Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus

Autor: Jens Luebeck, Alvin Wei Tian Ng, Patricia C. Galipeau, Xiaohong Li, Carissa A. Sanchez, Annalise C. Katz-Summercorn, Hoon Kim, Sriganesh Jammula, Yudou He, Scott M. Lippman, Roel G. W. Verhaak, Carlo C. Maley, Ludmil B. Alexandrov, Brian J. Reid, Rebecca C. Fitzgerald, Thomas G. Paulson, Howard Y. Chang, Sihan Wu, Vineet Bafna, Paul S. Mischel

Publikováno v: Luebeck, J, Ng, A W T, Galipeau, P C, Li, X, Sanchez, C A, Katz-Summercorn, A C, Kim, H, Jammula, S, He, Y, Lippman, S M, Verhaak, R G W, Maley, C C, Alexandrov, L B, Reid, B J, Fitzgerald, R C, Paulson, T G, Chang, H Y, Wu, S, Bafna, V & Mischel, P S 2023, ' Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus ', Nature, vol. 616, no. 7958, pp. 798-805 . https://doi.org/10.1038/s41586-023-05937-5
Nature, 616(7958), 798-805. Nature Publishing Group

Oncogene amplification on extrachromosomal DNA (ecDNA) drives the evolution of tumours and their resistance to treatment, and is associated with poor outcomes for patients with cancer1–6. At present, it is unclear whether ecDNA is a later manifesta

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http://www.scopus.com/inward/record.url?scp=85152435510&partnerID=8YFLogxK

Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas

Autor: Ng, Alvin Wei Tian, Contino, Gianmarco, Killcoyne, Sarah, Devonshire, Ginny, Hsu, Ray, Abbas, Sujath, Su, Jing, Redmond, Aisling M., Weaver, Jamie M.J., Eldridge, Matthew D., Tavaré, Simon, Grehan, Nicola, Nutzinger, Barbara, Fidziukiewicz, Elwira, Freeman, Adam, Smyth, Elizabeth C., O’Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Cheah, Calvin, Coles, Hannah, Flint, Connor, Eldridge, Matthew, Secrier, Maria, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H., Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R., Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O’Neill, J. Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Scott, Michael, Turkington, Richard, McManus, Damian, Coleman, Helen

Publikováno v: Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium, Ng, A W T, Contino, G, Killcoyne, S, Devonshire, G, Hsu, R, Abbas, S, Su, J, Redmond, A M, Weaver, J M J, Eldridge, M D, Tavaré, S, Grehan, N, Nutzinger, B, Fidziukiewicz, E, Freeman, A, Smyth, E C, O’Donovan, M, Miremadi, A, Malhotra, S, Tripathi, M, Cheah, C, Coles, H, Flint, C, Eldridge, M, Secrier, M, Jammula, S, Davies, J, Crichton, C, Carroll, N, Hardwick, R H, Safranek, P, Hindmarsh, A, Sujendran, V, Hayes, S J, Ang, Y, Sharrocks, A, Preston, S R, Bagwan, I, Save, V, Skipworth, R J E, Hupp, T R, O’Neill, J R, Tucker, O, Beggs, A, Taniere, P, Puig, S, Scott, M, Turkington, R, McManus, D & Coleman, H 2022, ' Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas ', Communications Biology, vol. 5, 335 . https://doi.org/10.1038/s42003-022-03238-7

Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed structural variations (SV) wi

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Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases

Autor: An, Jiyuan, Gharahkhani, Puya, Law, Matthew H., Ong, Jue-Sheng, Han, Xikun, Olsen, Catherine M., Neale, Rachel E., Lai, John, Vaughan, Tom L., Gockel, Ines, Thieme, René, Böhmer, Anne C., Jankowski, Janusz, Fitzgerald, Rebecca C., Schumacher, Johannes, Palles, Claire, Whiteman, David C., MacGregor, Stuart, Gammon, Marilie D., Corley, Douglas A., Shaheen, Nicholas J., Bird, Nigel C., Hardie, Laura J., Murray, Liam J., Reid, Brian J., Chow, Wong-Ho, Risch, Harvey A., Ye, Weimin, Liu, Geoffrey, Romero, Yvonne, Bernstein, Leslie, Wu, Anna H., Agee, M., Alipanahi, B., Auton, A., Bell, R. K., Bryc, K., Elson, S. L., Fontanillas, P., Furlotte, N. A., Hinds, D. A., Huber, K. E., Kleinman, A., Litterman, N. K., McIntyre, M. H., Mountain, J. L., Noblin, E. S., Northover, C. A. M., Pitts, S. J., Sathirapongsasuti, J. Fah, Sazonova, O. V., Shelton, J. F., Shringarpure, S., Tian, C., Tung, J. Y., Vacic, V., Wilson, C. H.

Funder: The Swedish Esophageal Cancer Study was funded by grants (R01 CA57947-03) from the National Cancer Institute he California Tobacco Related Research Program (3RT-0122; and; 10RT-0251) Marit Peterson Fund for Melanoma Research. CIDR is supporte

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https://www.repository.cam.ac.uk/handle/1810/310289

Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma

Autor: Mourikis, Thanos P., Benedetti, Lorena, Foxall, Elizabeth, Temelkovski, Damjan, Nulsen, Joel, Perner, Juliane, Cereda, Matteo, Lagergren, Jesper, Howell, Michael, Yau, Christopher, Fitzgerald, Rebecca C., Scaffidi, Paola, Ciccarelli, Francesca D., Noorani, Ayesha, Edwards, Paul A. W., Elliott, Rachael Fels, Grehan, Nicola, Nutzinger, Barbara, Hughes, Caitriona, Fidziukiewicz, Elwira, Bornschein, Jan, MacRae, Shona, Crawte, Jason, Northrop, Alex, Contino, Gianmarco, Li, Xiaodun, De La Rue, Rachel, Katz-Summercorn, Annalise, Abbas, Sujath, Loureda, Daniel, O’Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Tavaré, Simon, Lynch, Andy G., Eldridge, Matthew, Secrier, Maria, Bower, Lawrence, Devonshire, Ginny, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R., Oakes, Sarah, Bagwan, Izhar, Save, Vicki, Skipworth, Richard J. E., Hupp, Ted R., Robert O’Neill, J., Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Underwood, Timothy J., Walker, Robert C., Grace, Ben L., Barr, Hugh, Shepherd, Neil, Old, Oliver, Gossage, James, Davies, Andrew, Chang, Fuju, Zylstra, Janine, Mahadeva, Ula, Goh, Vicky, Sanders, Grant, Berrisford, Richard, Harden, Catherine, Lewis, Mike, Cheong, Ed, Kumar, Bhaskar, Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Igali, Laszlo, Scott, Michael, Sothi, Sharmila, Suortamo, Sari, Lishman, Suzy, Hanna, George B., Peters, Christopher J., Moorthy, Krishna, Grabowska, Anna, Turkington, Richard, McManus, Damian, Khoo, David, Fickling, Will

The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in in

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