Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Autor: Stefan C. Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester, Ignacio Vázquez-García, Kortine Kleinheinz, Dimitri G. Livitz, Salem Malikic, Nilgun Donmez, Subhajit Sengupta, Pavana Anur, Clemency Jolly, Marek Cmero, Daniel Rosebrock, Steven E. Schumacher, Yu Fan, Matthew Fittall, Ruben M. Drews, Xiaotong Yao, Thomas B.K. Watkins, Juhee Lee, Matthias Schlesner, Hongtu Zhu, David J. Adams, Nicholas McGranahan, Charles Swanton, Gad Getz, Paul C. Boutros, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Inigo Martincorena, Florian Markowetz, Ville Mustonen, Ke Yuan, Moritz Gerstung, Paul T. Spellman, Wenyi Wang, Quaid D. Morris, David C. Wedge, Peter Van Loo, Santiago Gonzalez, David D. Bowtell, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Roland Eils, Dale W. Garsed, Gavin Ha, Lara Jerman, Henry Lee-Six, Thomas J. Mitchell, Layla Oesper, Myron Peto, Benjamin J. Raphael, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Lincoln D. Stein, Oliver Spiro, Shankar Vembu, David A. Wheeler, Tsun-Po Yang

Publikováno v: Cell, vol 184, iss 8
PCAWG Evolution and Heterogeneity Working Group, PCAWG Consortium & Wedge, D C 2021, ' Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes ', Cell, vol. 184, no. 8, pp. 2239-2254.e39 . https://doi.org/10.1016/j.cell.2021.03.009
Cell

Summary Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bb531f63564192b68acc8f428aac07cd
http://hdl.handle.net/10138/330238

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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Zechen, Chong, Oliver, Drechsel, Lewis Jonathan Dursi, Roland, Eils, Shadrielle M, G Espiritu, Robert, S Fulton, Shengjie, Gao, Josep L, L Gelpi, Mark, B Gerstein, Santiago, Gonzalez, Ivo, G Gut, Faraz, Hach, Michael, C Heinold, Jonathan, Hinton, Taobo, Hu, Vincent, Huang, Huang, Yi, Barbara, Hutter, David, R Jones, Jongsun, Jung, Natalie, Jäger, Hyung-Lae, Kim, Kortine, Kleinheinz, Sushant, Kumar, Yogesh, Kumar, Christopher, M Lalansingh, Ivica, Letunic, Dimitri, Livitz, Eric, Z Ma, Yosef, E Maruvka, R Jay Mashl, Andrew, Menzies, Ana, Milovanovic, Morten Muhlig Nielsen, Stephan, Ossowski, Nagarajan, Paramasivam, Jakob Skou Pedersen, Marc, D Perry, Montserrat, Puiggròs, Keiran, M Raine, Esther, Rheinbay, Romina, Royo, S Cenk Sahinalp, Iman, Sarrafi, Matthias, Schlesner, Jared, T Simpson, Lucy, Stebbings, Miranda, D Stobbe, Jon, W Teague, Grace, Tiao, David, Torrents, Jeremiah, A Wala, Jiayin, Wang, Sebastian, M Waszak, Joachim, Weischenfeldt, Michael, C Wendl, Johannes, Werner, 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Publikováno v: Nature Communications, 11(1):4748. Nature Publishing Group
Nature communications, 11(1):4748. Nature Publishing Group
Nature communications, 11 (1
NATURE COMMUNICATIONS
Nature Communications, 11 (1)
Nature Communications, Vol 11, Iss 1, Pp 1-27 (2020)
Bailey, M H, Meyerson, W U, Dursi, L J, Wang, L B, Dong, G, Liang, W W, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, M H, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, Weischenfeldt, J, Brunak, S, Ding, L, Favero, F, MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium 2020, ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ', Nature Communications, vol. 11, no. 1, 4748 . https://doi.org/10.1038/s41467-020-18151-y
Bailey, Matthew H; Meyerson, William U; Dursi, Lewis Jonathan; Wang, Liang-Bo; Dong, Guanlan; Liang, Wen-Wei; Weerasinghe, Amila; Li, Shantao; Kelso, Sean; Saksena, Gordon; Ellrott, Kyle; Wendl, Michael C; Wheeler, David A; Getz, Gad; Simpson, Jared T; Gerstein, Mark B; Ding, Li (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11(1), p. 4748. Springer Nature 10.1038/s41467-020-18151-y
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Bailey, M H, Meyerson, W U, Dursi, L J, Wang, L B, Dong, G, Liang, W W, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, M H, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium 2020, ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ', Nature Communications, vol. 11, no. 1, 4748 . https://doi.org/10.1038/s41467-020-18151-y
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MC3 Working Group: Rehan Akbani21, Pavana Anur22, Matthew H. Bailey1,2,3, Alex Buchanan9, Kami Chiotti9, Kyle Covington12,23, Allison Creason9, Li Ding1,2,3,20, Kyle Ellrott9, Yu Fan21, Steven Foltz1,2, Gad Getz8,14,15,16, Walker Hale12, David Haussl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79caf69aa08507159a37977adcb4937b
https://www.bib.irb.hr/1104730

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

Autor: Marc Dabad, John Douglas Mcpherson, Xose S. Puente, Liu Xi, Ivo Gut, Anne-Marie Patch, Semin Lee, Cyriac Kandoth, Ruben M. Drews, Charlotte Anderson, Eivind Hovig, Paul C. Boutros, Peter J. Campbell, Louis Letourneau, Paolo Ribeca, Hidewaki Nakagawa, Natalie Jäger, Daniel Vodak, Thomas J. Hudson, Anne Sophie Sertier, Pablo H. Hennings-Yeomans, John Zhang, Philip Ginsbach, Laurie Tonon, Emanuele Raineri, Sahil Seth, Sophia Derdak, Benedikt Brors, David T. W. Jones, Minghui He, Sergi Beltran, Rafael Valdés-Mas, David Torrents, Singer Ma, Myron Peto, Nagarajan Paramasivam, Matthew D. Eldridge, Robert E. Denroche, Paul T. Spellman, Francesc Castro Giner, Roland Eils, Timothy Beck, Sigve Nakken, Daniela S. Gerhard, Lawrence E. Heisler, Jared T. Simpson, Víctor Quesada, Rolf Kabbe, Andy G. Lynch, Patrick S. Tarpey, Lawrence Bower, Akihiro Fujimoto, Barbara Hutter, Matthias Schlesner, Marta Gut, Ivo Buchhalter, David A. Wheeler, Takafumi N. Yamaguchi, Simon Heath, Nicholas J. Harding, Tyler Alioto

The emergence of next generation DNA sequencing technology is enabling high-resolution cancer genome analysis. Large-scale projects like the International Cancer Genome Consortium (ICGC) are systematically scanning cancer genomes to identify recurren

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https://doi.org/10.1101/012997

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Autor: Matthew D. Eldridge, Sasithorn Chotewutmontri, Susanne Gröbner, Eivind Hovig, Ivo Gut, Minghui He, Hidewaki Nakagawa, Charlotte Anderson, Rafael Valdés-Mas, Lars Feuerbach, Sergi Beltran, Adam Butler, Nagarajan Paramasivam, John Douglas Mcpherson, Akihiro Fujimoto, Ann-Marie Patch, Ivo Buchhalter, Laurie Tonon, Stefan M. Pfister, Víctor Quesada, Jon W. Teague, Sabine Schmidt, David T. W. Jones, Sahil Seth, David Torrents, Singer Ma, Marta Gut, Semin Lee, Robert E. Denroche, Carlos López-Otín, Andy G. Lynch, David A. Wheeler, Takafumi N. Yamaguchi, Lucy Stebbings, Ruben M. Drews, Roland Eils, Marc Dabad, Tyler Alioto, Barbara Hutter, Rebecca Shepherd, Peter Lichter, Sigve Nakken, Daniel Vodak, Simon Heath, Rolf Kabbe, Christopher Previti, Paul T. Spellman, Nicola Waddell, Jared T. Simpson, John V. Pearson, Timothy Beck, Patrick S. Tarpey, Daniela S. Gerhard, Andrew Menzies, Francesc Castro Giner, Paolo Ribeca, Nicholas J. Harding, Liu Xi, Nicolle Diessl, Emanuele Raineri, Lawrence E. Heisler, Jonathan Hinton, Xose S. Puente, Cyriac Kandoth, Natalie Jäger, David T. Jones, Matthias Schlesner, Louis Letourneau, Sean M. Grimmond, Elias Campo, Peter J. Campbell, Keiran Raine, Lawrence Bower, Michael Heinold, Andrey Korshunov, Thomas J. Hudson, Anne Sophie Sertier, Benedikt Brors, Sophia Derdak, Paul C. Boutros, Myron Peto, John Zhang, Philip Ginsbach

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Financial support was provided by the consortium projects READNA under grant agreement FP7 Health-F4- 2008-201418, ESGI under grant agreement 262055, GEUVADIS under grant agreement 261123 of the European Commission Framework Programme 7, ICGC-CLL thr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6c50ea0ec3ca8190514a6be077f87e3b
http://hdl.handle.net/2445/120214