Author: "Liang, Sheng-Ben" - Searchworks@Jio Institute Digital Library Search Results

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51. Osteoclast-like Giant Cell Tumor of the Pancreas with Metastases to Gallbladder and Lymph Nodes. A Case Report

Author: Sun, A-Ping, primary, Ohtsuki, Yuji, additional, Liang, Sheng-Ben, additional, Sonobe, Hiroshi, additional, Iwata, Jun, additional, Furihata, Mutsuo, additional, Takeuchi, Tamotsu, additional, Qiu, Yue, additional, Chen, Bing-Kun, additional, Watanabe, Ryohei, additional, and Ohmori, Katsusuke, additional
Published: 1998
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52. Tetrasomy 12 in ovarian tumors of thecoma-fibroma group: A fluorescence in situ hybridization analysis using paraffin sections.

Author: Sonobe, Hiroshi, Liang, Sheng-Ben, Taguchi, Takahiro, Takeuchi, Tamotsu, Furihata, Mutsuo, Yuri, Kazunari, and Ohtsuki, Yuji
Subjects: *TUMORS, *FIBROMAS, *IN situ hybridization
Abstract: Recent cytogenetical studies have indicated that trisomy 12 is a feature of ovarian tumors in the thecoma-fibroma group. Ten cases of these ovarian tumors were studied in total, including two thecomas, two fibrothecomas, four fibromas, one cellular fibroma and one fibrosarcoma, to clarify the relationship between polysomy 12 and proliferative activity in these tumors. Each formalin-fixed, paraffin-embedded tumor tissue was examined by fluorescence in situ hybridization to determine copy numbers of chromosome 12 and by immunohistochemical staining of Ki-67 for evaluation of tumor cell proliferation. Gains of trisomy 12 were found in seven of the 10 cases, and the percentage of cells with tetrasomy 12, but not that of cells with trisomy 12, was significantly and positively correlated with percentage of Ki-67-positive cells, but significantly and inversely correlated with patient age. These findings suggest that tetrasomy 12 is an age-related aberration of chromosome 12 in ovarian tumors of the thecoma-fibroma group, and that such tumors exhibit more active proliferation in younger patients. [ABSTRACT FROM AUTHOR]
Published: 2001

53. Expression of T-Cadherin (CDH13, H-Cadherin) in Human Brain and ItsCharacteristics as a Negative Growth Regulator of Epidermal Growth Factor inNeuroblastoma Cells.

Author: Takeuchi, Tamotsu, Misaki, Akiko, Liang, Sheng-Ben, Tachibana, Akiko, Hayashi, Nakanobu, Sonobe, Hiroshi, and Ohtsuki, Yuji
Subjects: EPIDERMAL growth factor, NEUROBLASTOMA, CENTRAL nervous system
Abstract: Abstract: In the present study, we first examined the expression of T-cadherin in human CNS by northern blot analysis, immunohistochemical staining, and in situ hybridization. Northern blot analysis demonstrated expression of T-cadherin in human adult cerebral cortex, medulla, thalamus, and midbrain. Immunohistochemical staining with a newly generated monoclonal antibody, designated MA-511, revealed strong expression of T-cadherin in neural cell surface membrane and neurites in adult cerebral cortex, medulla oblongata, and nucleus olivaris. Little or no expression of T-cadherin was found in spinal cord. We further examined T-cadherin expression in various developing nervous systems, and found that T-cadherin expression was lower in developing brain than in adult brain. In situ hybridization revealed that neural cells in medulla oblongata and nucleus olivaris, but not in spinal cord, possessed T-cadherin molecules. We transfected T-cadherin-negative TGW and NH-12 neuroblastoma cells with a T-cadherin cDNA-containing expression vector. T-cadherin-expressing neuroblastoma cells lost mitogenic proliferative response to epidermal growth factor. Epidermal growth factor is known to be required for proliferation of neural stem cells. This finding, together with those of the present study, suggests that T-cadherin functions as a negative regulator of neural cell growth. [ABSTRACT FROM AUTHOR]
Published: 2000
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54. Overexpression of c-MetProtein in Human Thyroid Tumors Correlated with Lymph Node Metastasis and Clinicopathologic Stage

Author: Chen, Bing-Kun, Ohtsuki, Yuji, Furihata, Mutsuo, Takeuchi, Tamotsu, Iwata, Jun, Liang, Sheng-Ben, and Sonobe, Hiroshi
Abstract: To examine the expression of c-Metprotein in thyroid tumors and the correlation of c-Metprotein expression with lymph node metastasis (LNM) and pathological stage, 111 papillary thyroid carcinomas (PTC), including 44 with synchronous LNM, and 117 follicular adenomas (FA) were immunohistochemically examined using dewaxed sections of formalin-fixed, paraffin-embedded tissues.Immunohistochemical results were confirmed by Western blot analysis.For PTC, positive immunostaining was observed in 107 of 111 (96.4%) cases and was diffusely present in either cytoplasm and nucleus, or only cytoplasm or only nucleus of cancer cells at varying intensities.Staining tended to be stronger in the periphery of cancer cell nests.Positive reaction was also found in 44 of 117 (37.6%) cases of FA.However, the extent and intensity of c-Metimmunostaining in FA were far less than those in PTC (p < 0.0001).Forty-four PTC cases (39.6%) exhibited LNM, and the extent and intensity of c-Metexpression were significantly correlated with both LNM (p < 0.0001) and pathological stage (p < 0.0001).No significant correlation of c-Metexpression with age, sex or tumor size was found.Our findings suggest that PTC expresses c-Metprotein much more strongly and intensively than does FA, and that strong and intense overexpression of c-Metprotein may be an indicator of the presence of lymph node metastasis and advanced pathological stage of papillary thyroid carcinoma.
Published: 1999
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55. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Author: Meyerson, William U., Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Li, Yize, Kelso, Sean, Wendl, Michael C., Simpson, Jared T., Akbani, Rehan, Anur, Pavana, Bailey, Matthew H., Buchanan, Alex, Chiotti, Kami, Covington, Kyle, Creason, Allison, Ding, Li, Ellrott, Kyle, Fan, Yu, Foltz, Steven, Getz, Gad, Hale, Walker, Haussler, David, Hess, Julian M., Hutter, Carolyn M., Kandoth, Cyriac, Kasaian, Katayoon, Kasapi, Melpomeni, Larson, Dave, Leshchiner, Ignaty, Letaw, John, Ma, Singer, McLellan, Michael D., Men, Yifei, Mills, Gordon B., Niu, Beifang, Peto, Myron, Radenbaugh, Amie, Reynolds, Sheila M., Saksena, Gordon, Sofia, Heidi, Stewart, Chip, Struck, Adam J., Stuart, Joshua M., Wang, Wenyi, Weinstein, John N., Wheeler, David A., Wong, Christopher K., Xi, Liu, Ye, Kai, Bieg, Matthias, Boutros, Paul C., Buchhalter, Ivo, Butler, Adam P., Chen, Ken, Chong, Zechen, Drechsel, Oliver, Jonathan Dursi, Lewis, Eils, Roland, Espiritu, Shadrielle M. G., Fulton, Robert S., Gao, Shengjie, Gelpi, Josep L. L., Gerstein, Mark B., Gonzalez, Santiago, Gut, Ivo G., Hach, Faraz, Heinold, Michael C., Hinton, Jonathan, Hu, Taobo, Huang, Vincent, Huang, Yi, Hutter, Barbara, Jones, David R., Jung, Jongsun, Jäger, Natalie, Kim, Hyung-Lae, Kleinheinz, Kortine, Kumar, Sushant, Kumar, Yogesh, Lalansingh, Christopher M., Letunic, Ivica, Livitz, Dimitri, Ma, Eric Z., Maruvka, Yosef E., Mashl, R. Jay, Menzies, Andrew, Milovanovic, Ana, Nielsen, Morten Muhlig, Ossowski, Stephan, Paramasivam, Nagarajan, Pedersen, Jakob Skou, Perry, Marc D., Puiggròs, Montserrat, Raine, Keiran M., Rheinbay, Esther, Royo, Romina, Sahinalp, S. Cenk, Sarrafi, Iman, Schlesner, Matthias, Stebbings, Lucy, Stobbe, Miranda D., Teague, Jon W., Tiao, Grace, Torrents, David, Wala, Jeremiah A., Wang, Jiayin, Waszak, Sebastian M., Weischenfeldt, Joachim, Werner, Johannes, Wu, Zhenggang, Xue, Hong, Yakneen, Sergei, Yamaguchi, Takafumi N., Yellapantula, Venkata D., Yung, Christina K., Zhang, Junjun, Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, 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, Amin, Samirkumar B., Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J., Ang, Yeng, Antonello, Davide, 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 R., Awadalla, Philip, Aymerich, Marta, Bader, Gary D., Baez-Ortega, Adrian, Bailey, Peter J., 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, 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., Biankin, Andrew V., 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 D. L., 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 J. C., Bruzos, Alicia L., Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H., Busanovich, John, Bustamante, Carlos D., 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, Campbell, Peter J., 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., 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, Jung Kyoon, Choi, Wan, Chomienne, Christine, 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, 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, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C., Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Shuai, Dinh, Huy Q., Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T., Drapkin, Ronny, Drews, Ruben M., Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J., Dunn, Michael, 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, El-Naggar, Adel, Eldridge, Matthew, Erkek, Serap, Escaramis, Georgia, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E., Faltas, Bishoy M., Fan, Daiming, Faquin, William C., Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L., Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A., Fink, J. Lynn, 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., Fonseca, Nuno A., Foster, Christopher S., Fox, Natalie S., Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C., Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A., Furuta, Mayuko, Futreal, P. Andrew, Füllgrabe, Anja, Gabriel, Stacey B., Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Garraway, Levi, Garred, Øystein, Garrison, Erik, Garsed, Dale W., Gehlenborg, Nils, George, Joshy, Gerhard, Daniela S., Gerhauser, Clarissa, Gershenwald, Jeffrey E., Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H., Gibbs, Richard A., Gill, Anthony J., Gill, Pelvender, Giri, Dilip D., Glodzik, Dominik, Gnanapragasam, Vincent J., Goebler, Maria Elisabeth, Goldman, Mary J., Gomez, Carmen, 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, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E., Habermann, Nina, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C., Hamilton, Anne, Hamilton, Mark P., Han, Leng, Hanna, George B., Hansmann, Martin, Haradhvala, Nicholas J., Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O., Harrington, Eoghan, Hasegawa, Takanori, 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., Heins, Zachary, Heisler, Lawrence E., Hellstrom-Lindberg, Eva, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J., Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hilmarsdottir, Holmfridur, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A., Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I., Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z., Hollingsworth, Michael A., Holmes, Oliver, Holt, Robert A., Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H., Hooijer, Gerrit K., Hornshøj, Henrik, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P., Hruban, Ralph H., Hu, Jianhong, Hua, Xing, Huang, Kuan-Lin, Huang, Mei, Huang, Mi Ni, Huber, Wolfgang, Hudson, Thomas J., Hummel, Michael, Hung, Jillian A., Huntsman, David, Hupp, Ted R., Huse, Jason, Huska, Matthew R., Hübschmann, Daniel, Iacobuzio-Donahue, Christine A., Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B., Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, S. M. Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose M. G., 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, Johnson, Rory, Johnson, Todd A., Jolly, Clemency, Joly, Yann, Jonasson, Jon G., Jones, Corbin D., Jones, David T. W., Jones, Nic, Jones, Steven J. M., Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kaiser, Vera B., Kakavand, Hojabr, Kalimuthu, Sangeetha, Von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, 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., Kellis, Manolis, Kench, James G., Kennedy, Catherine J., Kerssemakers, Jules N. A., Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K., Kim, Youngwook, King, Tari A., Klapper, Wolfram, Klimczak, Leszek J., Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M., Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O., 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, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H., Laird, Peter W., Lakhani, Sunil R., Lalonde, Emilie, Lamaze, Fabien C., Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta M. S., Lawerenz, Chris, Lawlor, Rita T., Lawrence, Michael S., Lazar, Alexander J., Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R., Leongamornlert, Daniel A., Letourneau, Louis, Levine, Douglas A., Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H., Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, W. M., Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V., Lopez-Guillermo, Armando, Lou, Shaoke, 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, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T., Maitra, Arindam, Majumder, Partha P., Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J., Mantovani-Löffler, Luisa, Marchal, Kathleen, 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 W. M., Martin, Sancha, Martin-Subero, Jose I., Martincorena, Iñigo, Martinez-Fundichely, Alexander, Massie, Charlie E., Matthew, Thomas J., Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D., McPherson, John D., McPherson, John R., McPherson, Treasa A., Meier, Samuel R., Meng, Alice, Meng, Shaowu, Merrett, Neil D., Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A., Mihaiescu, George L., Mijalkovic, Sanja, Mijalkovic-Lazic, Ana Mijalkovic, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A., Miller, David K., Miller, Jessica K., 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., Muiños, Ferran, Mularoni, Loris, 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, Nakagawa, Hidewaki, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio C. P., 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, Ott, German, Ouellette, B. F. Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, 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., Petersen, Gloria M., 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, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R., Prinz, Manuel, Pritchard, Antonia L., Prokopec, Stephenie D., Provenzano, Elena, Puente, Xose S., Puig, Sonia, Pulido-Tamayo, Sergio, Pupo, Gulietta M., Purdie, Colin A., Quinn, Michael C., Rabionet, Raquel, Rader, Janet S., Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Raphael, Benjamin J., Rathmell, W. Kimryn, Rausch, Tobias, Reifenberger, Guido, Reimand, Jüri, Reis-Filho, Jorge, Reuter, Victor, Reyes-Salazar, Iker, Reyna, Matthew A., 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 H. A., Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C., Rosenwald, Andreas, Rowe, Edward W., Rozen, Steven G., Rubanova, Yulia, Rubin, Mark A., Rubio-Perez, Carlota, 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, Salichos, Leonidas, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S., Sanchez-Vega, Francisco, Sander, Chris, Sanders, Grant, Sarin, Rajiv, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn P. M., Scardoni, Maria, Scarlett, Christopher J., Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E., Schilhabel, Markus B., Schlomm, Thorsten, Schmidt, Heather K., Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schumacher, Steven E., 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., Shackleton, Mark, Shah, Nimish C., Shahabi, Sagedeh, Shang, Catherine A., Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, 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, Shrestha, Raunak, Shringarpure, Suyash S., Shriver, Craig, Shuai, Shimin, Sidiropoulos, Nikos, Siebert, Reiner, Sieuwerts, Anieta M., Sieverling, Lina, Signoretti, Sabina, Sikora, Katarzyna O., Simbolo, Michele, Simon, Ronald, Simons, Janae V., Simpson, Peter T., Singer, Samuel, Sinnott-Armstrong, Nasa, 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., Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D., Stenhouse, Alasdair, Stilgenbauer, Stephan, Stratton, Michael R., Stretch, Jonathan R., 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, 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 F., 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., Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz H. P., Tsao, Ming, Tsunoda, Tatsuhiko, Tubio, Jose M. C., 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 P. C., Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, Raghavan, K. Vijay, Viksna, Juris, Vilain, Ricardo E., Villasante, Izar, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M., Waddell, Nicola, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Linghua, Wang, Qi, Wang, Yumeng, Wang, Zhining, Waring, Paul M., Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y., Wedge, David C., Weichenhan, Dieter, Weinberger, Paul, Weisenberger, Daniel J., Welch, Ian, Whalley, Justin P., 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, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Yachida, Shinichi, Yamaguchi, Rui, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y., Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Yoon, Christopher J., Yoon, Sung-Soo, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Zaikova, Olga, Zamora, Jorge, Zapatka, Marc, Zenklusen, Jean C., Zenz, Thorsten, Zeps, Nikolajs, Zhang, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, 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 H. M., Van De Vijver, Marc J., Van’t Veer, L., and Von Mering, Christian
Subjects: 692/4028/67/69, 706/648/697/129/2043, 631/114/2399, article, 45/23, 139, 631/1647/2217/748, 3. Good health
Abstract: Funder: NCI U24CA211006, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.

56. Sex differences in oncogenic mutational processes

Author: Prokopec, Stephenie D., Sun, Ren X., Yousif, Fouad, Schmitz, Nathaniel, Al-Shahrour, Fatima, Atwal, Gurnit, 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., Jiao, Wei, Kaiser, Vera B., Karlić, Rosa, 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., Polak, Paz, Rheinbay, Esther, Rubin, Mark A., Semple, Colin A., Sgroi, Dennis C., Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D., Stobbe, Miranda D., Thai, Kevin, Wright, Derek W., Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, 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 R., 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 D. L., 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 J. C., 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., Demeulemeester, Jonas, Demidov, German M., Demircioğlu, Deniz, Dennis, Nening M., Denroche, Robert E., Dentro, Stefan C., Desai, Nikita, Deshwar, Amit G., Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C., Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, 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 M. G., Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E., Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L., Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A., Fink, J. Lynn, 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., Fonseca, Nuno A., Foster, Christopher S., Fox, Natalie S., Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, 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., Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W., Gehlenborg, Nils, Gelpi, Josep L. L., George, Joshy, Gerhard, Daniela S., Gerhauser, Clarissa, Gershenwald, Jeffrey E., Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H., Gibbs, Richard A., 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, Grossman, Robert L., Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G., Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E., Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C., Hamilton, Anne, Hamilton, Mark P., Han, Leng, Hanna, George B., Hansmann, Martin, Haradhvala, Nicholas J., Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O., 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, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J., Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hess, Julian M., Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I., Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z., Hollingsworth, Michael A., Holmes, Oliver, Holt, Robert A., Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H., Hooijer, Gerrit K., Hornshøj, Henrik, 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., Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, S. M. Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose M. G., 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, Johansson, Peter A., Johns, Amber L., Johns, Jeremy, Johnson, Rory, Johnson, Todd A., Jolly, Clemency, Joly, Yann, Jonasson, Jon G., Jones, Corbin D., Jones, David R., Jones, David T. W., Jones, Nic, Jones, Steven J. M., Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kakavand, Hojabr, Kalimuthu, Sangeetha, Von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S., Katai, Hitoshi, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D., Kazakoff, Stephen H., Kazanov, Marat D., Keays, Maria, Kebebew, Electron, Kefford, Richard F., Kellis, Manolis, Kench, James G., Kennedy, Catherine J., Kerssemakers, Jules N. A., Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K., Kim, Youngwook, King, Tari A., Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J., Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M., Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O., 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, Sushant, Kumar, Yogesh, Kundra, Ritika, 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, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta M. S., Lawerenz, Chris, Lawlor, Rita T., Lawrence, Michael S., Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, 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, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, W. M., Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V., Lopez-Guillermo, Armando, Lou, Shaoke, 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, Ma, Eric Z., Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T., Maitra, Arindam, Majumder, Partha P., Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J., Mantovani-Löffler, Luisa, Marchal, Kathleen, 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 W. 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M., Van De Vijver, Marc J., Veer, L. Van’t, and Von Mering, Christian
Subjects: 692/4028/67/69, ComputingMilieux_THECOMPUTINGPROFESSION, 45, 631/67/68, 692/4028/67/395, 38/23, 631/114/2785, article, ComputingMilieux_LEGALASPECTSOFCOMPUTING, 119, 10. No inequality, GeneralLiterature_MISCELLANEOUS, 3. Good health
Abstract: Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790, Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762, Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196, Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376, Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.

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

Author: Meyerson, William U., Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Kelso, Sean, Wendl, Michael C., Simpson, Jared T., Akbani, Rehan, Anur, Pavana, Bailey, Matthew H., Buchanan, Alex, Chiotti, Kami, Covington, Kyle, Creason, Allison, Ding, Li, Ellrott, Kyle, Fan, Yu, Foltz, Steven, Getz, Gad, Hale, Walker, Haussler, David, Hess, Julian M., Hutter, Carolyn M., Kandoth, Cyriac, Kasaian, Katayoon, Kasapi, Melpomeni, Larson, Dave, Leshchiner, Ignaty, Letaw, John, Ma, Singer, McLellan, Michael D., Men, Yifei, Mills, Gordon B., Niu, Beifang, Peto, Myron, Radenbaugh, Amie, Reynolds, Sheila M., Saksena, Gordon, Sofia, Heidi, Stewart, Chip, Struck, Adam J., Stuart, Joshua M., Wang, Wenyi, Weinstein, John N., Wheeler, David A., Wong, Christopher K., Xi, Liu, Ye, Kai, Bieg, Matthias, Boutros, Paul C., Buchhalter, Ivo, Butler, Adam P., Chen, Ken, Chong, Zechen, Drechsel, Oliver, Jonathan Dursi, Lewis, Eils, Roland, Espiritu, Shadrielle M. G., Fulton, Robert S., Gao, Shengjie, Gelpi, Josep L. L., Gerstein, Mark B., Gonzalez, Santiago, Gut, Ivo G., Hach, Faraz, Heinold, Michael C., Hinton, Jonathan, Hu, Taobo, Huang, Vincent, Huang, Yi, Hutter, Barbara, Jones, David R., Jung, Jongsun, Jäger, Natalie, Kim, Hyung-Lae, Kleinheinz, Kortine, Kumar, Sushant, Kumar, Yogesh, Lalansingh, Christopher M., Letunic, Ivica, Livitz, Dimitri, Ma, Eric Z., Maruvka, Yosef E., Mashl, R. Jay, Menzies, Andrew, Milovanovic, Ana, Nielsen, Morten Muhlig, Ossowski, Stephan, Paramasivam, Nagarajan, Pedersen, Jakob Skou, Perry, Marc D., Puiggròs, Montserrat, Raine, Keiran M., Rheinbay, Esther, Royo, Romina, Sahinalp, S. Cenk, Sarrafi, Iman, Schlesner, Matthias, Stebbings, Lucy, Stobbe, Miranda D., Teague, Jon W., Tiao, Grace, Torrents, David, Wala, Jeremiah A., Wang, Jiayin, Waszak, Sebastian M., Weischenfeldt, Joachim, Werner, Johannes, Wu, Zhenggang, Xue, Hong, Yakneen, Sergei, Yamaguchi, Takafumi N., Yellapantula, Venkata D., Yung, Christina K., Zhang, Junjun, Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, 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, Amin, Samirkumar B., Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J., Ang, Yeng, Antonello, Davide, 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 R., Awadalla, Philip, Aymerich, Marta, Bader, Gary D., Baez-Ortega, Adrian, Bailey, Peter J., 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, 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., Biankin, Andrew V., 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 D. L., 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 J. C., Bruzos, Alicia L., Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H., Busanovich, John, Bustamante, Carlos D., 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, Campbell, Peter J., 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., 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, Jung Kyoon, Choi, Wan, Chomienne, Christine, 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, 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, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C., Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Shuai, Dinh, Huy Q., Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T., Drapkin, Ronny, Drews, Ruben M., Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J., Dunn, Michael, 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, El-Naggar, Adel, Eldridge, Matthew, Erkek, Serap, Escaramis, Georgia, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E., Faltas, Bishoy M., Fan, Daiming, Faquin, William C., Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L., Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A., Fink, J. Lynn, 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., Fonseca, Nuno A., Foster, Christopher S., Fox, Natalie S., Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C., Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A., Furuta, Mayuko, Futreal, P. 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M., Van De Vijver, Marc J., Van’t Veer, L., and Von Mering, Christian
Subjects: 692/4028/67/69, 706/648/697/129/2043, 631/114/2399, article, 45/23, 139, 631/1647/2217/748, 3. Good health
Abstract: Funder: NCI U24CA211006, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.

58. Pan-cancer analysis of whole genomes

Author: Campbell, Peter J., Getz, Gad, Korbel, Jan O., Stuart, Joshua M., Jennings, Jennifer L., Stein, Lincoln D., Perry, Marc D., Nahal-Bose, Hardeep K., Ouellette, B. F. Francis, Li, Constance H., Rheinbay, Esther, Nielsen, G. Petur, Sgroi, Dennis C., Wu, Chin-Lee, Faquin, William C., Deshpande, Vikram, Boutros, Paul C., Lazar, Alexander J., Hoadley, Katherine A., Louis, David N., Dursi, L. Jonathan, Yung, Christina K., Bailey, Matthew H., Saksena, Gordon, Raine, Keiran M., Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun, Wang, Wenyi, Wheeler, David A., Ding, Li, Simpson, Jared T., O’Connor, Brian D., Yakneen, Sergei, Ellrott, Kyle, Miyoshi, Naoki, Butler, Adam P., Royo, Romina, Shorser, Solomon I., Vazquez, Miguel, Rausch, Tobias, Tiao, Grace, Waszak, Sebastian M., Rodriguez-Martin, Bernardo, Shringarpure, Suyash, Wu, Dai-Ying, Demidov, German M., Delaneau, Olivier, Hayashi, Shuto, Imoto, Seiya, Habermann, Nina, Segre, Ayellet V., Garrison, Erik, Cafferkey, Andy, Alvarez, Eva G., Heredia-Genestar, José María, Muyas, Francesc, Drechsel, Oliver, Bruzos, Alicia L., Temes, Javier, Zamora, Jorge, Baez-Ortega, Adrian, Kim, Hyung-Lae, Mashl, R. Jay, Ye, Kai, DiBiase, Anthony, Huang, Kuan-Lin, Letunic, Ivica, McLellan, Michael D., Newhouse, Steven J., Shmaya, Tal, Kumar, Sushant, Wedge, David C., Wright, Mark H., Yellapantula, Venkata D., Gerstein, Mark, Khurana, Ekta, Marques-Bonet, Tomas, Navarro, Arcadi, Bustamante, Carlos D., Siebert, Reiner, Nakagawa, Hidewaki, Easton, Douglas F., Ossowski, Stephan, Tubio, Jose M. C., De La Vega, Francisco M., Estivill, Xavier, Yuen, Denis, Mihaiescu, George L., Omberg, Larsson, Ferretti, Vincent, Sabarinathan, Radhakrishnan, Pich, Oriol, Gonzalez-Perez, Abel, Taylor-Weiner, Amaro, Fittall, Matthew W., Demeulemeester, Jonas, Tarabichi, Maxime, Roberts, Nicola D., Van Loo, Peter, Cortés-Ciriano, Isidro, Urban, Lara, Park, Peter, Zhu, Bin, Pitkänen, Esa, Li, Yilong, Saini, Natalie, Klimczak, Leszek J., Weischenfeldt, Joachim, Sidiropoulos, Nikos, Alexandrov, Ludmil B., Rabionet, Raquel, Escaramis, Georgia, Bosio, Mattia, Holik, Aliaksei Z., Susak, Hana, Prasad, Aparna, Erkek, Serap, Calabrese, Claudia, Raeder, Benjamin, Harrington, Eoghan, Mayes, Simon, Turner, Daniel, Juul, Sissel, Roberts, Steven A., Song, Lei, Koster, Roelof, Mirabello, Lisa, Hua, Xing, Tanskanen, Tomas J., Tojo, Marta, Chen, Jieming, Aaltonen, Lauri A., Rätsch, Gunnar, Schwarz, Roland F., Butte, Atul J., Brazma, Alvis, Chanock, Stephen J., Chatterjee, Nilanjan, Stegle, Oliver, Harismendy, Olivier, Bova, G. Steven, Gordenin, Dmitry A., Haan, David, Sieverling, Lina, Feuerbach, Lars, Chalmers, Don, Joly, Yann, Knoppers, Bartha, Molnár-Gábor, Fruzsina, Phillips, Mark, Thorogood, Adrian, Townend, David, Goldman, Mary, Fonseca, Nuno A., Xiang, Qian, Craft, Brian, Piñeiro-Yáñez, Elena, Muñoz, Alfonso, Petryszak, Robert, Füllgrabe, Anja, Al-Shahrour, Fatima, Keays, Maria, Haussler, David, Weinstein, John, Huber, Wolfgang, Valencia, Alfonso, Papatheodorou, Irene, Zhu, Jingchun, Fan, Yu, Torrents, David, Bieg, Matthias, Chen, Ken, Chong, Zechen, Cibulskis, Kristian, Eils, Roland, Fulton, Robert S., Gelpi, Josep L., Gonzalez, Santiago, Gut, Ivo G., Hach, Faraz, Heinold, Michael, Hu, Taobo, Huang, Vincent, Hutter, Barbara, Jäger, Natalie, Jung, Jongsun, Kumar, Yogesh, Lalansingh, Christopher, Leshchiner, Ignaty, Livitz, Dimitri, Ma, Eric Z., Maruvka, Yosef E., Milovanovic, Ana, Nielsen, Morten Muhlig, Paramasivam, Nagarajan, Pedersen, Jakob Skou, Puiggròs, Montserrat, Sahinalp, S. Cenk, Sarrafi, Iman, Stewart, Chip, Stobbe, Miranda D., Wala, Jeremiah A., Wang, Jiayin, Wendl, Michael, Werner, Johannes, Wu, Zhenggang, Xue, Hong, Yamaguchi, Takafumi N., Yellapantula, Venkata, Davis-Dusenbery, Brandi N., Grossman, Robert L., Kim, Youngwook, Heinold, Michael C., Hinton, Jonathan, Jones, David R., Menzies, Andrew, Stebbings, Lucy, Hess, Julian M., Rosenberg, Mara, Dunford, Andrew J., Gupta, Manaswi, Imielinski, Marcin, Meyerson, Matthew, Beroukhim, Rameen, Reimand, Jüri, Dhingra, Priyanka, Favero, Francesco, Dentro, Stefan, Wintersinger, Jeff, Rudneva, Vasilisa, Park, Ji Wan, Hong, Eun Pyo, Heo, Seong Gu, Kahles, André, Lehmann, Kjong-Van, Soulette, Cameron M., Shiraishi, Yuichi, Liu, Fenglin, He, Yao, Demircioğlu, Deniz, Davidson, Natalie R., Greger, Liliana, Li, Siliang, Liu, Dongbing, Stark, Stefan G., Zhang, Fan, Amin, Samirkumar B., Bailey, Peter, Chateigner, Aurélien, Frenkel-Morgenstern, Milana, Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Lamaze, Fabien C., Li, Chang, Li, Xiaobo, Li, Xinyue, Liu, Xingmin, Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Ojesina, Akinyemi I., Pan-Hammarström, Qiang, Park, Peter J., Pedamallu, Chandra Sekhar, Su, Hong, Tan, Patrick, Teh, Bin Tean, Wang, Jian, Xiong, Heng, Ye, Chen, Yung, Christina, Zhang, Xiuqing, Zheng, Liangtao, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Wu, Kui, Yang, Huanming, Göke, Jonathan, Zhang, Zemin, Brooks, Angela N., Fittall, Matthew W, Martincorena, Iñigo, Rubio-Perez, Carlota, Juul, Malene, Schumacher, Steven, Shapira, Ofer, Tamborero, David, Mularoni, Loris, Hornshøj, Henrik, Deu-Pons, Jordi, Muiños, Ferran, Bertl, Johanna, Guo, Qianyun, Bazant, Wojciech, Barrera, Elisabet, Al-Sedairy, Sultan T., Aretz, Axel, Bell, Cindy, Betancourt, Miguel, Buchholz, Christiane, Calvo, Fabien, Chomienne, Christine, Dunn, Michael, Edmonds, Stuart, Green, Eric, Gupta, Shailja, Hutter, Carolyn M., Jegalian, Karine, Jones, Nic, Lu, Youyong, Nakagama, Hitoshi, Nettekoven, Gerd, Planko, Laura, Scott, David, Shibata, Tatsuhiro, Shimizu, Kiyo, Stratton, Michael R., Yugawa, Takashi, Tortora, Giampaolo, VijayRaghavan, K., Zenklusen, Jean C., Knoppers, Bartha M., Aminou, Brice, Bartolome, Javier, Boroevich, Keith A., Boyce, Rich, Buchanan, Alex, Byrne, Niall J., Chen, Zhaohong, Cho, Sunghoon, Choi, Wan, Clapham, Peter, Dow, Michelle T., Dursi, Lewis Jonathan, Eils, Juergen, Farcas, Claudiu, Fayzullaev, Nodirjon, Flicek, Paul, Heath, Allison P., Hofmann, Oliver, Hong, Jongwhi H., Hudson, Thomas J., Hübschmann, Daniel, Ivkovic, Sinisa, Jeon, Seung-Hyup, Jiao, Wei, Kabbe, Rolf, Kahles, Andre, Kerssemakers, Jules N. A., Kim, Hyunghwan, Kim, Jihoon, Koscher, Michael, Koures, Antonios, Kovacevic, Milena, Lawerenz, Chris, Liu, Jia, Mijalkovic, Sanja, Mijalkovic-Lazic, Ana Mijalkovic, Miyano, Satoru, Nastic, Mia, Nicholson, Jonathan, Ocana, David, Ohi, Kazuhiro, Ohno-Machado, Lucila, Pihl, Todd D., Prinz, Manuel, Radovic, Petar, Short, Charles, Sofia, Heidi J., Spring, Jonathan, Struck, Adam J., Tijanic, Nebojsa, Vicente, David, Wang, Zhining, Williams, Ashley, Woo, Youngchoon, Wright, Adam J., Yang, Liming, Hamilton, Mark P., Johnson, Todd A., Kahraman, Abdullah, Kellis, Manolis, Polak, Paz, Sallari, Richard, Sinnott-Armstrong, Nasa, Von Mering, Christian, Beltran, Sergi, Gerhard, Daniela S., Gut, Marta, Trotta, Jean-Rémi, Whalley, Justin P., Niu, Beifang, Espiritu, Shadrielle M. G., Gao, Shengjie, Huang, Yi, Lalansingh, Christopher M., Teague, Jon W., Wendl, Michael C., Abascal, Federico, Bader, Gary D., Bandopadhayay, Pratiti, Barenboim, Jonathan, Brunak, Søren, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Choi, Jung Kyoon, Diamanti, Klev, Fink, J. Lynn, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W., Haradhvala, Nicholas J., Harmanci, Arif O., Helmy, Mohamed, Herrmann, Carl, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Isaev, Keren, Izarzugaza, Jose M. G., Johnson, Rory, Juul, Randi Istrup, Kim, Jaegil, Kim, Jong K., Komorowski, Jan, Lanzós, Andrés, Larsson, Erik, Lee, Donghoon, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martinez-Fundichely, Alexander, McGillivray, Patrick D., Meyerson, William, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pons, Tirso, Pulido-Tamayo, Sergio, Reyes-Salazar, Iker, Reyna, Matthew A., Rubin, Mark A., Salichos, Leonidas, Sander, Chris, Schumacher, Steven E., Shackleton, Mark, Shen, Ciyue, Shrestha, Raunak, Shuai, Shimin, Tsunoda, Tatsuhiko, Umer, Husen M., Uusküla-Reimand, Liis, Verbeke, Lieven P. C., Wadelius, Claes, Wadi, Lina, Warrell, Jonathan, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, Lawrence, Michael S., Raphael, Benjamin J., Bailey, Peter J., Craft, David, Goldman, Mary J., Aburatani, Hiroyuki, Binder, Hans, Dinh, Huy Q., Heath, Simon C., Hoffmann, Steve, Imbusch, Charles David, Kretzmer, Helene, Laird, Peter W., Martin-Subero, Jose I., Nagae, Genta, Shen, Hui, Wang, Qi, Weichenhan, Dieter, Zhou, Wanding, Berman, Benjamin P., Brors, Benedikt, Plass, Christoph, Akdemir, Kadir C., Bowtell, David D. L., Burns, Kathleen H., Busanovich, John, Chan, Kin, Dueso-Barroso, Ana, Edwards, Paul A., Etemadmoghadam, Dariush, Haber, James E., Jones, David T. W., Ju, Young Seok, Kazanov, Marat D., Koh, Youngil, Kumar, Kiran, Lee, Eunjung Alice, Lee, Jake June-Koo, Lynch, Andy G., Macintyre, Geoff, Markowetz, Florian, Navarro, Fabio C. P., Pearson, John V., Rippe, Karsten, Scully, Ralph, Villasante, Izar, Waddell, Nicola, Yang, Lixing, Yao, Xiaotong, Yoon, Sung-Soo, Zhang, Cheng-Zhong, Bergstrom, Erik N., Boot, Arnoud, Covington, Kyle, Fujimoto, Akihiro, Huang, Mi Ni, Islam, S. M. Ashiqul, McPherson, John R., Morganella, Sandro, Mustonen, Ville, Ng, Alvin Wei Tian, Prokopec, Stephenie D., Vázquez-García, Ignacio, Wu, Yang, Yousif, Fouad, Yu, Willie, Rozen, Steven G., Rudneva, Vasilisa A., Shringarpure, Suyash S., Turner, Daniel J., Xia, Tian, Atwal, Gurnit, Chang, David K., Cooke, Susanna L., Faltas, Bishoy M., Haider, Syed, Kaiser, Vera B., Karlić, Rosa, Kato, Mamoru, Kübler, Kirsten, Margolin, Adam, Martin, Sancha, Nik-Zainal, Serena, P’ng, Christine, Semple, Colin A., Smith, Jaclyn, Sun, Ren X., Thai, Kevin, Wright, Derek W., Yuan, Ke, Biankin, Andrew V., Garraway, Levi, Grimmond, Sean M., Adams, David J., Anur, Pavana, Cao, Shaolong, Christie, Elizabeth L., Cmero, Marek, Cun, Yupeng, Dawson, Kevin J., Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Gerstung, Moritz, Ha, Gavin, Haase, Kerstin, Jerman, Lara, Ji, Yuan, Jolly, Clemency, Lee, Juhee, Lee-Six, Henry, Malikic, Salem, Mitchell, Thomas J., Morris, Quaid D., Oesper, Layla, Peifer, Martin, Peto, Myron, Rosebrock, Daniel, Rubanova, Yulia, Salcedo, Adriana, Sengupta, Subhajit, Shi, Ruian, Shin, Seung Jun, Spiro, Oliver, Vembu, Shankar, Wintersinger, Jeffrey A., Yang, Tsun-Po, Yu, Kaixian, Zhu, Hongtu, Spellman, Paul T., Weinstein, John N., Chen, Yiwen, Fujita, Masashi, Han, Leng, Hasegawa, Takanori, Komura, Mitsuhiro, Li, Jun, Mizuno, Shinichi, Shimizu, Eigo, Wang, Yumeng, Xu, Yanxun, Yamaguchi, Rui, Yang, Fan, Yang, Yang, Yoon, Christopher J., Yuan, Yuan, Liang, Han, Alawi, Malik, Borozan, Ivan, Brewer, Daniel S., Cooper, Colin S., Desai, Nikita, Grundhoff, Adam, Iskar, Murat, Su, Xiaoping, Zapatka, Marc, Lichter, Peter, Alsop, Kathryn, Bruxner, Timothy J. C., Christ, Angelika N., Cordner, Stephen M., Cowin, Prue A., Drapkin, Ronny, Fereday, Sian, George, Joshy, Hamilton, Anne, Holmes, Oliver, Hung, Jillian A., Kassahn, Karin S., Kazakoff, Stephen H., Kennedy, Catherine J., Leonard, Conrad R., Mileshkin, Linda, Miller, David K., Arnau, Gisela Mir, Mitchell, Chris, Newell, Felicity, Nones, Katia, Patch, Ann-Marie, Quinn, Michael C., Taylor, Darrin F., Thorne, Heather, Traficante, Nadia, Vedururu, Ravikiran, Waddell, Nick M., Waring, Paul M., Wood, Scott, Xu, Qinying, DeFazio, Anna, Anderson, Matthew J., Antonello, Davide, Barbour, Andrew P., Bassi, Claudio, Bersani, Samantha, Cataldo, Ivana, Chantrill, Lorraine A., Chiew, Yoke-Eng, Chou, Angela, Cingarlini, Sara, Cloonan, Nicole, Corbo, Vincenzo, Davi, Maria Vittoria, Duthie, Fraser R., Gill, Anthony J., Graham, Janet S., Harliwong, Ivon, Jamieson, Nigel B., Johns, Amber L., Kench, James G., Landoni, Luca, Lawlor, Rita T., Mafficini, Andrea, Merrett, Neil D., Miotto, Marco, Musgrove, Elizabeth A., Nagrial, Adnan M., Oien, Karin A., Pajic, Marina, Pinese, Mark, Robertson, Alan J., Rooman, Ilse, Rusev, Borislav C., Samra, Jaswinder S., Scardoni, Maria, Scarlett, Christopher J., Scarpa, Aldo, Sereni, Elisabetta, Sikora, Katarzyna O., Simbolo, Michele, Taschuk, Morgan L., Toon, Christopher W., Vicentini, Caterina, Wu, Jianmin, Zeps, Nikolajs, Behren, Andreas, Burke, Hazel, Cebon, Jonathan, Dagg, Rebecca A., De Paoli-Iseppi, Ricardo, Dutton-Regester, Ken, Field, Matthew A., Fitzgerald, Anna, Hersey, Peter, Jakrot, Valerie, Johansson, Peter A., Kakavand, Hojabr, Kefford, Richard F., Lau, Loretta M. S., Long, Georgina V., Pickett, Hilda A., Pritchard, Antonia L., Pupo, Gulietta M., Saw, Robyn P. M., Schramm, Sarah-Jane, Shang, Catherine A., Shang, Ping, Spillane, Andrew J., Stretch, Jonathan R., Tembe, Varsha, Thompson, John F., Vilain, Ricardo E., Wilmott, James S., Yang, Jean Y., Hayward, Nicholas K., Mann, Graham J., Scolyer, Richard A., Bartlett, John, Bavi, Prashant, Chadwick, Dianne E., Chan-Seng-Yue, Michelle, Cleary, Sean, Connor, Ashton A., Czajka, Karolina, Denroche, Robert E., Dhani, Neesha C., Eagles, Jenna, Gallinger, Steven, Grant, Robert C., Hedley, David, Hollingsworth, Michael A., Jang, Gun Ho, Johns, Jeremy, Kalimuthu, Sangeetha, Liang, Sheng-Ben, Lungu, Ilinca, Luo, Xuemei, Mbabaali, Faridah, McPherson, Treasa A., Miller, Jessica K., Moore, Malcolm J., Notta, Faiyaz, Pasternack, Danielle, Petersen, Gloria M., Roehrl, Michael H. A., Sam, Michelle, Selander, Iris, Serra, Stefano, Shahabi, Sagedeh, Thayer, Sarah P., Timms, Lee E., Wilson, Gavin W., Wilson, Julie M., Wouters, Bradly G., McPherson, John D., Beck, Timothy A., Bhandari, Vinayak, Collins, Colin C., Fleshner, Neil E., Fox, Natalie S., Fraser, Michael, Heisler, Lawrence E., Lalonde, Emilie, Livingstone, Julie, Meng, Alice, Sabelnykova, Veronica Y., Shiah, Yu-Jia, Van Der Kwast, Theodorus, Bristow, Robert G., Ding, Shuai, Fan, Daiming, Li, Lin, Nie, Yongzhan, Xiao, Xiao, Xing, Rui, Yang, Shanlin, Yu, Yingyan, Zhou, Yong, Banks, Rosamonde E., Bourque, Guillaume, Brennan, Paul, Letourneau, Louis, Riazalhosseini, Yasser, Scelo, Ghislaine, Vasudev, Naveen, Viksna, Juris, Lathrop, Mark, Tost, Jörg, Ahn, Sung-Min, Aparicio, Samuel, Arnould, Laurent, Aure, M. R., Bhosle, Shriram G., Birney, Ewan, Borg, Ake, Boyault, Sandrine, Brinkman, Arie B., Brock, Jane E., Broeks, Annegien, Børresen-Dale, Anne-Lise, Caldas, Carlos, Chin, Suet-Feung, Davies, Helen, Desmedt, Christine, Dirix, Luc, Dronov, Serge, Ehinger, Anna, Eyfjord, Jorunn E., Fatima, Aquila, Foekens, John A., Futreal, P. Andrew, Garred, Øystein, Giri, Dilip D., Glodzik, Dominik, Grabau, Dorthe, Hilmarsdottir, Holmfridur, Hooijer, Gerrit K., Jacquemier, Jocelyne, Jang, Se Jin, Jonasson, Jon G., Jonkers, Jos, Kim, Hyung-Yong, King, Tari A., Knappskog, Stian, Kong, Gu, Krishnamurthy, Savitri, Lakhani, Sunil R., Langerød, Anita, Larsimont, Denis, Lee, Hee Jin, Lee, Jeong-Yeon, Lee, Ming Ta Michael, Lingjærde, Ole Christian, MacGrogan, Gaetan, Martens, John W. M., O’Meara, Sarah, Pauporté, Iris, Pinder, Sarah, Pivot, Xavier, Provenzano, Elena, Purdie, Colin A., Ramakrishna, Manasa, Ramakrishnan, Kamna, Reis-Filho, Jorge, Richardson, Andrea L., Ringnér, Markus, Rodriguez, Javier Bartolomé, Rodríguez-González, F. Germán, Romieu, Gilles, Salgado, Roberto, Sauer, Torill, Shepherd, Rebecca, Sieuwerts, Anieta M., Simpson, Peter T., Smid, Marcel, Sotiriou, Christos, Span, Paul N., Stefánsson, Ólafur Andri, Stenhouse, Alasdair, Stunnenberg, Henk G., Sweep, Fred, Tan, Benita Kiat Tee, Thomas, Gilles, Thompson, Alastair M., Tommasi, Stefania, Treilleux, Isabelle, Tutt, Andrew, Ueno, Naoto T., Van Laere, Steven, Van Den Eynden, Gert G., Vermeulen, Peter, Viari, Alain, Vincent-Salomon, Anne, Wong, Bernice H., Yates, Lucy, Zou, Xueqing, Van Deurzen, Carolien H. M., Van De Vijver, Marc J., Van’t Veer, Laura, Ammerpohl, Ole, Aukema, Sietse, Bergmann, Anke K., Bernhart, Stephan H., Borkhardt, Arndt, Borst, Christoph, Burkhardt, Birgit, Claviez, Alexander, Goebler, Maria Elisabeth, Haake, Andrea, Haas, Siegfried, Hansmann, Martin, Hoell, Jessica I., Hummel, Michael, Karsch, Dennis, Klapper, Wolfram, Kneba, Michael, Kreuz, Markus, Kube, Dieter, Küppers, Ralf, Lenze, Dido, Loeffler, Markus, López, Cristina, Mantovani-Löffler, Luisa, Möller, Peter, Ott, German, Radlwimmer, Bernhard, Richter, Julia, Rohde, Marius, Rosenstiel, Philip C., Rosenwald, Andreas, Schilhabel, Markus B., Schreiber, Stefan, Stadler, Peter F., Staib, Peter, Stilgenbauer, Stephan, Sungalee, Stephanie, Szczepanowski, Monika, Toprak, Umut H., Trümper, Lorenz H. P., Wagener, Rabea, Zenz, Thorsten, Hovestadt, Volker, Von Kalle, Christof, Kool, Marcel, Korshunov, Andrey, Landgraf, Pablo, Lehrach, Hans, Northcott, Paul A., Pfister, Stefan M., Reifenberger, Guido, Warnatz, Hans-Jörg, Wolf, Stephan, Yaspo, Marie-Laure, Assenov, Yassen, Gerhauser, Clarissa, Minner, Sarah, Schlomm, Thorsten, Simon, Ronald, Sauter, Guido, Sültmann, Holger, Biswas, Nidhan K., Maitra, Arindam, Majumder, Partha P., Sarin, Rajiv, Barbi, Stefano, Bonizzato, Giada, Cantù, Cinzia, Dei Tos, Angelo P., Fassan, Matteo, Grimaldi, Sonia, Luchini, Claudio, Malleo, Giuseppe, Marchegiani, Giovanni, Milella, Michele, Paiella, Salvatore, Pea, Antonio, Pederzoli, Paolo, Ruzzenente, Andrea, Salvia, Roberto, Sperandio, Nicola, Arai, Yasuhito, Hama, Natsuko, Hiraoka, Nobuyoshi, Hosoda, Fumie, Nakamura, Hiromi, Ojima, Hidenori, Okusaka, Takuji, Totoki, Yasushi, Urushidate, Tomoko, Fukayama, Masashi, Ishikawa, Shumpei, Katai, Hitoshi, Katoh, Hiroto, Komura, Daisuke, Rokutan, Hirofumi, Saito-Adachi, Mihoko, Suzuki, Akihiro, Taniguchi, Hirokazu, Tatsuno, Kenji, Ushiku, Tetsuo, Yachida, Shinichi, Yamamoto, Shogo, Aikata, Hiroshi, Arihiro, Koji, Ariizumi, Shun-Ichi, Chayama, Kazuaki, Furuta, Mayuko, Gotoh, Kunihito, Hayami, Shinya, Hirano, Satoshi, Kawakami, Yoshiiku, Maejima, Kazuhiro, Nakamura, Toru, Nakano, Kaoru, Ohdan, Hideki, Sasaki-Oku, Aya, Tanaka, Hiroko, Ueno, Masaki, Yamamoto, Masakazu, Yamaue, Hiroki, Choo, Su Pin, Cutcutache, Ioana, Khuntikeo, Narong, Ong, Choon Kiat, Pairojkul, Chawalit, Popescu, Irinel, Ahn, Keun Soo, Aymerich, Marta, Lopez-Guillermo, Armando, López-Otín, Carlos, Puente, Xose S., Campo, Elias, Amary, Fernanda, Baumhoer, Daniel, Behjati, Sam, Bjerkehagen, Bodil, Futreal, P. A., Myklebost, Ola, Pillay, Nischalan, Tarpey, Patrick, Tirabosco, Roberto, Zaikova, Olga, Flanagan, Adrienne M., Boultwood, Jacqueline, Bowen, David T., Cazzola, Mario, Green, Anthony R., Hellstrom-Lindberg, Eva, Malcovati, Luca, Nangalia, Jyoti, Papaemmanuil, Elli, Vyas, Paresh, Ang, Yeng, Barr, Hugh, Beardsmore, Duncan, Eldridge, Matthew, Gossage, James, Grehan, Nicola, Hanna, George B., Hayes, Stephen J., Hupp, Ted R., Khoo, David, Lagergren, Jesper, Lovat, Laurence B., MacRae, Shona, O’Donovan, Maria, O’Neill, J. Robert, Parsons, Simon L., Preston, Shaun R., Puig, Sonia, Roques, Tom, Sanders, Grant, Sothi, Sharmila, Tavaré, Simon, Tucker, Olga, Turkington, Richard, Underwood, Timothy J., Welch, Ian, Fitzgerald, Rebecca C., Berney, Daniel M., De Bono, Johann S., Cahill, Declan, Camacho, Niedzica, Dennis, Nening M., Dudderidge, Tim, Edwards, Sandra E., Fisher, Cyril, Foster, Christopher S., Ghori, Mohammed, Gill, Pelvender, Gnanapragasam, Vincent J., Gundem, Gunes, Hamdy, Freddie C., Hawkins, Steve, Hazell, Steven, Howat, William, Isaacs, William B., Karaszi, Katalin, Kay, Jonathan D., Khoo, Vincent, Kote-Jarai, Zsofia, Kremeyer, Barbara, Kumar, Pardeep, Lambert, Adam, Leongamornlert, Daniel A., Livni, Naomi, Lu, Yong-Jie, Luxton, Hayley J., Marsden, Luke, Massie, Charlie E., Matthews, Lucy, Mayer, Erik, McDermott, Ultan, Merson, Sue, Neal, David E., Ng, Anthony, Nicol, David, Ogden, Christopher, Rowe, Edward W., Shah, Nimish C., Thomas, Sarah, Thompson, Alan, Verrill, Clare, Visakorpi, Tapio, Warren, Anne Y., Whitaker, Hayley C., Zhang, Hongwei, Van As, Nicholas, Eeles, Rosalind A., Abeshouse, Adam, Agrawal, Nishant, Akbani, Rehan, Al-Ahmadie, Hikmat, Albert, Monique, Aldape, Kenneth, Ally, Adrian, Appelbaum, Elizabeth L., Armenia, Joshua, Asa, Sylvia, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barnholtz-Sloan, Jill, Bathe, Oliver F., Baylin, Stephen B., Benz, Christopher, Berchuck, Andrew, Berrios, Mario, Bigner, Darell, Birrer, Michael, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bosenberg, Marcus, Bowlby, Reanne, Boyd, Jeffrey, Broaddus, Russell R., Brock, Malcolm, Brooks, Denise, Bullman, Susan, Caesar-Johnson, Samantha J., Carey, Thomas E., Carlsen, Rebecca, Cerfolio, Robert, Chandan, Vishal S., Chen, Hsiao-Wei, Cherniack, Andrew D., Chien, Jeremy, Cho, Juok, Chuah, Eric, Cibulskis, Carrie, Cope, Leslie, Cordes, Matthew G., Curley, Erin, Czerniak, Bogdan, Danilova, Ludmila, Davis, Ian J., Defreitas, Timothy, Demchok, John A., Dhalla, Noreen, Dhir, Rajiv, Doddapaneni, HarshaVardhan, El-Naggar, Adel, Felau, Ina, Ferguson, Martin L., Finocchiaro, Gaetano, Fong, Kwun M., Frazer, Scott, Friedman, William, Fronick, Catrina C., Fulton, Lucinda A., Gabriel, Stacey B., Gao, Jianjiong, Gehlenborg, Nils, Gershenwald, Jeffrey E., Ghossein, Ronald, Giama, Nasra H., Gibbs, Richard A., Gomez, Carmen, Govindan, Ramaswamy, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Heins, Zachary, Hepperla, Austin J., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Hruban, Ralph H., Hu, Jianhong, Huang, Mei, Huntsman, David, Huse, Jason, Iacobuzio-Donahue, Christine A., Ittmann, Michael, Jayaseelan, Joy C., Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J. M., Juhl, Hartmut, Kang, Koo Jeong, Karlan, Beth, Kasaian, Katayoon, Kebebew, Electron, Kim, Hark Kyun, Korchina, Viktoriya, Kundra, Ritika, Lai, Phillip H., Lander, Eric, Le, Xuan, Lee, Darlene, Levine, Douglas A., Lewis, Lora, Ley, Tim, Li, Haiyan Irene, Lin, Pei, Linehan, W. M., Liu, Fei Fei, Lu, Yiling, Lype, Lisa, Ma, Yussanne, Maglinte, Dennis T., Mardis, Elaine R., Marks, Jeffrey, Marra, Marco A., Matthew, Thomas J., Mayo, Michael, McCune, Karen, Meier, Samuel R., Meng, Shaowu, Mieczkowski, Piotr A., Mikkelsen, Tom, Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morrison, Carl, Mose, Lisle E., Moser, Catherine D., Mungall, Andrew J., Mungall, Karen, Mutch, David, Muzny, Donna M., Myers, Jerome, Newton, Yulia, Noble, Michael S., O’Donnell, Peter, O’Neill, Brian Patrick, Ochoa, Angelica, Park, Joong-Won, Parker, Joel S., Pass, Harvey, Pastore, Alessandro, Pennell, Nathan A., Perou, Charles M., Petrelli, Nicholas, Potapova, Olga, Rader, Janet S., Ramalingam, Suresh, Rathmell, W. Kimryn, Reuter, Victor, Reynolds, Sheila M., Ringel, Matthew, Roach, Jeffrey, Roberts, Lewis R., Robertson, A. Gordon, Sadeghi, Sara, Saller, Charles, Sanchez-Vega, Francisco, Schadendorf, Dirk, Schein, Jacqueline E., Schmidt, Heather K., Schultz, Nikolaus, Seethala, Raja, Senbabaoglu, Yasin, Shelton, Troy, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Shriver, Craig, Signoretti, Sabina, Simons, Janae V., Singer, Samuel, Sipahimalani, Payal, Skelly, Tara J., Smith-McCune, Karen, Socci, Nicholas D., Soloway, Matthew G., Sood, Anil K., Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thompson, R. Houston, Thorne, Leigh B., Tsao, Ming, Umbricht, Christopher, Van Den Berg, David J., Van Meir, Erwin G., Veluvolu, Umadevi, Voet, Douglas, Wang, Linghua, Weinberger, Paul, Weisenberger, Daniel J., Wigle, Dennis, Wilkerson, Matthew D., Wilson, Richard K., Winterhoff, Boris, Wiznerowicz, Maciej, Wong, Tina, Wong, Winghing, Xi, Liu, Yau, Christina, Zhang, Hailei, Zhang, Hongxin, and Zhang, Jiashan
Subjects: article, 3. Good health
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5, 6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8, 9; and evaluates a range of more-specialized features of cancer genomes8, 10–18.

59. Sex differences in oncogenic mutational processes

Author: Prokopec, Stephenie D., Sun, Ren X., Yousif, Fouad, Schmitz, Nathaniel, Al-Shahrour, Fatima, Atwal, Gurnit, 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., Jiao, Wei, Kaiser, Vera B., Karlić, Rosa, 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., Polak, Paz, Rheinbay, Esther, Rubin, Mark A., Semple, Colin A., Sgroi, Dennis C., Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D., Stobbe, Miranda D., Thai, Kevin, Wright, Derek W., Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, 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 R., 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 D. L., 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 J. C., 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., Demeulemeester, Jonas, Demidov, German M., Demircioğlu, Deniz, Dennis, Nening M., Denroche, Robert E., Dentro, Stefan C., Desai, Nikita, Deshwar, Amit G., Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C., Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, 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 M. G., Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E., Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L., Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A., Fink, J. Lynn, 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., Fonseca, Nuno A., Foster, Christopher S., Fox, Natalie S., Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, 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., Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W., Gehlenborg, Nils, Gelpi, Josep L. L., George, Joshy, Gerhard, Daniela S., Gerhauser, Clarissa, Gershenwald, Jeffrey E., Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H., Gibbs, Richard A., 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, Grossman, Robert L., Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G., Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E., Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C., Hamilton, Anne, Hamilton, Mark P., Han, Leng, Hanna, George B., Hansmann, Martin, Haradhvala, Nicholas J., Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O., 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, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J., Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hess, Julian M., Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I., Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z., Hollingsworth, Michael A., Holmes, Oliver, Holt, Robert A., Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H., Hooijer, Gerrit K., Hornshøj, Henrik, 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., Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, S. M. Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose M. G., 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, Johansson, Peter A., Johns, Amber L., Johns, Jeremy, Johnson, Rory, Johnson, Todd A., Jolly, Clemency, Joly, Yann, Jonasson, Jon G., Jones, Corbin D., Jones, David R., Jones, David T. W., Jones, Nic, Jones, Steven J. M., Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kakavand, Hojabr, Kalimuthu, Sangeetha, Von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S., Katai, Hitoshi, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D., Kazakoff, Stephen H., Kazanov, Marat D., Keays, Maria, Kebebew, Electron, Kefford, Richard F., Kellis, Manolis, Kench, James G., Kennedy, Catherine J., Kerssemakers, Jules N. A., Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K., Kim, Youngwook, King, Tari A., Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J., Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M., Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O., 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, Sushant, Kumar, Yogesh, Kundra, Ritika, 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, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta M. S., Lawerenz, Chris, Lawlor, Rita T., Lawrence, Michael S., Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, 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, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, W. M., Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V., Lopez-Guillermo, Armando, Lou, Shaoke, 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, Ma, Eric Z., Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T., Maitra, Arindam, Majumder, Partha P., Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J., Mantovani-Löffler, Luisa, Marchal, Kathleen, 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 W. M., Martin-Subero, Jose I., Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E., Mashl, R. Jay, Massie, Charlie E., Matthew, Thomas J., Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D., 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, Meyerson, William, Mieczkowski, Piotr A., Mihaiescu, George L., Mijalkovic, Sanja, Mijalkovic-Lazic, Ana Mijalkovic, 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., Muiños, Ferran, Mularoni, Loris, 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., Nakagama, Hitoshi, Nakagawa, Hidewaki, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio C. P., 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, Morten Muhlig, 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, Ong, Chovon Kiat, Ossowski, Stephan, Ott, German, Ouellette, B. F. 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M., Van De Vijver, Marc J., Veer, L. Van’t, and Von Mering, Christian
Subjects: 692/4028/67/69, ComputingMilieux_THECOMPUTINGPROFESSION, 45, 631/67/68, 692/4028/67/395, 38/23, 631/114/2785, article, ComputingMilieux_LEGALASPECTSOFCOMPUTING, 119, 10. No inequality, GeneralLiterature_MISCELLANEOUS, 3. Good health
Abstract: Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790, Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762, Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196, Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376, Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.

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

Author: Meyerson, William U., Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Li, Yize, Kelso, Sean, Wendl, Michael C., Simpson, Jared T., Akbani, Rehan, Anur, Pavana, Bailey, Matthew H., Buchanan, Alex, Chiotti, Kami, Covington, Kyle, Creason, Allison, Ding, Li, Ellrott, Kyle, Fan, Yu, Foltz, Steven, Getz, Gad, Hale, Walker, Haussler, David, Hess, Julian M., Hutter, Carolyn M., Kandoth, Cyriac, Kasaian, Katayoon, Kasapi, Melpomeni, Larson, Dave, Leshchiner, Ignaty, Letaw, John, Ma, Singer, McLellan, Michael D., Men, Yifei, Mills, Gordon B., Niu, Beifang, Peto, Myron, Radenbaugh, Amie, Reynolds, Sheila M., Saksena, Gordon, Sofia, Heidi, Stewart, Chip, Struck, Adam J., Stuart, Joshua M., Wang, Wenyi, Weinstein, John N., Wheeler, David A., Wong, Christopher K., Xi, Liu, Ye, Kai, Bieg, Matthias, Boutros, Paul C., Buchhalter, Ivo, Butler, Adam P., Chen, Ken, Chong, Zechen, Drechsel, Oliver, Jonathan Dursi, Lewis, Eils, Roland, Espiritu, Shadrielle M. G., Fulton, Robert S., Gao, Shengjie, Gelpi, Josep L. L., Gerstein, Mark B., Gonzalez, Santiago, Gut, Ivo G., Hach, Faraz, Heinold, Michael C., Hinton, Jonathan, Hu, Taobo, Huang, Vincent, Huang, Yi, Hutter, Barbara, Jones, David R., Jung, Jongsun, Jäger, Natalie, Kim, Hyung-Lae, Kleinheinz, Kortine, Kumar, Sushant, Kumar, Yogesh, Lalansingh, Christopher M., Letunic, Ivica, Livitz, Dimitri, Ma, Eric Z., Maruvka, Yosef E., Mashl, R. Jay, Menzies, Andrew, Milovanovic, Ana, Nielsen, Morten Muhlig, Ossowski, Stephan, Paramasivam, Nagarajan, Pedersen, Jakob Skou, Perry, Marc D., Puiggròs, Montserrat, Raine, Keiran M., Rheinbay, Esther, Royo, Romina, Sahinalp, S. Cenk, Sarrafi, Iman, Schlesner, Matthias, Stebbings, Lucy, Stobbe, Miranda D., Teague, Jon W., Tiao, Grace, Torrents, David, Wala, Jeremiah A., Wang, Jiayin, Waszak, Sebastian M., Weischenfeldt, Joachim, Werner, Johannes, Wu, Zhenggang, Xue, Hong, Yakneen, Sergei, Yamaguchi, Takafumi N., Yellapantula, Venkata D., Yung, Christina K., Zhang, Junjun, Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, 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, Amin, Samirkumar B., Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J., Ang, Yeng, Antonello, Davide, 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 R., Awadalla, Philip, Aymerich, Marta, Bader, Gary D., Baez-Ortega, Adrian, Bailey, Peter J., 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, 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., Biankin, Andrew V., 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 D. L., 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 J. C., Bruzos, Alicia L., Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H., Busanovich, John, Bustamante, Carlos D., 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, Campbell, Peter J., 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., 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, Jung Kyoon, Choi, Wan, Chomienne, Christine, 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, 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, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C., Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Shuai, Dinh, Huy Q., Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T., Drapkin, Ronny, Drews, Ruben M., Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J., Dunn, Michael, 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, El-Naggar, Adel, Eldridge, Matthew, Erkek, Serap, Escaramis, Georgia, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E., Faltas, Bishoy M., Fan, Daiming, Faquin, William C., Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L., Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A., Fink, J. Lynn, 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., Fonseca, Nuno A., Foster, Christopher S., Fox, Natalie S., Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C., Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A., Furuta, Mayuko, Futreal, P. Andrew, Füllgrabe, Anja, Gabriel, Stacey B., Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Garraway, Levi, Garred, Øystein, Garrison, Erik, Garsed, Dale W., Gehlenborg, Nils, George, Joshy, Gerhard, Daniela S., Gerhauser, Clarissa, Gershenwald, Jeffrey E., Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H., Gibbs, Richard A., Gill, Anthony J., Gill, Pelvender, Giri, Dilip D., Glodzik, Dominik, Gnanapragasam, Vincent J., Goebler, Maria Elisabeth, Goldman, Mary J., Gomez, Carmen, 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, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E., Habermann, Nina, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C., Hamilton, Anne, Hamilton, Mark P., Han, Leng, Hanna, George B., Hansmann, Martin, Haradhvala, Nicholas J., Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O., Harrington, Eoghan, Hasegawa, Takanori, 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., Heins, Zachary, Heisler, Lawrence E., Hellstrom-Lindberg, Eva, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J., Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hilmarsdottir, Holmfridur, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A., Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I., Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z., Hollingsworth, Michael A., Holmes, Oliver, Holt, Robert A., Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H., Hooijer, Gerrit K., Hornshøj, Henrik, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P., Hruban, Ralph H., Hu, Jianhong, Hua, Xing, Huang, Kuan-Lin, Huang, Mei, Huang, Mi Ni, Huber, Wolfgang, Hudson, Thomas J., Hummel, Michael, Hung, Jillian A., Huntsman, David, Hupp, Ted R., Huse, Jason, Huska, Matthew R., Hübschmann, Daniel, Iacobuzio-Donahue, Christine A., Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B., Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, S. M. Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose M. G., 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, Johnson, Rory, Johnson, Todd A., Jolly, Clemency, Joly, Yann, Jonasson, Jon G., Jones, Corbin D., Jones, David T. W., Jones, Nic, Jones, Steven J. M., Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kaiser, Vera B., Kakavand, Hojabr, Kalimuthu, Sangeetha, Von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, 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., Kellis, Manolis, Kench, James G., Kennedy, Catherine J., Kerssemakers, Jules N. A., Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K., Kim, Youngwook, King, Tari A., Klapper, Wolfram, Klimczak, Leszek J., Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M., Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O., 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, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H., Laird, Peter W., Lakhani, Sunil R., Lalonde, Emilie, Lamaze, Fabien C., Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta M. S., Lawerenz, Chris, Lawlor, Rita T., Lawrence, Michael S., Lazar, Alexander J., Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R., Leongamornlert, Daniel A., Letourneau, Louis, Levine, Douglas A., Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H., Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, W. M., Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V., Lopez-Guillermo, Armando, Lou, Shaoke, 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, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T., Maitra, Arindam, Majumder, Partha P., Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J., Mantovani-Löffler, Luisa, Marchal, Kathleen, 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 W. M., Martin, Sancha, Martin-Subero, Jose I., Martincorena, Iñigo, Martinez-Fundichely, Alexander, Massie, Charlie E., Matthew, Thomas J., Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D., McPherson, John D., McPherson, John R., McPherson, Treasa A., Meier, Samuel R., Meng, Alice, Meng, Shaowu, Merrett, Neil D., Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A., Mihaiescu, George L., Mijalkovic, Sanja, Mijalkovic-Lazic, Ana Mijalkovic, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A., Miller, David K., Miller, Jessica K., 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., Muiños, Ferran, Mularoni, Loris, 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, Nakagawa, Hidewaki, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio C. P., 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, Ott, German, Ouellette, B. F. Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, 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., Petersen, Gloria M., 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, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R., Prinz, Manuel, Pritchard, Antonia L., Prokopec, Stephenie D., Provenzano, Elena, Puente, Xose S., Puig, Sonia, Pulido-Tamayo, Sergio, Pupo, Gulietta M., Purdie, Colin A., Quinn, Michael C., Rabionet, Raquel, Rader, Janet S., Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Raphael, Benjamin J., Rathmell, W. 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A., Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C., Rosenwald, Andreas, Rowe, Edward W., Rozen, Steven G., Rubanova, Yulia, Rubin, Mark A., Rubio-Perez, Carlota, 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, Salichos, Leonidas, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S., Sanchez-Vega, Francisco, Sander, Chris, Sanders, Grant, Sarin, Rajiv, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn P. M., Scardoni, Maria, Scarlett, Christopher J., Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E., Schilhabel, Markus B., Schlomm, Thorsten, Schmidt, Heather K., Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schumacher, Steven E., 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., Shackleton, Mark, Shah, Nimish C., Shahabi, Sagedeh, Shang, Catherine A., Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, 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, Shrestha, Raunak, Shringarpure, Suyash S., Shriver, Craig, Shuai, Shimin, Sidiropoulos, Nikos, Siebert, Reiner, Sieuwerts, Anieta M., Sieverling, Lina, Signoretti, Sabina, Sikora, Katarzyna O., Simbolo, Michele, Simon, Ronald, Simons, Janae V., Simpson, Peter T., Singer, Samuel, Sinnott-Armstrong, Nasa, 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., Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D., Stenhouse, Alasdair, Stilgenbauer, Stephan, Stratton, Michael R., Stretch, Jonathan R., 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, 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 F., 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., Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz H. P., Tsao, Ming, Tsunoda, Tatsuhiko, Tubio, Jose M. C., 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 P. C., Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, Raghavan, K. 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M., Van De Vijver, Marc J., Van’t Veer, L., and Von Mering, Christian
Subjects: 692/4028/67/69, 706/648/697/129/2043, 631/114/2399, article, 45/23, 139, 631/1647/2217/748, 3. Good health
Abstract: Funder: NCI U24CA211006, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.

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

Author: Meyerson, William U., Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Li, Yize, Kelso, Sean, Wendl, Michael C., Simpson, Jared T., Akbani, Rehan, Anur, Pavana, Bailey, Matthew H., Buchanan, Alex, Chiotti, Kami, Covington, Kyle, Creason, Allison, Ding, Li, Ellrott, Kyle, Fan, Yu, Foltz, Steven, Getz, Gad, Hale, Walker, Haussler, David, Hess, Julian M., Hutter, Carolyn M., Kandoth, Cyriac, Kasaian, Katayoon, Kasapi, Melpomeni, Larson, Dave, Leshchiner, Ignaty, Letaw, John, Ma, Singer, McLellan, Michael D., Men, Yifei, Mills, Gordon B., Niu, Beifang, Peto, Myron, Radenbaugh, Amie, Reynolds, Sheila M., Saksena, Gordon, Sofia, Heidi, Stewart, Chip, Struck, Adam J., Stuart, Joshua M., Wang, Wenyi, Weinstein, John N., Wheeler, David A., Wong, Christopher K., Xi, Liu, Ye, Kai, Bieg, Matthias, Boutros, Paul C., Buchhalter, Ivo, Butler, Adam P., Chen, Ken, Chong, Zechen, Drechsel, Oliver, Jonathan Dursi, Lewis, Eils, Roland, Espiritu, Shadrielle M. G., Fulton, Robert S., Gao, Shengjie, Gelpi, Josep L. L., Gerstein, Mark B., Gonzalez, Santiago, Gut, Ivo G., Hach, Faraz, Heinold, Michael C., Hinton, Jonathan, Hu, Taobo, Huang, Vincent, Huang, Yi, Hutter, Barbara, Jones, David R., Jung, Jongsun, Jäger, Natalie, Kim, Hyung-Lae, Kleinheinz, Kortine, Kumar, Sushant, Kumar, Yogesh, Lalansingh, Christopher M., Letunic, Ivica, Livitz, Dimitri, Ma, Eric Z., Maruvka, Yosef E., Mashl, R. Jay, Menzies, Andrew, Milovanovic, Ana, Nielsen, Morten Muhlig, Ossowski, Stephan, Paramasivam, Nagarajan, Pedersen, Jakob Skou, Perry, Marc D., Puiggròs, Montserrat, Raine, Keiran M., Rheinbay, Esther, Royo, Romina, Sahinalp, S. Cenk, Sarrafi, Iman, Schlesner, Matthias, Stebbings, Lucy, Stobbe, Miranda D., Teague, Jon W., Tiao, Grace, Torrents, David, Wala, Jeremiah A., Wang, Jiayin, Waszak, Sebastian M., Weischenfeldt, Joachim, Werner, Johannes, Wu, Zhenggang, Xue, Hong, Yakneen, Sergei, Yamaguchi, Takafumi N., Yellapantula, Venkata D., Yung, Christina K., Zhang, Junjun, Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, 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, Amin, Samirkumar B., Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J., Ang, Yeng, Antonello, Davide, 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 R., Awadalla, Philip, Aymerich, Marta, Bader, Gary D., Baez-Ortega, Adrian, Bailey, Peter J., 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, 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., Biankin, Andrew V., 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 D. L., 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 J. 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M., Van De Vijver, Marc J., Van’t Veer, L., and Von Mering, Christian
Subjects: 692/4028/67/69, 706/648/697/129/2043, 631/114/2399, article, 45/23, 139, 631/1647/2217/748, 3. Good health
Abstract: Funder: NCI U24CA211006, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.

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61 results on '"Liang, Sheng-Ben"'

51. Osteoclast-like Giant Cell Tumor of the Pancreas with Metastases to Gallbladder and Lymph Nodes. A Case Report

52. Tetrasomy 12 in ovarian tumors of thecoma-fibroma group: A fluorescence in situ hybridization analysis using paraffin sections.

53. Expression of T-Cadherin (CDH13, H-Cadherin) in Human Brain and ItsCharacteristics as a Negative Growth Regulator of Epidermal Growth Factor inNeuroblastoma Cells.

54. Overexpression of c-MetProtein in Human Thyroid Tumors Correlated with Lymph Node Metastasis and Clinicopathologic Stage

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

56. Sex differences in oncogenic mutational processes

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

58. Pan-cancer analysis of whole genomes

59. Sex differences in oncogenic mutational processes

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

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

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61 results on '"Liang, Sheng-Ben"'

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