
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Moghul, Masood, Cazzaniga, Walter, Croft, Fionnuala, Kinsella, Netty, Cahill, Declan, and James, Nicholas David
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PROSTATE cancer ,MOBILE health ,MIDDLE-income countries ,CANCER patients ,MEDICAL screening ,EARLY detection of cancer - Abstract
Prostate cancer, the most common cause of cancer in men in the UK and one of the most common around the world to date, has no consensus on screening. Multiple large-scale trials from around the world have produced conflicting outcomes in cancer-specific and overall mortality. A main part of the issue is the PSA test, which has a high degree of variability, making it challenging to set PSA thresholds, as well as limited specificity. Prostate cancer has a predisposition in men from black backgrounds, and outcomes are worse in men of lower socioeconomic groups. Mobile targeted case finding, focusing on high-risk groups, may be a solution to help those that most need it. The aim of this systematic review was to review the evidence for mobile testing for prostate cancer. A review of all mobile screening studies for prostate cancer was performed in accordance with the Cochrane guidelines and the PRISMA statement. Of the 629 unique studies screened, 6 were found to be eligible for the review. The studies dated from 1973 to 2017 and came from four different continents, with around 30,275 men being screened for prostate cancer. Detection rates varied from 0.6% in the earliest study to 8.2% in the latest study. The challenge of early diagnosis of potentially lethal prostate cancer remains an issue for developed and low- and middle-income countries alike. Although further studies are needed, mobile screening of a targeted population with streamlined investigation and referral pathways combined with raising awareness in those communities may help make the case for screening for prostate cancer. [ABSTRACT FROM AUTHOR]
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- 2023
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30. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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31. Combined burden and functional impact tests for cancer driver discovery using DriverPower
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Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reimand, Jüri, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Gallinger, Steven, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Boutros, Paul C, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Hersey, Peter, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jihoon, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Larsimont, Denis, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Siliang, Li, Xiaobo, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reis-Filho, Jorge, Reuter, Victor, Reynolds, Sheila M, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Saini, Natalie, Saito-Adachi, Mihoko, Salcedo, Adriana, Salgado, Roberto, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shelton, Troy, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shringarpure, Suyash S, Shriver, Craig, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Villasante, Izar, 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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32. Integrative pathway enrichment analysis of multivariate omics data
- Author
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
- Published
- 2023
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33. Pathway and network analysis of more than 2500 whole cancer genomes
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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34. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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35. Genomic footprints of activated telomere maintenance mechanisms in cancer
- Author
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Sieverling, Lina, Hong, Chen, Koser, Sandra D, Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M, Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J, Eils, Roland, Schlesner, Matthias, Akdemir, Kadir C, Alvarez, Eva G, Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C, Bowtell, David DL, Brors, Benedikt, Burns, Kathleen H, Campbell, Peter J, Chan, Kin, Chen, Ken, Dueso-Barroso, Ana, Dunford, Andrew J, Edwards, Paul A, Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W, Gerstein, Mark, Gordenin, Dmitry A, Haan, David, Haber, James E, Hess, Julian M, Imielinski, Marcin, Jones, David TW, Ju, Young Seok, Kazanov, Marat D, Klimczak, Leszek J, Koh, Youngil, Korbel, Jan O, Kumar, Kiran, Lee, Eunjung Alice, Lee, Jake June-Koo, Li, Yilong, Lynch, Andy G, Macintyre, Geoff, Markowetz, Florian, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Meyerson, Matthew, Miyano, Satoru, Nakagawa, 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Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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36. Are you now a good surgeon? T2 positive margin status as a quality outcome measure following radical prostatectomy
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Damani, Arees, Van Hemelrijck, Mieke, Wulaningsih, Wahyu, Crawley, Danielle, and Cahill, Declan
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- 2017
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37. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates
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Buhigas, Claudia, Warren, Anne Y., Leung, Wing-Kit, Whitaker, Hayley C., Luxton, Hayley J., Hawkins, Steve, Kay, Jonathan, Butler, Adam, Xu, Yaobo, Woodcock, Dan J., Merson, Sue, Frame, Fiona M., Sahli, Atef, Abascal, Federico, Gihawi, Abraham, Lambert, Adam, Thompson, Alan, Futreal, Andrew, Menzies, Andrew, Baddage, Anne, Ng, Anthony, Sahil, Atef, Kremeyer, Barbara, Al-Lazikani, Bissan, Massie, Charlie, Greenman, Christopher, Ogden, Christopher, Verrill, Clare, Fisher, Cyril, Berney, Dan, Burns, Dan, Leongamornlert, Daniel, Jones, David, Nicol, David, Wedge, David C., Cahill, Declan, Easton, Douglas, Rowe, Edward, Riabchenko, Ekaterina, Bancroft, Elizabeth, Mayer, Erik, Anokian, Ezequiel, Hamdy, Freddie, Park, Gahee, Pelvender, Gill, Leeman, Gregory, Gundem, Gunes, Zhang, Hongwei, Mills, Ian G., Zhang, Jingjing, Teague, Jon, Zamora, Jorge, Karaszi, Katalin, Raine, Kieran, Matthews, Lucy, Stebbings, Lucy, Alexandrov, Ludmil B., Marsden, Luke, Ahmed, Mahbubl, Nykter, Matti, Ghori, Mohammed, Livni, Naomi, Dennis, Nening, Van As, Nicholas, Camacho, Niedzica, Shah, Nimish, Kumar, Pardeep, Van Loo, Peter, Lach, Radoslaw, Edwards, Sandra, Pita, Sara, Field, Sarah J., Thomas, Sarah, Tavaré, Simon, Scalabrino, Stefania, Hazell, Steven, McLaren, Stuart, Visakorpi, Tapio, Mitchell, Thomas J., Dudderidge, Tim, Dadaev, Tokhir, McDermott, Ultan, Bo, Valeria, Haberland, Valeriia, Gnanapragasam, Vincent, Khoo, Vincent, Howat, William, Jie-Lu, Yong, Yu, Yongwei, Kote-Jarai, Zsofia, Martincorena, Iñigo, Bova, G. Steven, Foster, Christopher S., Campbell, Peter, Maitland, Norman J., Neal, David E., Massie, Charlie E., Lynch, Andy G., Eeles, Rosalind A., Cooper, Colin S., Brewer, Daniel S., Group, CRUK-ICGC Prostate Cancer, University of St Andrews. School of Medicine, University of St Andrews. Statistics, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. St Andrews Bioinformatics Unit, University of St Andrews. Cellular Medicine Division, Tampere University, BioMediTech, Group, CRUK-ICGC Prostate Cancer, Apollo - University of Cambridge Repository, Lynch, Andy G [0000-0002-7876-7338], and Brewer, Daniel S [0000-0003-4753-9794]
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Male ,Cancer Research ,Prostatic Hyperplasia ,Normal tissue ,Mutational signatures ,QH426 Genetics ,Clonal expansions ,Field effect ,RC0254 ,Ecology,Evolution & Ethology ,SDG 3 - Good Health and Well-being ,NCAD ,Humans ,QH426 ,Computational & Systems Biology ,MCC ,Human Biology & Physiology ,Prostate cancer ,Benign prostatic hyperplasia ,Nucleotides ,RC0254 Neoplasms. Tumors. Oncology (including Cancer) ,Research ,Prostate ,Prostatic Neoplasms ,DAS ,Genomics ,Tumour Biology ,Clone Cells ,Oncology ,Molecular Medicine ,3111 Biomedicine ,Genetics & Genomics - Abstract
Background Up to 80% of cases of prostate cancer present with multifocal independent tumour lesions leading to the concept of a field effect present in the normal prostate predisposing to cancer development. In the present study we applied Whole Genome DNA Sequencing (WGS) to a group of morphologically normal tissue (n = 51), including benign prostatic hyperplasia (BPH) and non-BPH samples, from men with and men without prostate cancer. We assess whether the observed genetic changes in morphologically normal tissue are linked to the development of cancer in the prostate. Results Single nucleotide variants (P = 7.0 × 10–03, Wilcoxon rank sum test) and small insertions and deletions (indels, P = 8.7 × 10–06) were significantly higher in morphologically normal samples, including BPH, from men with prostate cancer compared to those without. The presence of subclonal expansions under selective pressure, supported by a high level of mutations, were significantly associated with samples from men with prostate cancer (P = 0.035, Fisher exact test). The clonal cell fraction of normal clones was always higher than the proportion of the prostate estimated as epithelial (P = 5.94 × 10–05, paired Wilcoxon signed rank test) which, along with analysis of primary fibroblasts prepared from BPH specimens, suggests a stromal origin. Constructed phylogenies revealed lineages associated with benign tissue that were completely distinct from adjacent tumour clones, but a common lineage between BPH and non-BPH morphologically normal tissues was often observed. Compared to tumours, normal samples have significantly less single nucleotide variants (P = 3.72 × 10–09, paired Wilcoxon signed rank test), have very few rearrangements and a complete lack of copy number alterations. Conclusions Cells within regions of morphologically normal tissue (both BPH and non-BPH) can expand under selective pressure by mechanisms that are distinct from those occurring in adjacent cancer, but that are allied to the presence of cancer. Expansions, which are probably stromal in origin, are characterised by lack of recurrent driver mutations, by almost complete absence of structural variants/copy number alterations, and mutational processes similar to malignant tissue. Our findings have implications for treatment (focal therapy) and early detection approaches.
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- 2022
38. Management of men with lower urinary tract symptoms referred for prostate radiotherapy
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Holloway, Nicola, primary, Ribeiro, Luis, additional, Bosco, Cecilia, additional, Van Hemelrijck, Mieke, additional, Seth, Jai, additional, Nitkunan, Tharani, additional, Nicol, David, additional, Cahill, Declan, additional, Withington, John, additional, Kinsella, Janette, additional, and Wong, Kathie, additional
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- 2022
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39. A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology
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Yamamoto, Hidekazu, Nir, Dror, Vyas, Lona, Chang, Richard T., Popert, Rick, Cahill, Declan, Challacombe, Ben, Dasgupta, Prokar, and Chandra, Ashish
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- 2014
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40. Hand-Assisted Laparoscopic Nephrectomy
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Rozet, François, Cahill, Declan, Desgrandchamps, François, de la Rosette, Jean J.M.C.H., editor, and Gill, Inderbir S., editor
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- 2005
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41. Developing a consensus statement for psychosocial support in active surveillance for prostate cancer
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Beckmann, Kerri, primary, Cahill, Declan, additional, Brown, Christian, additional, Van Hemelrijck, Mieke, additional, and Kinsella, Netty, additional
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- 2022
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42. MP57-08 SELECTIVE RADICAL PROSTATECTOMY IN GRADE GROUP 1 PROSTATE CANCER
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Moghul, Masood, primary, Mcnally, Claire, additional, Kaur, Kaljit, additional, Kinsella, Netty, additional, Dafydd, Derfel, additional, Sohaib, Aslam, additional, Hazell, Steve, additional, and Cahill, Declan, additional
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- 2022
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43. MP15-17 RETZIUS-SPARING ROBOT ASSISTED RADICAL PROSTATECTOMY HAS SIMILAR 1-YEAR FUNCTIONAL AND ONCOLOGICAL OUTCOMES AS STANDARD ROBOT-ASSISTED RADICAL PROSTATECTOMY: RESULTS FROM A HIGH VOLUME UK CENTRE
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Umari, Paolo, primary, Narain, Tushar Aditya, additional, Eden, Dominic, additional, Cahill, Declan, additional, Eden, Christopher, additional, and Sooriakumaran, Prasanna, additional
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- 2022
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44. Pre‐biopsy 3‐Tesla MRI and targeted biopsy of the index prostate cancer: correlation with robot‐assisted radical prostatectomy
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Patel, Uday, Dasgupta, Prokar, Challacombe, Ben, Cahill, Declan, Brown, Christian, Patel, Roshnee, and Kirby, Roger
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- 2017
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45. Correction to: Robot-assisted laparoscopic pyeloplasty: a single-centre experience
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Wood, Thomas Charles, Raison, Nicholas, Elhage, Oussama, Ahmed, Kamran, Cahill, Declan, Challacombe, Benjamin J., Khan, Muhammad Shamim, and Dasgupta, Prokar
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- 2018
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46. A prospective prostate cancer screening programme for men with pathogenic variants in mismatch repair genes (IMPACT): initial results from an international prospective study
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Bancroft, Elizabeth K, primary, Page, Elizabeth C, additional, Brook, Mark N, additional, Thomas, Sarah, additional, Taylor, Natalie, additional, Pope, Jennifer, additional, McHugh, Jana, additional, Jones, Ann-Britt, additional, Karlsson, Questa, additional, Merson, Susan, additional, Ong, Kai Ren, additional, Hoffman, Jonathan, additional, Huber, Camilla, additional, Maehle, Lovise, additional, Grindedal, Eli Marie, additional, Stormorken, Astrid, additional, Evans, D Gareth, additional, Rothwell, Jeanette, additional, Lalloo, Fiona, additional, Brady, Angela F, additional, Bartlett, Marion, additional, Snape, Katie, additional, Hanson, Helen, additional, James, Paul, additional, McKinley, Joanne, additional, Mascarenhas, Lyon, additional, Syngal, Sapna, additional, Ukaegbu, Chinedu, additional, Side, Lucy, additional, Thomas, Tessy, additional, Barwell, Julian, additional, Teixeira, Manuel R, additional, Izatt, Louise, additional, Suri, Mohnish, additional, Macrae, Finlay A, additional, Poplawski, Nicola, additional, Chen-Shtoyerman, Rakefet, additional, Ahmed, Munaza, additional, Musgrave, Hannah, additional, Nicolai, Nicola, additional, Greenhalgh, Lynn, additional, Brewer, Carole, additional, Pachter, Nicholas, additional, Spigelman, Allan D, additional, Azzabi, Ashraf, additional, Helfand, Brian T, additional, Halliday, Dorothy, additional, Buys, Saundra, additional, Ramon y Cajal, Teresa, additional, Donaldson, Alan, additional, Cooney, Kathleen A, additional, Harris, Marion, additional, McGrath, John, additional, Davidson, Rosemarie, additional, Taylor, Amy, additional, Cooke, Peter, additional, Myhill, Kathryn, additional, Hogben, Matthew, additional, Aaronson, Neil K, additional, Ardern-Jones, Audrey, additional, Bangma, Chris H, additional, Castro, Elena, additional, Dearnaley, David, additional, Dias, Alexander, additional, Dudderidge, Tim, additional, Eccles, Diana M, additional, Green, Kate, additional, Eyfjord, Jorunn, additional, Falconer, Alison, additional, Foster, Christopher S, additional, Gronberg, Henrik, additional, Hamdy, Freddie C, additional, Johannsson, Oskar, additional, Khoo, Vincent, additional, Lilja, Hans, additional, Lindeman, Geoffrey J, additional, Lubinski, Jan, additional, Axcrona, Karol, additional, Mikropoulos, Christos, additional, Mitra, Anita V, additional, Moynihan, Clare, additional, Ni Raghallaigh, Holly, additional, Rennert, Gad, additional, Collier, Rebecca, additional, Offman, Judith, additional, Kote-Jarai, Zsofia, additional, Eeles, Rosalind A, additional, Adams, Lisa, additional, Adlard, Julian, additional, Alfonso, Rosa, additional, Ali, Saira, additional, Andrew, Angela, additional, Araújo, Luís, additional, Azam, Nazya, additional, Ball, Darran, additional, Barker, Queenstone, additional, Basevitch, Alon, additional, Benton, Barbara, additional, Berlin, Cheryl, additional, Bermingham, Nicola, additional, Biller, Leah, additional, Bloss, Angela, additional, Bradford, Matilda, additional, Bradshaw, Nicola, additional, Branson, Amy, additional, Brendler, Charles, additional, Brennan, Maria, additional, Bulman, Barbara, additional, Burgess, Lucy, additional, Cahill, Declan, additional, Callard, Alice, additional, Calvo Verges, Nuria, additional, Cardoso, Marta, additional, Carter, Vanda, additional, Catanzaro, Mario, additional, Chamberlain, Anthony, additional, Chapman, Cyril, additional, Chong, Michael, additional, Clark, Caroline, additional, Clowes, Virginia, additional, Cogley, Lyn, additional, Cole, Trevor, additional, Compton, Cecilia, additional, Conner, Tom, additional, Cookson, Sandra, additional, Cornford, Philip, additional, Costello, Philandra, additional, Coulier, Laura, additional, Davies, Michaela, additional, Dechet, Christopher, additional, DeSouza, Bianca, additional, Devlin, Gemma, additional, Douglas, Fiona, additional, Douglas, Emma, additional, Dudakia, Darshna, additional, Duncan, Alexis, additional, Ellery, Natalie, additional, Everest, Sarah, additional, Freemantle, Sue, additional, Frydenberg, Mark, additional, Fuller, Debbie, additional, Gabriel, Camila, additional, Gale, Madeline, additional, Garcia, Lynda, additional, Gay, Simona, additional, Genova, Elena, additional, George, Angela, additional, Georgiou, Demetra, additional, Gisbert, Alexandra, additional, Gleeson, Margaret, additional, Glover, Wayne, additional, Gnanapragasam, Vincent, additional, Goff, Sally, additional, Goldgar, David, additional, Gonçalves, Nuno, additional, Goodman, Selina, additional, Gorrie, Jennifer, additional, Gott, Hannah, additional, Grant, Anna, additional, Gray, Catherine, additional, Griffiths, Julie, additional, Gupwell, Karin, additional, Gurasashvili, Jana, additional, Hanslien, Eldbjørg, additional, Haraldsdottir, Sigurdis, additional, Hart, Rachel, additional, Hartigan, Catherine, additional, Hawkes, Lara, additional, Heaton, Tricia, additional, Henderson, Alex, additional, Henrique, Rui, additional, Hilario, Kathrine, additional, Hill, Kathryn, additional, Hulick, Peter, additional, Hunt, Clare, additional, Hutchings, Melanie, additional, Ibitoye, Rita, additional, Inglehearn, Thomas, additional, Ireland, Joanna, additional, Islam, Farah, additional, Ismail, Siti, additional, Jacobs, Chris, additional, James, Denzil, additional, Jenkins, Sharon, additional, Jobson, Irene, additional, Johnstone, Anne, additional, Jones, Oliver, additional, Josefsberg Ben-Yehoshua, Sagi, additional, Kaemba, Beckie, additional, Kaul, Karen, additional, Kemp, Zoe, additional, Kinsella, Netty, additional, Klehm, Margaret, additional, Kockelbergh, Roger, additional, Kohut, Kelly, additional, Kosicka-Slawinska, Monika, additional, Kulkarni, Anjana, additional, Kumar, Pardeep, additional, Lam, Jimmy, additional, LeButt, Mandy, additional, Leibovici, Dan, additional, Lim, Ramona, additional, Limb, Lauren, additional, Lomas, Claire, additional, Longmuir, Mark, additional, López, Consol, additional, Magnani, Tiziana, additional, Maia, Sofia, additional, Maiden, Jessica, additional, Male, Alison, additional, Manalo, Merrie, additional, Martin, Phoebe, additional, McBride, Donna, additional, McGuire, Michael, additional, McMahon, Romayne, additional, McNally, Claire, additional, McVeigh, Terri, additional, Melzer, Ehud, additional, Mencias, Mark, additional, Mercer, Catherine, additional, Mitchell, Gillian, additional, Mora, Josefina, additional, Morton, Catherine, additional, Moss, Cathryn, additional, Murphy, Morgan, additional, Murphy, Declan, additional, Mzazi, Shumi, additional, Nadolski, Maria, additional, Newlin, Anna, additional, Nogueira, Pedro, additional, O'Keefe, Rachael, additional, O'Toole, Karen, additional, O'Connell, Shona, additional, Ogden, Chris, additional, Okoth, Linda, additional, Oliveira, Jorge, additional, Paez, Edgar, additional, Palou, Joan, additional, Park, Linda, additional, Patel, Nafisa, additional, Paulo Souto, João, additional, Pearce, Allison, additional, Peixoto, Ana, additional, Perez, Kimberley, additional, Petelin, Lara, additional, Pichert, Gabriella, additional, Poile, Charlotte, additional, Potter, Alison, additional, Preitner, Nadia, additional, Purnell, Helen, additional, Quinn, Ellen, additional, Radice, Paolo, additional, Rankin, Brigette, additional, Rees, Katie, additional, Renton, Caroline, additional, Richardson, Kate, additional, Risby, Peter, additional, Rogers, Jason, additional, Ruderman, Maggie, additional, Ruiz, April, additional, Sajoo, Anaar, additional, Salvatore, Natale, additional, Sands, Victoria, additional, Sanguedolce, Francesco, additional, Sattar, Ayisha, additional, Saunders, Kathryn, additional, Schofield, Lyn, additional, Scott, Rodney, additional, Searle, Anne, additional, Sehra, Ravinder, additional, Selkirk, Christina, additional, Shackleton, Kylie, additional, Shanley, Sue, additional, Shaw, Adam, additional, Shevrin, Daniel, additional, Shipman, Hannah, additional, Sidat, Zahirah, additional, Siguake, Kas, additional, Simon, Kate, additional, Smyth, Courtney, additional, Snadden, Lesley, additional, Solanky, Nita, additional, Solomons, Joyce, additional, Sorrentino, Margherita, additional, Stayner, Barbara, additional, Stephenson, Robert, additional, Stoffel, Elena, additional, Thomas, Maggie, additional, Thompson, Alan, additional, Tidey, Lizzie, additional, Tischkowitz, Marc, additional, Torokwa, Audrey, additional, Townshend, Sharron, additional, Treherne, Katy, additional, Tricker, Karen, additional, Trinh, Quoc-Dien, additional, Tripathi, Vishakha, additional, Turnbull, Clare, additional, Valdagni, Riccardo, additional, Van As, Nicholas, additional, Venne, Vickie, additional, Verdon, Lizzie, additional, Vitellaro, Marco, additional, Vogel, Kristen, additional, Walker, Lisa, additional, Watford, Amy, additional, Watt, Cathy, additional, Weintroub, Ilana, additional, Weiss, Shelly, additional, Weissman, Scott, additional, Weston, Michelle, additional, Wiggins, Jennifer, additional, Wise, Gillian, additional, Woodhouse, Christopher, additional, Yesildag, Pembe, additional, Youngs, Alice, additional, Yurgelun, Matthew, additional, and Zollo, Fabiana, additional
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- 2021
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47. Oncological outcomes of robotic-assisted radical prostatectomy after more than 5 years
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Billia, Michele, Elhage, Oussama, Challacombe, Benjamin, Cahill, Declan, Popert, Rick, Holmes, Kathy, Kirby, Roger Sinclair, and Dasgupta, Prokar
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- 2014
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48. IS THERE A ROLE FOR CHOLINE PET SCANNING IN SALVAGE PROSTATECTOMY?: MP57-02
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Goonewardene, Sanchia, Bletcher, Gideon, Catterwell, Rick, Cahill, Declan, Persad, Raj, Gillatt, David, Challacombe, Ben, Dasgupta, Prokar, and Popert, Rick
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- 2016
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49. SALVAGE RADICAL PROSTATECTOMY COMPLICATIONS AND FUNCTIONAL OUTCOMES: OPEN VERSUS ROBOTIC PROCEDURES.: MP50-03
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Gontero, Paolo, Marra, Giancarlo, Alessio, Paolo, Oderda, Marco, Palazzetti, Anna, Pisano, Francesca, Battaglia, Antonino, Munegato, Stefania, Filippini, Claudia, Frea, Bruno, Munoz, Fernando, Linares, Estefania, Salas, Raphael Sanchez, Goonewardene, Sanchia, Dasgupta, Prokar, Cahill, Declan, Challacombe, Ben, Gillatt, David, Persad, Raj, Palou, Juan, Joniau, Steven, Smelzo, Salvatore, Piechaud, Thierry, De La Taille, Alexandre, Roupret, Morgan, Tilki, Derya, and Popert, Rick
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- 2016
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50. Developing a consensus statement for psychosocial support in active surveillance for prostate cancer.
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Beckmann, Kerri, Cahill, Declan, Brown, Christian, Van Hemelrijck, Mieke, and Kinsella, Netty
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- 2023
- Full Text
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