المؤلفون: Turkington, RC, Knight, LA, Blayney, JK, Secrier, M, Douglas, R, Parkes, EE, Sutton, EK, Stevenson, L, McManus, D, Halliday, S, McCavigan, AM, Logan, GE, Walker, SM, Steele, CJ, Perner, J, Bornschein, J, MacRae, S, Miremadi, A, McCarron, E, McQuaid, S, Arthur, K, James, JA, Eatock, MM, O'Neill, R, Noble, F, Underwood, TJ, Harkin, DP, Salto-Tellez, M, Fitzgerald, RC, Kennedy, RD, Noorani, A, Edwards, PAW, Grehan, N, Nutzinger, B, Hughes, C, Fidziukiewicz, E, Crawte, J, Northrop, A, Contino, G, Li, XD, de la Rue, R, O'Donovan, M, Malhotra, S, Tripathi, M, Tavare, S, Lynch, AG, Eldridge, M, Bower, L, Devonshire, G, Jammula, S, Davies, J, Crichton, C, Carroll, N, Safranek, P, Hindmarsh, A, Sujendran, V, Hayes, SJ, Ang, Y, Preston, SR, Oakes, S, Bagwan, I, Save, V, Skipworth, RJE, Hupp, TR, Tucker, O, Beggs, A, Taniere, P, Puig, S, Owsley, J, Barr, H, Shepherd, N, Old, O, Lagergren, J, Gossage, J, Davies, A, Chang, FJ, Zylstra, J, Mahadeva, U, Goh, V, Ciccarelli, FD, Sanders, G, Berrisford, R, Harden, C, Lewis, M, Cheong, E, Kumar, B, Parsons, SL, Soomro, I, Kaye, P, Saunders, J, Lovat, L, Haidry, R, Igali, L, Scott, M, Sothi, S, Suortamo, S, Lishman, S, Hanna, GB, Moorthy, K, Peters, CJ, Grabowska, A, Coleman, H

المصدر: Gut. 68(11):1918-1927

مصطلحات موضوعية: Medicin och hälsovetenskap

الوصول الحر: http://kipublications.ki.se/Default.aspx?queryparsed=id:142430259Test

المؤلفون: Bornschein, J, Wernisch, L, Secrier, M, Miremadi, A, Perner, J, MacRae, S, O'Donovan, M, Newton, R, Menon, S, Bower, L, Eldridge, MD, Devonshire, G, Cheah, C, Turkington, R, Hardwick, RH, Selgrad, M, Venerito, M, Malfertheiner, P, Fitzgerald, RC, Noorani, A, Elliott, RF, Edwards, PAW, Grehan, N, Nutzinger, B, Crawte, J, Chettouh, H, Contino, G, Li, XD, Gregson, E, Zeki, S, de la Rue, R, Malhotra, S, Tavare, S, Lynch, AG, Smith, ML, Davies, J, Crichton, C, Carroll, N, Safranek, P, Hindmarsh, A, Sujendran, V, Hayes, SJ, Ang, Y, Preston, SR, Oakes, S, Bagwan, I, Save, V, Skipworth, RJE, Hupp, TR, O'Neill, JR, Tucker, O, Beggs, A, Taniere, P, Puig, S, Underwood, TJ, Noble, F, Owsley, J, Barr, H, Shepherd, N, Old, O, Lagergren, J, Gossage, J, Davies, A, Chang, FJ, Zylstra, J, Goh, V, Ciccarelli, FD, Sanders, G, Berrisford, R, Harden, C, Bunting, D, Lewis, M, Cheong, E, Kumar, B, Parsons, SL, Soomro, I, Kaye, P, Saunders, J, Lovat, L, Haidry, R, Eneh, V, Igali, L, Scott, M, Sothi, S, Suortamo, S, Lishman, S, Hanna, GB, Peters, CJ, Grabowska, A

المصدر: International journal of cancer. 145(12):3389-3401

مصطلحات موضوعية: Medicin och hälsovetenskap

الوصول الحر: http://kipublications.ki.se/Default.aspx?queryparsed=id:142099339Test

المؤلفون: Noorani, A, Bornschein, J, Lynch, AG, Secrier, M, Achilleos, A, Eldridge, M, Bower, L, Weaver, JMJ, Crawte, J, Ong, CA, Shannon, N, MacRae, S, Grehan, N, Nutzinger, B, O'Donovan, M, Hardwick, R, Tavare, S, Fitzgerald, RC

المصدر: Genome research. 27(6):902-912

مصطلحات موضوعية: Medicin och hälsovetenskap

الوصول الحر: http://kipublications.ki.se/Default.aspx?queryparsed=id:135929671Test

المؤلفون: Madhu, B, Narita, M, Jauhiainen, A, Menon, S, Stubbs, M, Tavare, S, Griffiths, JR

المصدر: Metabolomics : Official journal of the Metabolomic Society. 11(6):1848-1863

مصطلحات موضوعية: Medicin och hälsovetenskap

الوصول الحر: http://kipublications.ki.se/Default.aspx?queryparsed=id:132267687Test

المؤلفون: Jammula, S, Katz-Summercorn, AC, Li, XD, Linossi, C, Smyth, E, Killcoyne, S, Biasci, D, Subash, VV, Abbas, S, Blasko, A, Devonshire, G, Grantham, A, Wronowski, F, O'Donovan, M, Grehan, N, Eldridge, MD, Tavare, S, Fitzgerald, RC

المصدر: Gastroenterology. 158(6):1682

مصطلحات موضوعية: Medicin och hälsovetenskap

الوصول الحر: http://kipublications.ki.se/Default.aspx?queryparsed=id:143823211Test

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Cope, L, Cordes, MG, Curley, E, Czerniak, B, Danilova, L, Davis, IJ, Defreitas, T, Demchok, JA, Dhalla, N, Dhir, R, Doddapaneni, H, El-Naggar, A, Felau, I, Ferguson, ML, Finocchiaro, G, Fong, KM, Frazer, S, Friedman, W, Fronick, CC, Fulton, LA, Gabriel, SB, Gao, J, Gehlenborg, N, Gershenwald, JE, Ghossein, R, Giama, NH, Gibbs, RA, Gomez, C, Govindan, R, Hayes, DN, Hegde, AM, Heiman, D, Heins, Z, Hepperla, AJ, Holbrook, A, Holt, RA, Hoyle, AP, Hruban, RH, Hu, J, Huang, M, Huntsman, D, Huse, J, Donahue, CAI, Ittmann, M, Jayaseelan, JC, Jefferys, SR, Jones, CD, Jones, SJM, Juhl, H, Kang, KJ, Karlan, B, Kasaian, K, Kebebew, E, Kim, HK, Korchina, V, Kundra, R, Lai, PH, Lander, E, Le, X, Levine, DA, Lewis, L, Ley, T, Li, HI, Lin, P, Linehan, WM, Liu, FF, Lu, Y, Lype, L, Ma, Y, Maglinte, DT, Mardis, ER, Marks, J, Marra, MA, Matthew, TJ, Mayo, M, McCune, K, Meier, SR, Meng, S, Mieczkowski, PA, Mikkelsen, T, Miller, CA, Mills, GB, Moore, RA, Morrison, C, Mose, LE, Moser, CD, Mungall, AJ, Mungall, K, Mutch, D, Muzny, DM, Myers, J, Newton, Y, Noble, MS, O'Donnell, P, O'Neill, BP, Ochoa, A, Parker, JS, Pass, H, Pastore, A, Pennell, NA, Perou, CM, Petrelli, N, Potapova, O, Rader, JS, Ramalingam, S, Rathmell, WK, Reuter, V, Reynolds, SM, Ringel, M, Roach, J, Roberts, LR, Robertson, AG, Sadeghi, S, Saller, C, Sanchez-Vega, F, Schadendorf, D, Schein, JE, Schmidt, HK, Schultz, N, Seethala, R, Senbabaoglu, Y, Shelton, T, Shi, Y, Shih, J, Shmulevich, I, Shriver, C, Signoretti, S, Simons, J, Singer, S, Sipahimalani, P, Skelly, TJ, McCune, KS, Socci, ND, Soloway, MG, Sood, AK, Tam, A, Tan, D, Tarnuzzer, R, Thiessen, N, Thompson, RH, Thorne, LB, Tsao, M, Umbricht, C, Van Den Berg, DJ, Van Meir, EG, Veluvolu, U, Voet, D, Wang, L, Weinberger, P, Weisenberger, DJ, Wigle, D, Wilkerson, MD, Wilson, RK, Winterhoff, B, Wiznerowicz, M, Wong, T, Wong, W, Xi, L, Yau, C

المصدر: Nature. 578(7793):82

مصطلحات موضوعية: Medicin och hälsovetenskap

الوصول الحر: http://kipublications.ki.se/Default.aspx?queryparsed=id:143672104Test

المؤلفون: Kuett, L, Catena, R, Özcan, A, Plüss, A, Ali, HR, Sa’d, MA, Alon, S, Aparicio, S, Battistoni, G, Balasubramanian, Shankar, Becker, R, Bodenmiller, B, Boyden, ES, Bressan, D, Bruna, A, Burger, M, Caldas, Carlos, Callari, M, Cannell, IG, Casbolt, H, Chornay, N, Cui, Y, Dariush, Aliakbar, Dinh, K, Emenari, A, Eyal-Lubling, Y, Fan, J, Fatemi, A, Fisher, E, González-Solares, EA, González-Fernández, C, Goodwin, D, Greenwood, W, Grimaldi, F, Hannon, GJ, Harris, S, Jauset, C, Joyce, JA, Karagiannis, ED, Kovačević, T, Kunes, R, Yoldaş, AK, Lai, D, Laks, E, Lee, H, Lee, M, Lerda, G, Li, Y, McPherson, A, Millar, N, Mulvey, CM, Nugent, I, O’Flanagan, CH, Paez-Ribes, M, Pearsall, I, Qosaj, F, Roth, AJ, Rueda, OM, Ruiz, T, Sawicka, K, Sepúlveda, LA, Shah, SP, Shea, A, Sinha, A, Smith, A, Tavaré, S, Tietscher, S, Vázquez-García, I, Vogl, SL, Walton, NA, Wassie, AT, Watson, SS, Weselak, J, Wild, SA, Williams, E, Windhager, J, Xia, C, Zheng, P, Zhuang, X, Schraml, P, Moch, H, de Souza, N

الوصف: A holistic understanding of tissue and organ structure and function requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous detection of up to 40 antigens and transcripts using metal-tagged antibodies but has so far been restricted to two-dimensional imaging. Here we report the development of 3D IMC for multiplexed 3D tissue analysis at single-cell resolution and demonstrate the utility of the technology by analysis of human breast cancer samples. The resulting 3D models reveal cellular and microenvironmental heterogeneity and cell-level tissue organization not detectable in two dimensions. 3D IMC will prove powerful in the study of phenomena occurring in 3D space such as tumor cell invasion and is expected to provide invaluable insights into cellular microenvironments and tissue architecture.

وصف الملف: application/pdf

العلاقة: https://www.repository.cam.ac.uk/handle/1810/332671Test

الإتاحة: https://doi.org/10.17863/CAM.80116Test
https://www.repository.cam.ac.uk/handle/1810/332671Test

المؤلفون: Ng, AWT, Contino, G, Killcoyne, S, Devonshire, G, Hsu, R, Abbas, S, Su, J, Redmond, AM, Weaver, JMJ, Eldridge, MD, Tavaré, S, Grehan, N, Nutzinger, B, Fidziukiewicz, E, Freeman, A, Smyth, EC, 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, RH, Safranek, P, Hindmarsh, A, Sujendran, V, Hayes, SJ, Ang, Y, Sharrocks, A, Preston, SR, Bagwan, I, Save, V, Skipworth, RJE, Hupp, TR, O’Neill, JR, Tucker, O, Beggs, A, Taniere, P, Puig, S, Underwood, TJ, Walker, RC, Grace, BL, Lagergren, J, Gossage, J, Davies, A, Chang, F, Mahadeva, U, Goh, V, Ciccarelli, FD, Sanders, G, Berrisford, R, Chan, D, Cheong, E, Kumar, B, Sreedharan, L, Parsons, SL, Soomro, I, Kaye, P, Saunders, J, Lovat, L, Haidry, R, Scott, M, Sothi, S, Lishman, S, Hanna, GB, Peters, CJ, Moorthy, K, Grabowska, A, Turkington, R, McManus, D, Coleman, H, Petty, RD, Bartlett, F, Edwards, PAW, Fitzgerald, RC

المصدر: Communications Biology , 5 (1) , Article 335. (2022)

مصطلحات موضوعية: Adenocarcinoma, Esophageal Neoplasms, Genome, Human, Histone Acetyltransferases, Humans, Whole Genome Sequencing

الوصف: 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) with a predominance of deletions, tandem duplications and inter-chromosome junctions that could be identified as LINE-1 mobile element (ME) insertions. Complex clusters of rearrangements resembling breakage-fusion-bridge cycles or extrachromosomal circular DNA accounted for 22% of complex SVs affecting known oncogenes. Counting SV events affecting known driver genes substantially increased the recurrence rates of these drivers. After excluding fragile sites, we identified 51 candidate new drivers in genomic regions disrupted by SVs, including ETV5, KAT6B and CLTC. RUNX1 was the most recurrently altered gene (24%), with many deletions inactivating the RUNT domain but preserved the reading frame, suggesting an altered protein product. These findings underscore the importance of identification of SV events in OAC with implications for targeted therapies.

وصف الملف: text

العلاقة: https://discovery.ucl.ac.uk/id/eprint/10153324/1/s42003-022-03238-7.pdfTest; https://discovery.ucl.ac.uk/id/eprint/10153324Test/

الإتاحة: https://discovery.ucl.ac.uk/id/eprint/10153324/1/s42003-022-03238-7.pdfTest
https://discovery.ucl.ac.uk/id/eprint/10153324Test/

المؤلفون: Buhigas, C, Warren, AY, Leung, WK, Whitaker, HC, Luxton, HJ, Hawkins, S, Kay, J, Butler, A, Xu, Y, Woodcock, DJ, Merson, S, Frame, FM, Sahli, A, Abascal, F, Gihawi, A, Lambert, A, Thompson, A, Futreal, A, Menzies, A, Baddage, A, Ng, A, Sahil, A, Kremeyer, B, Al-Lazikani, B, Massie, C, Greenman, C, Ogden, C, Verrill, C, Fisher, C, Berney, D, Burns, D, Leongamornlert, D, Jones, D, Nicol, D, Wedge, D, Cahill, D, Easton, D, Rowe, E, Riabchenko, E, Bancroft, E, Mayer, E, Anokian, E, Hamdy, F, Park, G, Pelvender, G, Leeman, G, Gundem, G, Zhang, H, Mills, IG, Zhang, J, Teague, J, Zamora, J, Karaszi, K, Raine, K, Matthews, L, Stebbings, L, Alexandrov, LB, Marsden, L, Ahmed, M, Nykter, M, Ghori, M, Livni, N, Dennis, N, Van As, N, Camacho, N, Shah, N, Kumar, P, Van Loo, P, Lach, R, Edwards, S, Pita, S, Field, SJ, Thomas, S, Tavaré, S, Scalabrino, S, Hazell, S, McLaren, S, Visakorpi, T, Mitchell, TJ, Dudderidge, T, Dadaev, T, McDermott, U, Bo, V, Haberland, V, Gnanapragasam, V, Khoo, V, Howat, W, Jie-Lu, Y, Yu, Y, Kote-Jarai, Z, Martincorena, I, Bova, GS, Foster, CS, Campbell, P, Maitland, NJ, Neal, DE, Massie, CE, Lynch, AG, Eeles, RA, Cooper, CS

المساهمون: CRUK-ICGC Prostate Cancer Group

مصطلحات موضوعية: prostate cancer, clonal expansions, genomics, normal tissue, benign prostatic hyperplasia, field effect, mutational signatures

الوصف: Availability of data and materials: The datasets generated during the current study are available in the European Genome-Phenome Archive repository, https://ega-archive.org/datasets/EGAD00001000689Test and https://ega-archive.org/datasets/EGAD00001004125Test. The variant calls generated are available from the corresponding author on reasonable request. ; Supplementary information is available online at https://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-022-01644-3#Sec18Test . ; Copyright © The Author(s) 2022. 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 ...

وصف الملف: 1 - 16; Electronic

العلاقة: Molecular Cancer; ORCID iDs: Valeriia Haberland orcid:0000-0002-3874-0683; 183; Buhigas, C., CRUK-ICGC Prostate Cancer Group et al. (2022) 'The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates', Molecular Cancer, 21 (1), 183, pp. 1 - 13. doi:10.1186/s12943-022-01644-3.; https://bura.brunel.ac.uk/handle/2438/27308Test; https://doi.org/10.1186/s12943-022-01644-3Test

الإتاحة: https://doi.org/10.1186/s12943-022-01644-3Test
https://bura.brunel.ac.uk/handle/2438/27308Test

المؤلفون: Mourikis, TP, Benedetti, L, Foxall, E, Temelkovski, D, Nulsen, J, Perner, J, Cereda, M, Lagergren, J, Howell, M, Yau, C, Fitzgerald, RC, Scaffidi, P, Noorani, A, Edwards, PAW, Elliott, RF, Grehan, N, Nutzinger, B, Hughes, C, Fidziukiewicz, E, Bornschein, J, MacRae, S, Crawte, J, Northrop, A, Contino, G, Li, XD, de la Rue, R, Katz-Summercorn, A, Abbas, S, Loureda, D, O'Donovan, M, Miremadi, A, Malhotra, S, Tripathi, M, Tavare, S, Lynch, AG, Eldridge, M, Secrier, M, Bower, L, Devonshire, G, Jammula, S, Davies, J, Crichton, C, Carroll, N, Safranek, P, Hindmarsh, A, Sujendran, V, Hayes, SJ, Ang, Y, Sharrocks, A, Preston, SR, Oakes, S, Bagwan, I, Save, V, Skipworth, RJE, Hupp, TR, O'Neill, JR, Tucker, O, Beggs, A, Taniere, P, Puig, S, Underwood, TJ, Walker, RC, Grace, BL, Barr, H, Shepherd, N, Old, O, Gossage, J, Davies, A, Chang, F, Zylstra, J, Mahadeva, U, Goh, V, Sanders, G, Berrisford, R, Harden, C, Lewis, M, Cheong, E, Kumar, B, Parsons, SL, Soomro, I, Kaye, P, Saunders, J, Lovat, L, Haidry, R, Igali, L, Scott, M, Sothi, S, Suortamo, S, Lishman, S, Hanna, GB, Peters, CJ, Moorthy, K, Grabowska, A, Turkington, R, McManus, D, Khoo, D, Fickling, W, Ciccarelli, FD

المصدر: Nature communications. 10(1):3101

مصطلحات موضوعية: Medicin och hälsovetenskap

الوصول الحر: http://kipublications.ki.se/Default.aspx?queryparsed=id:141351228Test