Author: "Yu, Kaixian" - Searchworks@Jio Institute Digital Library Search Results

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117 results on '"Yu, Kaixian"'

1. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression

Author: Cao, Shaolong, Wang, Jennifer R, Ji, Shuangxi, Yang, Peng, Dai, Yaoyi, Guo, Shuai, Montierth, Matthew D, Shen, John Paul, Zhao, Xiao, Chen, Jingxiao, Lee, Jaewon James, Guerrero, Paola A, Spetsieris, Nicholas, Engedal, Nikolai, Taavitsainen, Sinja, Yu, Kaixian, Livingstone, Julie, Bhandari, Vinayak, Hubert, Shawna M, Daw, Najat C, Futreal, P Andrew, Efstathiou, Eleni, Lim, Bora, Viale, Andrea, Zhang, Jianjun, Nykter, Matti, Czerniak, Bogdan A, Brown, Powel H, Swanton, Charles, Msaouel, Pavlos, Maitra, Anirban, Kopetz, Scott, Campbell, Peter, Speed, Terence P, Boutros, Paul C, Zhu, Hongtu, Urbanucci, Alfonso, Demeulemeester, Jonas, Van Loo, Peter, and Wang, Wenyi
Subjects: Human Genome, Genetics, Cancer, 2.1 Biological and endogenous factors, Aetiology, Humans, Neoplasms, Genetic Heterogeneity, Genomics, RNA, Messenger, Disease Progression
Abstract: Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate and validate TmS in 6,590 patient tumors across 15 cancer types, identifying significant inter-tumor variability. Across cancers, high TmS is associated with increased risk of disease progression and death. TmS is influenced by cancer-specific patterns of gene alteration and intra-tumor genetic heterogeneity as well as by pan-cancer trends in metabolic dysregulation. Taken together, our results indicate that measuring cell-type-specific total mRNA expression in tumor cells predicts tumor phenotypes and clinical outcomes.
Published: 2022

2. The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

Author: Marinescu, Razvan V., Oxtoby, Neil P., Young, Alexandra L., Bron, Esther E., Toga, Arthur W., Weiner, Michael W., Barkhof, Frederik, Fox, Nick C., Eshaghi, Arman, Toni, Tina, Salaterski, Marcin, Lunina, Veronika, Ansart, Manon, Durrleman, Stanley, Lu, Pascal, Iddi, Samuel, Li, Dan, Thompson, Wesley K., Donohue, Michael C., Nahon, Aviv, Levy, Yarden, Halbersberg, Dan, Cohen, Mariya, Liao, Huiling, Li, Tengfei, Yu, Kaixian, Zhu, Hongtu, Tamez-Pena, Jose G., Ismail, Aya, Wood, Timothy, Bravo, Hector Corrada, Nguyen, Minh, Sun, Nanbo, Feng, Jiashi, Yeo, B. T. Thomas, Chen, Gang, Qi, Ke, Chen, Shiyang, Qiu, Deqiang, Buciuman, Ionut, Kelner, Alex, Pop, Raluca, Rimocea, Denisa, Ghazi, Mostafa M., Nielsen, Mads, Ourselin, Sebastien, Sorensen, Lauge, Venkatraghavan, Vikram, Liu, Keli, Rabe, Christina, Manser, Paul, Hill, Steven M., Howlett, James, Huang, Zhiyue, Kiddle, Steven, Mukherjee, Sach, Rouanet, Anais, Taschler, Bernd, Tom, Brian D. M., White, Simon R., Faux, Noel, Sedai, Suman, Oriol, Javier de Velasco, Clemente, Edgar E. V., Estrada, Karol, Aksman, Leon, Altmann, Andre, Stonnington, Cynthia M., Wang, Yalin, Wu, Jianfeng, Devadas, Vivek, Fourrier, Clementine, Raket, Lars Lau, Sotiras, Aristeidis, Erus, Guray, Doshi, Jimit, Davatzikos, Christos, Vogel, Jacob, Doyle, Andrew, Tam, Angela, Diaz-Papkovich, Alex, Jammeh, Emmanuel, Koval, Igor, Moore, Paul, Lyons, Terry J., Gallacher, John, Tohka, Jussi, Ciszek, Robert, Jedynak, Bruno, Pandya, Kruti, Bilgel, Murat, Engels, William, Cole, Joseph, Golland, Polina, Klein, Stefan, and Alexander, Daniel C.
Subjects: Quantitative Biology - Populations and Evolution, Statistics - Applications
Abstract: We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials., Comment: Presents final results of the TADPOLE competition. 60 pages, 7 tables, 14 figures
Published: 2020

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

Author: Dentro, Stefan C, Leshchiner, Ignaty, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G, Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Vázquez-García, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G, Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steven E, Fan, Yu, Fittall, Matthew, Drews, Ruben M, Yao, Xiaotong, Watkins, Thomas BK, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J, McGranahan, Nicholas, Swanton, Charles, Getz, Gad, Boutros, Paul C, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T, Wang, Wenyi, Morris, Quaid D, Wedge, David C, Van Loo, Peter, and PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium
Subjects: PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium, branching evolution, cancer driver genes, cancer evolution, intra-tumor heterogeneity, pan-cancer genomics, subclonal reconstruction, tumor phylogeny, whole-genome sequencing, Genetics, Cancer, Human Genome, 2.1 Biological and endogenous factors, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract: Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.
Published: 2021

4. The evolutionary history of 2,658 cancers

Author: Gerstung, Moritz, Jolly, Clemency, Leshchiner, Ignaty, Dentro, Stefan C, Gonzalez, Santiago, Rosebrock, Daniel, Mitchell, Thomas J, Rubanova, Yulia, Anur, Pavana, Yu, Kaixian, Tarabichi, Maxime, Deshwar, Amit, Wintersinger, Jeff, Kleinheinz, Kortine, Vázquez-García, Ignacio, Haase, Kerstin, Jerman, Lara, Sengupta, Subhajit, Macintyre, Geoff, Malikic, Salem, Donmez, Nilgun, Livitz, Dimitri G, Cmero, Marek, Demeulemeester, Jonas, Schumacher, Steven, Fan, Yu, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Boutros, Paul C, Bowtell, David D, Zhu, Hongtu, Getz, Gad, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S Cenk, Ji, Yuan, Peifer, Martin, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Wang, Wenyi, Morris, Quaid D, Spellman, Paul T, Wedge, David C, and Van Loo, Peter
Subjects: Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Rare Diseases, Brain Cancer, Brain Disorders, Human Genome, Cancer, 2.1 Biological and endogenous factors, Aetiology, DNA Repair, Evolution, Molecular, Gene Dosage, Genes, Tumor Suppressor, Genetic Variation, Genome, Human, Humans, Mutagenesis, Insertional, Neoplasms, PCAWG Evolution & Heterogeneity Working Group, PCAWG Consortium, General Science & Technology
Abstract: Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.
Published: 2020

5. Development of a one-day driving cycle for electric ride-hailing vehicles

Author: Qin, Xiaoran, Yu, Kaixian, Li, Hanqian, Dai, Feng, Liu, Haijiang, Yang, Hai, Ye, Jieping, and Zhu, Hongtu
Published: 2020
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6. Author Correction: The evolutionary history of 2,658 cancers

Author: Gerstung, Moritz, Jolly, Clemency, Leshchiner, Ignaty, Dentro, Stefan C., Gonzalez, Santiago, Rosebrock, Daniel, Mitchell, Thomas J., Rubanova, Yulia, Anur, Pavana, Yu, Kaixian, Tarabichi, Maxime, Deshwar, Amit, Wintersinger, Jeff, Kleinheinz, Kortine, Vázquez-García, Ignacio, Haase, Kerstin, Jerman, Lara, Sengupta, Subhajit, Macintyre, Geoff, Malikic, Salem, Donmez, Nilgun, Livitz, Dimitri G., Cmero, Marek, Demeulemeester, Jonas, Schumacher, Steven, Fan, Yu, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Boutros, Paul C., Bowtell, David D., Zhu, Hongtu, Getz, Gad, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., and Van Loo, Peter
Published: 2023
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7. BioKG: a comprehensive, high-quality biomedical knowledge graph for AI-powered, data-driven biomedical research

Author: Zhang, Yuan, primary, Pan, Feng, additional, Sui, Xin, additional, Yu, Kaixian, additional, Li, Keqiao, additional, Tian, Shubo, additional, Erdengasileng, Arslan, additional, Han, Qing, additional, Wang, Wanjing, additional, Wang, Jianan, additional, Wang, Jian, additional, Sun, Donghu, additional, Chung, Henry, additional, Zhou, Jun, additional, Zhou, Eric, additional, Lee, Ben, additional, Qiu, Xing, additional, Zhao, Tingting, additional, and Zhang, Jinfeng, additional
Published: 2023
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8. Radiomic analysis in prediction of Human Papilloma Virus status

Author: Yu, Kaixian, Zhang, Youyi, Yu, Yang, Huang, Chao, Liu, Rongjie, Li, Tengfei, Yang, Liuqing, Morris, Jeffrey S., Baladandayuthapani, Veerabhadran, and Zhu, Hongtu
Published: 2017
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9. Abstract 4272: Pan-cancer analysis of intra-tumor heterogeneity in 9,116 cancers using a novel regularized likelihood model

Author: Jiang, Yujie, primary, Yu, Kaixian, additional, Montierth, Matthew D., additional, Ji, Shuangxi, additional, Shin, Seung Jun, additional, Guo, Shuai, additional, Cao, Shaolong, additional, Tang, Yuxin, additional, Kopetz, Scott, additional, Msaouel, Pavlos, additional, Wang, Jennifer R., additional, Kimmel, Marek, additional, Van Loo, Peter, additional, Zhu, Hongtu, additional, and Wang, Wenyi, additional
Published: 2023
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10. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Author: Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, 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 MG, 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 LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, 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, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose MG, 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 TW, Jones, Nic, Jones, Steven JM, 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, Karlić, Rosa, 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 NA, 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, 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Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Yuan, Yuen, Denis, Yung, Christina K, 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 HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
Published: 2023
Full Text: View/download PDF

11. Combined burden and functional impact tests for cancer driver discovery using DriverPower

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Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reimand, Jüri, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, 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Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
Published: 2023
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12. Integrative pathway enrichment analysis of multivariate omics data

Author: Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pich, Oriol, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sabarinathan, Radhakrishnan, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Reimand, Jüri, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, 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Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, 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, Junjun, Zhang, Xiuqing, Zhang, Zemin, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, and Veer, L van’t
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
Published: 2023
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13. Pathway and network analysis of more than 2500 whole cancer genomes

Author: Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kellis, Manolis, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pons, Tirso, Reyes-Salazar, Iker, Rheinbay, Esther, Rubio-Perez, Carlota, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, 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Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
Published: 2023
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14. Divergent mutational processes distinguish hypoxic and normoxic tumours

Author: Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, 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, 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, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, 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, 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, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, 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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, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, 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, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
Published: 2023
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15. Genomic footprints of activated telomere maintenance mechanisms in cancer

Author: Sieverling, Lina, Hong, Chen, Koser, Sandra D, Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M, Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J, Eils, Roland, Schlesner, Matthias, Akdemir, Kadir C, Alvarez, Eva G, Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C, Bowtell, David DL, Brors, Benedikt, Burns, Kathleen H, Campbell, Peter J, Chan, Kin, Chen, Ken, Dueso-Barroso, Ana, Dunford, Andrew J, Edwards, Paul A, Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W, Gerstein, Mark, Gordenin, Dmitry A, Haan, David, Haber, James E, Hess, Julian M, Imielinski, Marcin, Jones, David TW, Ju, Young Seok, Kazanov, Marat D, Klimczak, Leszek J, Koh, Youngil, Korbel, Jan O, Kumar, Kiran, Lee, Eunjung Alice, Lee, Jake June-Koo, Li, Yilong, Lynch, Andy G, Macintyre, Geoff, Markowetz, Florian, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Meyerson, Matthew, Miyano, Satoru, Nakagawa, Hidewaki, Navarro, Fabio CP, Ossowski, Stephan, Pearson, John V, Puiggròs, Montserrat, Rippe, Karsten, Roberts, Nicola D, Roberts, Steven A, Rodriguez-Martin, Bernardo, Schumacher, Steven E, Scully, Ralph, Shackleton, Mark, Sidiropoulos, Nikos, Stewart, Chip, Torrents, David, MC Tubio, Jose, Villasante, Izar, Waddell, Nicola, Wala, Jeremiah A, Weischenfeldt, Joachim, Yang, Lixing, Yao, Xiaotong, Yoon, Sung-Soo, Zamora, Jorge, Zhang, Cheng-Zhong, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, 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, 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Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, 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 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Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, 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, William, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, 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Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pedamallu, Chandra Sekhar, Pedersen, Jakob Skou, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, 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, Raine, Keiran M, 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, Reynolds, Sheila M, Rheinbay, Esther, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Roach, Jeffrey, Roberts, Lewis R, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rubin, Mark A, Rubio-Perez, Carlota, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Sahinalp, S Cenk, Saini, Natalie, Saito-Adachi, Mihoko, Saksena, Gordon, 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, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, 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, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, 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, 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Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
Published: 2023
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16. Automatic extraction of protein-protein interactions using grammatical relationship graph

Author: Yu, Kaixian, Lung, Pei-Yau, Zhao, Tingting, Zhao, Peixiang, Tseng, Yan-Yuan, and Zhang, Jinfeng
Published: 2018
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17. Biological Network Inference With GRASP: A Bayesian Network Structure Learning Method Using Adaptive Sequential Monte Carlo

Author: Yu, Kaixian, primary, Cui, Zihan, additional, Sui, Xin, additional, Qiu, Xing, additional, and Zhang, Jinfeng, additional
Published: 2021
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18. Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer

Author: Cao, Shaolong, primary, Wang, Jennifer, additional, Ji, Shuangxi, additional, Yang, Peng, additional, Montierth, Matthew, additional, Guo, Shuai, additional, Shen, John Paul, additional, Zhao, Xiao, additional, Chen, Jingxiao, additional, Lee, Jaewon, additional, Guerrero, Paola, additional, Spetsieris, Nicholas, additional, Engedal, Nikolai, additional, Taavitsainen, Sinja, additional, Yu, Kaixian, additional, Livingstone, Julie, additional, Bhandari, Vinayak, additional, Hubert, Shawna, additional, Daw, Najat, additional, Futreal, Andrew, additional, Efstathiou, Eleni, additional, Lim, Bora, additional, Viale, Andrea, additional, Zhang, Jianjun, additional, Nykter, Matti, additional, Czerniak, Bogdan, additional, Msaouel, Pavlos, additional, Maitra, Anirban, additional, Kopetz, Scott, additional, Campbell, Peter, additional, Speed, Terence, additional, Boutros, Paul, additional, Zhu, Hongtu, additional, Urbanucci, Alfonso, additional, Demeulemeester, Jonas, additional, Loo, Peter Van, additional, and Wang, Wenyi, additional
Published: 2021
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19. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Author: Dentro, Stefan C., Leshchiner, Ignaty, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Vazquez-Garcia, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G., Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steven E., Fan, Yu, Fittall, Matthew, Drews, Ruben M., Yao, Xiaotong, Watkins, Thomas B. K., Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J., McGranahan, Nicholas, Swanton, Charles, Getz, Gad, Boutros, Paul C., Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T., Wang, Wenyi, Morris, Quaid D., Wedge, David C., Van Loo, Peter, Dentro, Stefan C., Leshchiner, Ignaty, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Vazquez-Garcia, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G., Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steven E., Fan, Yu, Fittall, Matthew, Drews, Ruben M., Yao, Xiaotong, Watkins, Thomas B. K., Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J., McGranahan, Nicholas, Swanton, Charles, Getz, Gad, Boutros, Paul C., Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T., Wang, Wenyi, Morris, Quaid D., Wedge, David C., and Van Loo, Peter
Abstract: Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1 %) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones, We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.
Published: 2021

20. The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

Author: Marinescu, Razvan V., Oxtoby, Neil P., Young, Alexandra L., Bron, Esther E., Toga, Arthur W., Weiner, Michael W., Barkhof, Frederik, Fox, Nick C., Eshaghi, Arman, Toni, Tina, Salaterski, Marcin, Lunina, Veronika, Ansart, Manon, Durrleman, Stanley, Lu, Pascal, Iddi, Samuel, Li, Dan, Thompson, Wesley K., Donohue, Michael C., Nahon, Aviv, Levy, Yarden, Halbersberg, Dan, Cohen, Mariya, Liao, Huiling, Li, Tengfei, Yu, Kaixian, Zhu, Hongtu, Tamez-Peña, José G., Ismail, Aya, Wood, Timothy, Bravo, Hector Corrada, Nguyen, Minh, Sun, Nanbo, Feng, Jiashi, Yeo, B.T. Thomas, Chen, Gang, Qi, Ke, Chen, Shiyang, Qiu, Deqiang, Buciuman, Ionut, Kelner, Alex, Pop, Raluca, Rimocea, Denisa, Ghazi, Mostafa M., Nielsen, Mads, Ourselin, Sebastien, Sørensen, Lauge, Venkatraghavan, Vikram, Liu, Keli, Rabe, Christina, Manser, Paul, Hill, Steven M., Howlett, James, Huang, Zhiyue, Kiddle, Steven, Mukherjee, Sach, Rouanet, Anaïs, Taschler, Bernd, Tom, Brian D. M., White, Simon R., Faux, Noel, Sedai, Suman, de Velasco Oriol, Javier, Clemente, Edgar E. V., Estrada, Karol, Aksman, Leon, Altmann, Andre, Stonnington, Cynthia M., Wang, Yalin, Wu, Jianfeng, Devadas, Vivek, Fourrier, Clementine, Raket, Lars Lau, Sotiras, Aristeidis, Erus, Guray, Doshi, Jimit, Davatzikos, Christos, Vogel, Jacob, Doyle, Andrew, Tam, Angela, Diaz-Papkovich, Alex, Jammeh, Emmanuel, Koval, Igor, Moore, Paul, Lyons, Terry J., Gallacher, John, Tohka, Jussi, Ciszek, Robert, Jedynak, Bruno, Pandya, Kruti, Bilgel, Murat, Engels, William, Cole, Joseph, Golland, Polina, Klein, Stefan, Alexander, Daniel C., Marinescu, Razvan V., Oxtoby, Neil P., Young, Alexandra L., Bron, Esther E., Toga, Arthur W., Weiner, Michael W., Barkhof, Frederik, Fox, Nick C., Eshaghi, Arman, Toni, Tina, Salaterski, Marcin, Lunina, Veronika, Ansart, Manon, Durrleman, Stanley, Lu, Pascal, Iddi, Samuel, Li, Dan, Thompson, Wesley K., Donohue, Michael C., Nahon, Aviv, Levy, Yarden, Halbersberg, Dan, Cohen, Mariya, Liao, Huiling, Li, Tengfei, Yu, Kaixian, Zhu, Hongtu, Tamez-Peña, José G., Ismail, Aya, Wood, Timothy, Bravo, Hector Corrada, Nguyen, Minh, Sun, Nanbo, Feng, Jiashi, Yeo, B.T. Thomas, Chen, Gang, Qi, Ke, Chen, Shiyang, Qiu, Deqiang, Buciuman, Ionut, Kelner, Alex, Pop, Raluca, Rimocea, Denisa, Ghazi, Mostafa M., Nielsen, Mads, Ourselin, Sebastien, Sørensen, Lauge, Venkatraghavan, Vikram, Liu, Keli, Rabe, Christina, Manser, Paul, Hill, Steven M., Howlett, James, Huang, Zhiyue, Kiddle, Steven, Mukherjee, Sach, Rouanet, Anaïs, Taschler, Bernd, Tom, Brian D. M., White, Simon R., Faux, Noel, Sedai, Suman, de Velasco Oriol, Javier, Clemente, Edgar E. V., Estrada, Karol, Aksman, Leon, Altmann, Andre, Stonnington, Cynthia M., Wang, Yalin, Wu, Jianfeng, Devadas, Vivek, Fourrier, Clementine, Raket, Lars Lau, Sotiras, Aristeidis, Erus, Guray, Doshi, Jimit, Davatzikos, Christos, Vogel, Jacob, Doyle, Andrew, Tam, Angela, Diaz-Papkovich, Alex, Jammeh, Emmanuel, Koval, Igor, Moore, Paul, Lyons, Terry J., Gallacher, John, Tohka, Jussi, Ciszek, Robert, Jedynak, Bruno, Pandya, Kruti, Bilgel, Murat, Engels, William, Cole, Joseph, Golland, Polina, Klein, Stefan, and Alexander, Daniel C.
Abstract: Accurate prediction of progression in subjects at risk of Alzheimer's disease is crucial for enrolling the right subjects in clinical trials. However, a prospective comparison of state-of-the-art algorithms for predicting disease onset and progression is currently lacking. We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of patient-specific biomarkers. On a limited, cross-sectional subset of the data emulating clinical trials, performance of the best algorithms at predicting clinical diagnosis decreased only slightly (2 pe
Published: 2021

21. CliP: subclonal architecture reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model

Author: Jiang, Yujie, primary, Yu, Kaixian, additional, Ji, Shuangxi, additional, Shin, Seung Jun, additional, Cao, Shaolong, additional, Montierth, Matthew D, additional, Huang, Licai, additional, Kopetz, Scott, additional, Msaouel, Pavlos, additional, Wang, Jennifer Rui, additional, Kimmel, Marek, additional, Zhu, Hongtu, additional, and Wang, Wenyi, additional
Published: 2021
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22. Inferring structural variant cancer cell fraction

Author: Cmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Corcoran, Niall M., Papenfuss, Tony, Hovens, Christopher M., Markowetz, Florian, Macintyre, Geoff, Adams, David J., Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Campbell, Peter J., Cao, Shaolong, Christie, Elizabeth L., Cun, Yupeng, Dawson, Kevin J., Demeulemeester, Jonas, Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew W., Garsed, Dale W., Gerstung, Moritz, Getz, Gad, Gonzalez, Santiago, Ha, Gavin, Haase, Kerstin, Imielinski, Marcin, Jerman, Lara, Ji, Yuan, Jolly, Clemency, Kleinheinz, Kortine, Lee, Juhee, Lee-Six, Henry, Leshchiner, Ignaty, Livitz, Dimitri, Malikic, Salem, Martincorena, Iñigo, Mitchell, Thomas J., Morris, Quaid D., Mustonen, Ville, Oesper, Layla, Peifer, Martin, Peto, Myron, Raphael, Benjamin J., Rosebrock, Daniel, Rubanova, Yulia, Sahinalp, S. Cenk, Salcedo, Adriana, Schlesner, Matthias, Schumacher, Steven E., Sengupta, Subhajit, Shi, Ruian, Shin, Seung Jun, Spellman, Paul T., Spiro, Oliver, Stein, Lincoln D., Tarabichi, Maxime, Van Loo, Peter, Vembu, Shankar, Vázquez-García, Ignacio, Wang, Wenyi, Wedge, David C., Wheeler, David A., Wintersinger, Jeffrey A., Yang, Tsun-Po, Yao, Xiaotong, Yu, Kaixian, Zhu, Hongtu, Cmero, Marek [0000-0001-7783-5530], Yuan, Ke [0000-0002-2318-1460], Ong, Cheng Soon [0000-0002-2302-9733], Papenfuss, Tony [0000-0002-1102-8506], Markowetz, Florian [0000-0002-2784-5308], Macintyre, Geoff [0000-0003-3906-467X], Apollo - University of Cambridge Repository, Dentro, SC, Wedge, DC, Yang, T-P, Organismal and Evolutionary Biology Research Programme, Institute of Biotechnology, Bioinformatics, and Department of Computer Science
Subjects: Male, 0301 basic medicine, Medizin, General Physics and Astronomy, Somatic evolution in cancer, Genome, 0302 clinical medicine, Gene Frequency, Neoplasms, 129, lcsh:Science, Cancer, Ovarian Neoplasms, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Multidisciplinary, Manchester Cancer Research Centre, Prostatic Neoplasms/genetics, Liver Neoplasms, 1184 Genetics, developmental biology, physiology, Neoplasms/genetics, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Ovarian Cancer, 3. Good health, 030220 oncology & carcinogenesis, 1181 Ecology, evolutionary biology, 139, Female, Algorithms, Human, 631/67, DNA Copy Number Variations, Science, In silico, Computational biology, Biology, Sensitivity and Specificity, Article, General Biochemistry, Genetics and Molecular Biology, Ovarian Neoplasms/genetics, 03 medical and health sciences, Rare Diseases, Machine learning, Genetics, PCAWG Evolution and Heterogeneity Working Group, medicine, Humans, Computer Simulation, ddc:610, Liver Neoplasms/genetics, Allele frequency, Whole genome sequencing, 45, Whole Genome Sequencing, Genome, Human, ResearchInstitutes_Networks_Beacons/mcrc, Human Genome, Breakpoint, Computational Biology, Prostatic Neoplasms, PCAWG Consortium, General Chemistry, Computational Biology/methods, 631/114/1305, 113 Computer and information sciences, Pancreatic Neoplasms/genetics, medicine.disease, Computational biology and bioinformatics, Pancreatic Neoplasms, 030104 developmental biology, lcsh:Q, Human genome, 631/114, 119, Digestive Diseases
Abstract: We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone’s performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity., The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.
Published: 2020

23. 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., Maria Heredia-Genestar, Jose, 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, Weiner, Amaro Taylor, Fittall, Matthew W., Demeulemeester, Jonas, Tarabichi, Maxime, Roberts, Nicola D., Van Loo, Peter, Cortes-Ciriano, Isidro, Urban, Lara, Park, Peter, Pitkaenen, 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., Ratsch, 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, Molnar-Gabor, Fruzsina, Phillips, Mark, Thorogood, Adrian, Townend, David, Goldman, Mary, Fonseca, Nuno A., Xiang, Qian, Craft, Brian, Pineiro-Yanez, Elena, Munoz, Alfonso, Petryszak, Robert, Fullgrabe, 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, Jaeger, 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, Puiggros, 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, Juri, Dhingra, Priyanka, Favero, Francesco, Dentro, Stefan, Wintersinger, Jeff, Rudneva, Vasilisa, Park, Ji Wan, Hong, Eun Pyo, Heo, Seong Gu, Kahles, Andre, Soulette, Cameron M., Shiraishi, Yuichi, Liu, Fenglin, He, Yao, Demircioglu, Deniz, Davidson, Natalie R., Greger, Liliana, Li, Siliang, Liu, Dongbing, Stark, Stefan G., Zhang, Fan, Amin, Samirkumar B., Bailey, Peter, Chateigner, Aurelien, 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-Hammarstrom, 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, Goke, Jonathan, Zhang, Zemin, Brooks, Angela N., Martincorena, Inigo, Rubio-Perez, Carlota, Juul, Malene, Schumacher, Steven, Shapira, Ofer, Tamborero, David, Mularoni, Loris, Hornshoj, Henrik, Deu-Pons, Jordi, Muinos, 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., Huebschmann, Daniel, Ivkovic, Sinisa, Jeon, Seung-Hyup, Jiao, Wei, Kabbe, Rolf, 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-Remi, 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, Soren, Fita, Joana Carlevaro, 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, Lanzos, Andres, Larsson, Erik, Lee, Donghoon, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Fundichely, Alexander Martinez, 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., Uuskula-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., Vazquez-Garcia, 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., Karlic, Rosa, Kato, Mamoru, Kubler, 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, Jorg, 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, Borresen-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, Oystein, 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., Langerod, Anita, Larsimont, Denis, Lee, Hee Jin, Lee, Jeong-Yeon, Lee, Ming Ta Michael, Lingjaerde, Ole Christian, MacGrogan, Gaetan, Martens, John W. M., O'Meara, Sarah, Pauporte, Iris, Pinder, Sarah, Pivot, Xavier, Provenzano, Elena, Purdie, Colin A., Ramakrishna, Manasa, Ramakrishnan, Kamna, Reis-Filho, Jorge, Richardson, Andrea L., Ringner, Markus, Rodriguez, Javier Bartolome, Rodriguez-Gonzalez, F. German, Romieu, Gilles, Salgado, Roberto, Sauer, Torill, Shepherd, Rebecca, Sieuwerts, Anieta M., Simpson, Peter T., Smid, Marcel, Sotiriou, Christos, Span, Paul N., Stefansson, Olafur 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, Kueppers, Ralf, Lenze, Dido, Loeffler, Markus, Lopez, Cristina, Mantovani-Loeffler, Luisa, Moeller, 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., Truemper, 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-Joerg, Wolf, Stephan, Yaspo, Marie-Laure, Assenov, Yassen, Gerhauser, Clarissa, Minner, Sarah, Schlomm, Thorsten, Simon, Ronald, Sauter, Guido, Sueltmann, Holger, Biswas, Nidhan K., Maitra, Arindam, Majumder, Partha P., Sarin, Rajiv, Barbi, Stefano, Bonizzato, Giada, Cantu, 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, Lopez-Otin, 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, Tavare, 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, Donahue, Christine A. Iacobuzio, 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., McCune, Karen Smith, 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, Zhang, Jiashan, 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., Maria Heredia-Genestar, Jose, 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, Weiner, Amaro Taylor, Fittall, Matthew W., Demeulemeester, Jonas, Tarabichi, Maxime, Roberts, Nicola D., Van Loo, Peter, Cortes-Ciriano, Isidro, Urban, Lara, Park, Peter, Pitkaenen, 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., Ratsch, 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, Molnar-Gabor, Fruzsina, Phillips, Mark, Thorogood, Adrian, Townend, David, Goldman, Mary, Fonseca, Nuno A., Xiang, Qian, Craft, Brian, Pineiro-Yanez, Elena, Munoz, Alfonso, Petryszak, Robert, Fullgrabe, 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, Jaeger, 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, Puiggros, 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, Juri, Dhingra, Priyanka, Favero, Francesco, Dentro, Stefan, Wintersinger, Jeff, Rudneva, Vasilisa, Park, Ji Wan, Hong, Eun Pyo, Heo, Seong Gu, Kahles, Andre, Soulette, Cameron M., Shiraishi, Yuichi, Liu, Fenglin, He, Yao, Demircioglu, Deniz, Davidson, Natalie R., Greger, Liliana, Li, Siliang, Liu, Dongbing, Stark, Stefan G., Zhang, Fan, Amin, Samirkumar B., Bailey, Peter, Chateigner, Aurelien, 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-Hammarstrom, 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, Goke, Jonathan, Zhang, Zemin, Brooks, Angela N., Martincorena, Inigo, Rubio-Perez, Carlota, Juul, Malene, Schumacher, Steven, Shapira, Ofer, Tamborero, David, Mularoni, Loris, Hornshoj, Henrik, Deu-Pons, Jordi, Muinos, 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., Huebschmann, Daniel, Ivkovic, Sinisa, Jeon, Seung-Hyup, Jiao, Wei, Kabbe, Rolf, 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-Remi, Whalley, Justin P., Niu, Beifang, Espiritu, Shadrielle M. 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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, Kueppers, Ralf, Lenze, Dido, Loeffler, Markus, Lopez, Cristina, Mantovani-Loeffler, Luisa, Moeller, 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., Truemper, Lorenz H. 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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 scale(1-3). 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 promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).
Published: 2020

24. A community effort to create standards for evaluating tumor subclonal reconstruction

Author: Salcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G., Deshwar, Amit G., David, Matei, Wilson, Nathan M., Dentro, Stefan, Wintersinger, Jeff A., Liu, Lydia Y., Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M., Buchanan, Alex, Lalansingh, Christopher M., P'ng, Christine, Anghel, Catalina V., Umar, Imaad, Lo, Bryan, Zou, William, Simpson, Jared T., Stuart, Joshua M., Anastassiou, Dimitris, Guan, Yuanfang, Ewing, Adam D., Ellrott, Kyle, Wedge, David C., Morris, Quaid, Van Loo, Peter, Boutros, Paul C., Jha, Alokkumar, Huang, Tanxiao, Yang, Tsun-Po, Peifer, Martin, Sahinalp, Cenk, Malikic, Salem, Vazquez-Garcia, Ignacio, Mustonen, Ville, Yang, Hsih-Te, Lee, Ken-Ray, Ji, Yuan, Sengupta, Subhajit, Rudewicz, Justine, Nikolski, Macha, Schaeverbeke, Quentin, Yuan, Ke, Markowetz, Florian, Macintyre, Geoff, Cmero, Marek, Chaudhary, Belal, Leshchiner, Ignaty, Livitz, Dimitri, Getz, Gad, Loher, Phillipe, Yu, Kaixian, Wang, Wenyi, Zhu, Hongtu, Salcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G., Deshwar, Amit G., David, Matei, Wilson, Nathan M., Dentro, Stefan, Wintersinger, Jeff A., Liu, Lydia Y., Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M., Buchanan, Alex, Lalansingh, Christopher M., P'ng, Christine, Anghel, Catalina V., Umar, Imaad, Lo, Bryan, Zou, William, Simpson, Jared T., Stuart, Joshua M., Anastassiou, Dimitris, Guan, Yuanfang, Ewing, Adam D., Ellrott, Kyle, Wedge, David C., Morris, Quaid, Van Loo, Peter, Boutros, Paul C., Jha, Alokkumar, Huang, Tanxiao, Yang, Tsun-Po, Peifer, Martin, Sahinalp, Cenk, Malikic, Salem, Vazquez-Garcia, Ignacio, Mustonen, Ville, Yang, Hsih-Te, Lee, Ken-Ray, Ji, Yuan, Sengupta, Subhajit, Rudewicz, Justine, Nikolski, Macha, Schaeverbeke, Quentin, Yuan, Ke, Markowetz, Florian, Macintyre, Geoff, Cmero, Marek, Chaudhary, Belal, Leshchiner, Ignaty, Livitz, Dimitri, Getz, Gad, Loher, Phillipe, Yu, Kaixian, Wang, Wenyi, and Zhu, Hongtu
Abstract: Methods for reconstructing tumor evolution are benchmarked in the DREAM Somatic Mutation Calling Tumour Heterogeneity Challenge. Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.
Published: 2020

25. Abstract PO-029: CliP: A model-based method for subclonal architecture reconstruction using regularized maximum likelihood estimation

Author: Jiang, Yujie, primary, Yu, Kaixian, additional, Zhu, Hongtu, additional, and Wang, Wenyi, additional
Published: 2020
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26. Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer

Author: Cao, Shaolong, primary, Wang, Jennifer R., additional, Ji, Shuangxi, additional, Yang, Peng, additional, Montierth, Matthew D., additional, Guo, Shuai, additional, Shen, John Paul, additional, Zhao, Xiao, additional, Chen, Jingxiao, additional, Lee, Jaewon James, additional, Guerrero, Paola A, additional, Spetsieris, Nicholas, additional, Engedal, Nikolai, additional, Taavitsainen, Sinja, additional, Yu, Kaixian, additional, Livingstone, Julie, additional, Bhandari, Vinayak, additional, Hubert, Shawna M, additional, Daw, Najat C., additional, Futreal, P. Andrew, additional, Efstathiou, Eleni, additional, Lim, Bora, additional, Viale, Andrea, additional, Zhang, Jianjun, additional, Nykter, Matti, additional, Czerniak, Bogdan A, additional, Msaouel, Pavlos, additional, Maitra, Anirban, additional, Kopetz, Scott, additional, Campbell, Peter, additional, Speed, Terence P., additional, Boutros, Paul C., additional, Zhu, Hongtu, additional, Urbanucci, Alfonso, additional, Demeulemeester, Jonas, additional, Van Loo, Peter, additional, and Wang, Wenyi, additional
Published: 2020
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27. Abstract 829: Global tumor transcriptional activity reveals aggressiveness across multiple cancers

Author: Cao, Shaolong, primary, Wang, Jennifer R., additional, Demeulemeester, Jonas, additional, Chen, Jingxiao, additional, Yu, Kaixian, additional, Yang, Peng, additional, Lim, Bora, additional, Urbanucci, Alfonso, additional, Campbell, Peter, additional, Zhu, Hongtu, additional, Van loo, Peter, additional, and Wang, Wenyi, additional
Published: 2020
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28. Characterizing Genetic Intra-Tumor Heterogeneity Across 2,658 Human Cancer Genomes

Author: Dentro, Stefan C., primary, Leshchiner, Ignaty, additional, Haase, Kerstin, additional, Tarabichi, Maxime, additional, Wintersinger, Jeff, additional, Deshwar, Amit G., additional, Yu, Kaixian, additional, Rubanova, Yulia, additional, Macintyre, Geoff, additional, Demeulemeester, Jonas, additional, Vázquez-García, Ignacio, additional, Kleinheinz, Kortine, additional, Livitz, Dimitri G., additional, Malikic, Salem, additional, Donmez, Nilgun, additional, Sengupta, Subhajit, additional, Anur, Pavana, additional, Jolly, Clemency, additional, Cmero, Marek, additional, Rosebrock, Daniel, additional, Schumacher, Steven, additional, Fan, Yu, additional, Fittall, Matthew, additional, Drews, Ruben M., additional, Yao, Xiaotong, additional, Lee, Juhee, additional, Schlesner, Matthias, additional, Zhu, Hongtu, additional, Adams, David J., additional, Getz, Gad, additional, Boutros, Paul C., additional, Imielinski, Marcin, additional, Beroukhim, Rameen, additional, Sahinalp, S. Cenk, additional, Ji, Yuan, additional, Peifer, Martin, additional, Martincorena, Inigo, additional, Markowetz, Florian, additional, Mustonen, Ville, additional, Yuan, Ke, additional, Gerstung, Moritz, additional, Spellman, Paul T., additional, Wang, Wenyi, additional, Morris, Quaid, additional, Wedge, David C., additional, Van Loo, Peter, additional, Group, PCAWG Evolution and Heterogeneity W, additional, and Consortium, PCAWG, additional
Published: 2020
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29. Assessment of network module identification across complex diseases

Author: Choobdar, Sarvenaz, Ahsen, Mehmet E., Natoli, Ted, Lysenko, Artem, Ma, Tianle, Mall, Raghvendra, Marbach, Daniel, Mattia, Tomasoni, Medvedovic, Mario, Menche, Jörg, Mercer, Johnathan, Micarelli, Elisa, Monaco, Alfonso, Narayan, Rajiv, Müller, Felix, Narykov, Oleksandr, Norman, Thea, Park, Sungjoon, Perfetto, Livia, Perrin, Dimitri, Pirrò, Stefano, Przytycka, Teresa M., DREAM Module Identification Challenge Consortium, Qian, Xiaoning, Raman, Karthik, Ramazzotti, Daniele, Ramsahai, Emilie, Ravindran, Balaraman, Rennert, Philip, Sáez Rodríguez, Julio, Schärfe, Charlotta, Sharan, Roded, Shi, Ning, Subramanian, Aravind, Shin, Wonho, Shu, Hai, Sinha, Himanshu, Slonim, Donna K., Spinelli, Lionel, Srinivasan, Suhas, Suver, Christine, Szklarczyk, Damian, Tangaro, Sabina, Zhang, Jitao D., Thiagarajan, Suresh, Tichit, Laurent, Tiede, Thorsten, Tripathi, Beethika, Tsherniak, Aviad, Tsunoda, Tatsuhiko, Türei, Dénes, Ullah, Ehsan, Vahedi, Golnaz, Valdeolivas, Alberto, Stolovitzky, Gustavo, Vivek, Jayaswal, von Mering, Christian, Waagmeester, Andra, Wang, Bo, Wang, Yijie, Weir, Barbara A., White, Shana, Winkler, Sebastian, Xu, Ke, Xu, Taosheng, Kutalik, Zoltán, Yan, Chunhua, Yang, Liuqing, Yu, Kaixian, Yu, Xiangtian, Zaffaroni, Gaia, Zaslavskiy, Mikhail, Zeng, Tao, Zhang, Lu, Zhang, Weijia, Lage, Kasper, Zhang, Lixia, Zhang, Xinyu, Zhang, Junpeng, Zhou, Xin, Zhou, Jiarui, Zhu, Hongtu, Zhu, Junjie, Zuccon, Guido, Crawford, Jake, Cowen, Lenore J., Bergmann, Sven, Aicheler, Fabian, Amoroso, Nicola, Arenas, Alex, Azhagesan, Karthik, Baker, Aaron, Banf, Michael, Batzoglou, Serafim, Tomasoni, Mattia, Baudot, Anaïs, Bellotti, Roberto, Boroevich, Keith A., Brun, Christine, Cai, Stanley, Caldera, Michael, Calderone, Alberto, Cesareni, Gianni, Chen, Weiqi, Fang, Tao, Chichester, Christine, Cowen, Lenore, Cui, Hongzhu, Dao, Phuong, De Domenico, Manlio, Dhroso, Andi, Didier, Gilles, Divine, Mathew, Lamparter, David, Del Sol, Antonio, Feng, Xuyang, Flores-Canales, Jose C., Fortunato, Santo, Gitter, Anthony, Gorska, Anna, Guan, Yuanfang, Guénoche, Alain, Gómez, Sergio, Lin, Junyuan, Hamza, Hatem, Hartmann, András, He, Shan, Heijs, Anton, Heinrich, Julian, Hescott, Benjamin, Hu, Xiaozhe, Hu, Ying, Huang, Xiaoqing, Hughitt, V. Keith, Jeon, Minji, Jeub, Lucas, Johnson, Nathan T., Joo, Keehyoung, Joung, InSuk, Jung, Sascha, Kalko, Susana G., Kamola, Piotr J., Kang, Jaewoo, Kaveelerdpotjana, Benjapun, Kim, Minjun, Kim, Yoo-Ah, Kohlbacher, Oliver, Korkin, Dmitry, Krzysztof, Kiryluk, Kunji, Khalid, Kutalik, Zoltàn, Lang-Brown, Sean, Le, Thuc Duy, Lee, Jooyoung, Lee, Sunwon, Lee, Juyong, Li, Dong, Li, Jiuyong, Liu, Lin, Loizou, Antonis, Luo, Zhenhua, Choobdar, Sarvenaz, Ahsen, Mehmet E., Crawford, Jake, Tomasoni, Mattia, Le, Thuc Duy, Li, Jiuyong, Liu, Lin, Zhang, W, Marbach, D, The DREAM Module Identification Challenge Consortium, Choobdar, S, Ahsen, M, Crawford, J, Tomasoni, M, Fang, T, Lamparter, D, Lin, J, Hescott, B, Hu, X, Mercer, J, Natoli, T, Narayan, R, Aicheler, F, Amoroso, N, Arenas, A, Azhagesan, K, Baker, A, Banf, M, Batzoglou, S, Baudot, A, Bellotti, R, Bergmann, S, Boroevich, K, Brun, C, Cai, S, Caldera, M, Calderone, A, Cesareni, G, Chen, W, Chichester, C, Cowen, L, Cui, H, Dao, P, De Domenico, M, Dhroso, A, Didier, G, Divine, M, del Sol, A, Feng, X, Flores-Canales, J, Fortunato, S, Gitter, A, Gorska, A, Guan, Y, Guenoche, A, Gomez, S, Hamza, H, Hartmann, A, He, S, Heijs, A, Heinrich, J, Hu, Y, Huang, X, Hughitt, V, Jeon, M, Jeub, L, Johnson, N, Joo, K, Joung, I, Jung, S, Kalko, S, Kamola, P, Kang, J, Kaveelerdpotjana, B, Kim, M, Kim, Y, Kohlbacher, O, Korkin, D, Krzysztof, K, Kunji, K, Kutalik, Z, Lage, K, Lang-Brown, S, Le, T, Lee, J, Lee, S, Li, D, Li, J, Liu, L, Loizou, A, Luo, Z, Lysenko, A, Ma, T, Mall, R, Mattia, T, Medvedovic, M, Menche, J, Micarelli, E, Monaco, A, Muller, F, Narykov, O, Norman, T, Park, S, Perfetto, L, Perrin, D, Pirro, S, Przytycka, T, Qian, X, Raman, K, Ramazzotti, D, Ramsahai, E, Ravindran, B, Rennert, P, Saez-Rodriguez, J, Scharfe, C, Sharan, R, Shi, N, Shin, W, Shu, H, Sinha, H, Slonim, D, Spinelli, L, Srinivasan, S, Subramanian, A, Suver, C, Szklarczyk, D, Tangaro, S, Thiagarajan, S, Tichit, L, Tiede, T, Tripathi, B, Tsherniak, A, Tsunoda, T, Turei, D, Ullah, E, Vahedi, G, Valdeolivas, A, Vivek, J, von Mering, C, Waagmeester, A, Wang, B, Wang, Y, Weir, B, White, S, Winkler, S, Xu, K, Xu, T, Yan, C, Yang, L, Yu, K, Yu, X, Zaffaroni, G, Zaslavskiy, M, Zeng, T, Zhang, J, Zhang, L, Zhang, X, Zhou, X, Zhou, J, Zhu, H, Zhu, J, Zuccon, G, Stolovitzky, G, Spinelli, Lionel, Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Theories and Approaches of Genomic Complexity (TAGC), DREAM Module Identification Challenge Consortium, Aicheler, F., Amoroso, N., Arenas, A., Azhagesan, K., Baker, A., Banf, M., Batzoglou, S., Baudot, A., Bellotti, R., Bergmann, S., Boroevich, K.A., Brun, C., Cai, S., Caldera, M., Calderone, A., Cesareni, G., Chen, W., Chichester, C., Choobdar, S., Cowen, L., Crawford, J., Cui, H., Dao, P., De Domenico, M., Dhroso, A., Didier, G., Divine, M., Del Sol, A., Fang, T., Feng, X., Flores-Canales, J.C., Fortunato, S., Gitter, A., Gorska, A., Guan, Y., Guénoche, A., Gómez, S., Hamza, H., Hartmann, A., He, S., Heijs, A., Heinrich, J., Hescott, B., Hu, X., Hu, Y., Huang, X., Hughitt, V.K., Jeon, M., Jeub, L., Johnson, N.T., Joo, K., Joung, I., Jung, S., Kalko, S.G., Kamola, P.J., Kang, J., Kaveelerdpotjana, B., Kim, M., Kim, Y.A., Kohlbacher, O., Korkin, D., Krzysztof, K., Kunji, K., Kutalik, Z., Lage, K., Lamparter, D., Lang-Brown, S., Le, T.D., Lee, J., Lee, S., Li, D., Li, J., Lin, J., Liu, L., Loizou, A., Luo, Z., Lysenko, A., Ma, T., Mall, R., Marbach, D., Mattia, T., Medvedovic, M., Menche, J., Mercer, J., Micarelli, E., Monaco, A., Müller, F., Narayan, R., Narykov, O., Natoli, T., Norman, T., Park, S., Perfetto, L., Perrin, D., Pirrò, S., Przytycka, T.M., Qian, X., Raman, K., Ramazzotti, D., Ramsahai, E., Ravindran, B., Rennert, P., Saez-Rodriguez, J., Schärfe, C., Sharan, R., Shi, N., Shin, W., Shu, H., Sinha, H., Slonim, D.K., Spinelli, L., Srinivasan, S., Subramanian, A., Suver, C., Szklarczyk, D., Tangaro, S., Thiagarajan, S., Tichit, L., Tiede, T., Tripathi, B., Tsherniak, A., Tsunoda, T., Türei, D., Ullah, E., Vahedi, G., Valdeolivas, A., Vivek, J., von Mering, C., Waagmeester, A., Wang, B., Wang, Y., Weir, B.A., White, S., Winkler, S., Xu, K., Xu, T., Yan, C., Yang, L., Yu, K., Yu, X., Zaffaroni, G., Zaslavskiy, M., Zeng, T., Zhang, J.D., Zhang, L., Zhang, W., Zhang, X., Zhang, J., Zhou, X., Zhou, J., Zhu, H., Zhu, J., and Zuccon, G.
Subjects: Identification methods, Cellular signalling networks, Computer science, Population genetics, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Gene regulatory network, DREAM challenge, network, modules, predictions, Genome-wide association study, Computational biology, Biochemistry, Models, Biological, Polymorphism, Single Nucleotide, Gene regulatory networks, Functional clustering, 03 medical and health sciences, Human disease, Humans, Disease, ddc:610, Protein Interaction Maps, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Network module, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Network topology, Gene Expression Profiling, Computational Biology, Cell Biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gene expression profiling, [SDV] Life Sciences [q-bio], Molecular network, Phenotype, Protein network, Network Module Identification, Analysis, Algorithms, Biotechnology, Genome-Wide Association Study
Abstract: Many bioinformatics methods have been proposed for reducing the complexity of large gene or protein networks into relevant subnetworks or modules. Yet, how such methods compare to each other in terms of their ability to identify disease-relevant modules in different types of network remains poorly understood. We launched the ‘Disease Module Identification DREAM Challenge’, an open competition to comprehensively assess module identification methods across diverse protein–protein interaction, signaling, gene co-expression, homology and cancer-gene networks. Predicted network modules were tested for association with complex traits and diseases using a unique collection of 180 genome-wide association studies. Our robust assessment of 75 module identification methods reveals top-performing algorithms, which recover complementary trait-associated modules. We find that most of these modules correspond to core disease-relevant pathways, which often comprise therapeutic targets. This community challenge establishes biologically interpretable benchmarks, tools and guidelines for molecular network analysis to study human disease biology., In this DREAM challenge, 75 methods for the identification of disease-relevant modules from molecular networks are compared and validated with GWAS data. The authors provide practical guidelines for users and establish benchmarks for network analysis.
Published: 2019

30. Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types

Author: Dentro, Stefan C., Leshchiner, Ignaty, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Vázquez-García, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G., Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Demeulemeester, Jonas, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steven, Fan, Yu, Fittall, Matthew, Drews, Ruben M., Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J., Getz, Gad, Boutros, Paul C., Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T., Wang, Wenyi, Morris, Quaid D., Wedge, David C., and Loo, Peter Van
Abstract: Summary Ongoing cancer evolution gives rise to intra-tumour heterogeneity (ITH), which is a major mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin and drivers of ITH across cancer types are poorly understood. Here, we extensively characterise ITH across 2,778 cancer whole genome sequences from 36 cancer types. We demonstrate that nearly all tumours (94.7%) with sufficient sequencing depth contain evidence of recent subclonal expansions, and that most cancer types show clear signs of positive selection in both clonal and subclonal protein coding variants. We find distinctive subclonal patterns of driver gene mutations, fusions, structural variation and copy-number alterations across cancer types. Dynamic, tumour type-specific changes of mutational processes between subclonal expansions shape differences between clonal and subclonal events. Our results underline the importance of ITH and its drivers in tumour evolution, and provide an unprecedented pan-cancer resource of extensively annotated subclonal events, laying a foundation for future cancer genomic studies.
Published: 2018
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31. Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases

Author: Choobdar, Sarvenaz, Ahsen, Mehmet E., Crawford, Jake, Tomasoni, Mattia, Fang, Tao, Lamparter, David, Lin, Junyuan, Hescott, Benjamin, Hu, Xiaozhe, Mercer, Johnathan, Natoli, Ted, Narayan, Rajiv, Subramanian, Aravind, Zhang, Jitao D., Stolovitzky, Gustavo, Kutalik, Zoltán, Lage, Kasper, Slonim, Donna K., Saez-Rodriguez, Julio, Cowen, Lenore J., Bergmann, Sven, Marbach, Daniel, Aicheler, Fabian, Amoroso, Nicola, Arenas, Alex, Azhagesan, Karthik, Baker, Aaron, Banf, Michael, Batzoglou, Serafim, Baudot, Anaïs, Bellotti, Roberto, Boroevich, Keith A., Brun, Christine, Cai, Stanley, Caldera, Michael, Calderone, Alberto, Cesareni, Gianni, Chen, Weiqi, Chichester, Christine, Cowen, Lenore, Cui, Hongzhu, Dao, Phuong, Domenico, Manlio De, Dhroso, Andi, Didier, Gilles, Divine, Mathew, Sol, Antonio del, Feng, Xuyang, Flores-Canales, Jose C., Fortunato, Santo, Gitter, Anthony, Gorska, Anna, Guan, Yuanfang, Guénoche, Alain, Gómez, Sergio, Hamza, Hatem, Hartmann, András, He, Shan, Heijs, Anton, Heinrich, Julian, Hu, Ying, Huang, Xiaoqing, Hughitt, V. Keith, Jeon, Minji, Jeub, Lucas, Johnson, Nathan, Joo, Keehyoung, Joung, InSuk, Jung, Sascha, Kalko, Susana G., Kamola, Piotr J., Kang, Jaewoo, Kaveelerdpotjana, Benjapun, Kim, Minjun, Kim, Yoo-Ah, Kohlbacher, Oliver, Korkin, Dmitry, Krzysztof, Kiryluk, Kunji, Khalid, Kutalik, Zoltàn, Lang-Brown, Sean, Le, Thuc Duy, Lee, Jooyoung, Lee, Sunwon, Lee, Juyong, Li, Dong, Li, Jiuyong, Liu, Lin, Loizou, Antonis, Luo, Zhenhua, Lysenko, Artem, Ma, Tianle, Mall, Raghvendra, Mattia, Tomasoni, Medvedovic, Mario, Menche, Jörg, Micarelli, Elisa, Monaco, Alfonso, Müller, Felix, Narykov, Oleksandr, Norman, Thea, Park, Sungjoon, Perfetto, Livia, Perrin, Dimitri, Pirrò, Stefano, Przytycka, Teresa M., Qian, Xiaoning, Raman, Karthik, Ramazzotti, Daniele, Ramsahai, Emilie, Ravindran, Balaraman, Rennert, Philip, Schärfe, Charlotta, Sharan, Roded, Shi, Ning, Shin, Wonho, Shu, Hai, Sinha, Himanshu, Spinelli, Lionel, Srinivasan, Suhas, Suver, Christine, Szklarczyk, Damian, Tangaro, Sabina, Thiagarajan, Suresh, Tichit, Laurent, Tiede, Thorsten, Tripathi, Beethika, Tsherniak, Aviad, Tsunoda, Tatsuhiko, Türei, Dénes, Ullah, Ehsan, Vahedi, Golnaz, Valdeolivas, Alberto, Vivek, Jayaswal, Mering, Christian von, Waagmeester, Andra, Wang, Bo, Wang, Yijie, Weir, Barbara A., White, Shana, Winkler, Sebastian, Xu, Ke, Xu, Taosheng, Yan, Chunhua, Yang, Liuqing, Yu, Kaixian, Yu, Xiangtian, Zaffaroni, Gaia, Zaslavskiy, Mikhail, Zeng, Tao, Zhang, Lu, Zhang, Weijia, Zhang, Lixia, Zhang, Xinyu, Zhang, Junpeng, Zhou, Xin, Zhou, Jiarui, Zhu, Hongtu, Zhu, Junjie, and Zuccon, Guido
Subjects: Identification methods, Molecular network, Computer science, Association (object-oriented programming), Key (cryptography), Open community, Genome-wide association study, Identification (biology), Computational biology, Disease
Abstract: Identification of modules in molecular networks is at the core of many current analysis methods in biomedical research. However, how well different approaches identify disease-relevant modules in different types of gene and protein networks remains poorly understood. We launched the “Disease Module Identification DREAM Challenge”, an open competition to comprehensively assess module identification methods across diverse protein-protein interaction, signaling, gene co-expression, homology, and cancer-gene networks. Predicted network modules were tested for association with complex traits and diseases using a unique collection of 180 genome-wide association studies (GWAS). Our critical assessment of 75 contributed module identification methods reveals novel top-performing algorithms, which recover complementary trait-associated modules. We find that most of these modules correspond to core disease-relevant pathways, which often comprise therapeutic targets and correctly prioritize candidate disease genes. This community challenge establishes benchmarks, tools and guidelines for molecular network analysis to study human disease biology (https://synapse.org/modulechallenge).
Published: 2018
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32. GRASP: a Bayesian network structure learning method using adaptive sequential Monte Carlo

Author: Yu, Kaixian, primary, Cui, Zihan, additional, Qiu, Xing, additional, and Zhang, Jinfeng, additional
Published: 2019
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33. Data Science Foundations: Geometry and Topology of Complex Hierarchic Systems and Big Data Analytics.

Author: Yu, Kaixian, primary
Published: 2019
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34. The evolutionary history of 2,658 cancers

Author: Jolly, Clemency, Gerstung, Moritz, Leshchiner, Ignaty, Dentro, Stefan C., Gonzalez, Santiago, Mitchell, Thomas J., Rubanova, Yulia, Anur, Pavana, Rosebrock, Daniel, Yu, Kaixian, Tarabichi, Maxime, Deshwar, Amit, Wintersinger, Jeff, Kleinheinz, Kortine, Vasquez-Garcia, Ignacio, Haase, Kerstin, Sengupta, Subhajit, Macintyre, Geoff, Malikic, Salem, Donmez, Nilgun, Livitz, Dimitri G., Cmero, Mark, Demeulemeester, Jonas, Schumacher, Steve, Fan, Yu, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Boutros, Paul C., Bowtell, David D., Zhu, Hongtu, Getz, Gad, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Markowetz, Florian, Mustonen, Ville, Juan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., Van Loo, Peter, Jolly, Clemency, Gerstung, Moritz, Leshchiner, Ignaty, Dentro, Stefan C., Gonzalez, Santiago, Mitchell, Thomas J., Rubanova, Yulia, Anur, Pavana, Rosebrock, Daniel, Yu, Kaixian, Tarabichi, Maxime, Deshwar, Amit, Wintersinger, Jeff, Kleinheinz, Kortine, Vasquez-Garcia, Ignacio, Haase, Kerstin, Sengupta, Subhajit, Macintyre, Geoff, Malikic, Salem, Donmez, Nilgun, Livitz, Dimitri G., Cmero, Mark, Demeulemeester, Jonas, Schumacher, Steve, Fan, Yu, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Boutros, Paul C., Bowtell, David D., Zhu, Hongtu, Getz, Gad, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Markowetz, Florian, Mustonen, Ville, Juan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., and Van Loo, Peter
Published: 2018

35. Pervasive intra-tumour heterogeneity and subclonal selection across cancer types

Author: Dentro, Stefan, Leshchiner, Ignaty, Haase, Kerstin, Wintersinger, Jeff, Deshwar, Amit, Tarabichi, Maxime, Rubanova, Yulia, Yu, Kaixian, Garcia, Ignacio Vazquez, Macintyre, Geoff, Kleinheinz, Kortine, Livitz, Dimitri, Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Ji, Yuan, Demeulemeester, Jonas, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steve, Fan, Yu, Fittall, Matthew, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David, Getz, Gad, Boutros, Paul, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, Cenk, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Wang, Wenyi, Spellman, Paul, Morris, Quaid, Wedge, David, Van Loo, Peter, Dentro, Stefan, Leshchiner, Ignaty, Haase, Kerstin, Wintersinger, Jeff, Deshwar, Amit, Tarabichi, Maxime, Rubanova, Yulia, Yu, Kaixian, Garcia, Ignacio Vazquez, Macintyre, Geoff, Kleinheinz, Kortine, Livitz, Dimitri, Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Ji, Yuan, Demeulemeester, Jonas, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steve, Fan, Yu, Fittall, Matthew, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David, Getz, Gad, Boutros, Paul, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, Cenk, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Wang, Wenyi, Spellman, Paul, Morris, Quaid, Wedge, David, and Van Loo, Peter
Published: 2018

36. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.

Author: Rubanova, Yulia, Shi, Ruian, Harrigan, Caitlin F., Li, Roujia, Wintersinger, Jeff, Sahin, Nil, Deshwar, Amit, PCAWG Evolution and Heterogeneity Working Group, Dentro, Stefan C., Leshchiner, Ignaty, Gerstung, Moritz, Jolly, Clemency, Haase, Kerstin, Tarabichi, Maxime, Deshwar, Amit G., Yu, Kaixian, Gonzalez, Santiago, Macintyre, Geoff, Adams, David J., and Anur, Pavana
Subjects: SOMATIC mutation, CANCER, GENE frequency, DECONVOLUTION (Mathematics)
Abstract: The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures that represent mutation types that co-occur in the same tumours. However, it remains unclear how mutation processes change during cancer evolution due to the lack of reliable methods to reconstruct evolutionary trajectories of mutational signature activity. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we present TrackSig, a new method that reconstructs these trajectories using optimal, joint segmentation and deconvolution of mutation type and allele frequencies from a single tumour sample. In simulations, we find TrackSig has a 3–5% activity reconstruction error, and 12% false detection rate. It outperforms an aggressive baseline in situations with branching evolution, CNA gain, and neutral mutations. Applied to data from 2658 tumours and 38 cancer types, TrackSig permits pan-cancer insight into evolutionary changes in mutational processes. Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data. [ABSTRACT FROM AUTHOR]
Published: 2020
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37. Machine Learning Applications in Head and Neck Radiation Oncology: Lessons From Open-Source Radiomics Challenges

Author: Elhalawani, Hesham, primary, Lin, Timothy A., additional, Volpe, Stefania, additional, Mohamed, Abdallah S. R., additional, White, Aubrey L., additional, Zafereo, James, additional, Wong, Andrew J., additional, Berends, Joel E., additional, AboHashem, Shady, additional, Williams, Bowman, additional, Aymard, Jeremy M., additional, Kanwar, Aasheesh, additional, Perni, Subha, additional, Rock, Crosby D., additional, Cooksey, Luke, additional, Campbell, Shauna, additional, Yang, Pei, additional, Nguyen, Khahn, additional, Ger, Rachel B., additional, Cardenas, Carlos E., additional, Fave, Xenia J., additional, Sansone, Carlo, additional, Piantadosi, Gabriele, additional, Marrone, Stefano, additional, Liu, Rongjie, additional, Huang, Chao, additional, Yu, Kaixian, additional, Li, Tengfei, additional, Yu, Yang, additional, Zhang, Youyi, additional, Zhu, Hongtu, additional, Morris, Jeffrey S., additional, Baladandayuthapani, Veerabhadran, additional, Shumway, John W., additional, Ghosh, Alakonanda, additional, Pöhlmann, Andrei, additional, Phoulady, Hady A., additional, Goyal, Vibhas, additional, Canahuate, Guadalupe, additional, Marai, G. Elisabeta, additional, Vock, David, additional, Lai, Stephen Y., additional, Mackin, Dennis S., additional, Court, Laurence E., additional, Freymann, John, additional, Farahani, Keyvan, additional, Kaplathy-Cramer, Jayashree, additional, and Fuller, Clifton D., additional
Published: 2018
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38. Abstract 3000: Pervasive intra-tumour heterogeneity and subclonal selection across cancer types

Author: Dentro, Stefan, primary, Leshchiner, Ignaty, additional, Haase, Kerstin, additional, Wintersinger, Jeff, additional, Deshwar, Amit, additional, Tarabichi, Maxime, additional, Rubanova, Yulia, additional, Yu, Kaixian, additional, Vázquez García, Ignacio, additional, Macintyre, Geoff, additional, Kleinheinz, Kortine, additional, Livitz, Dimitri, additional, Malikic, Salem, additional, Donmez, Nilgun, additional, Sengupta, Subhajit, additional, Ji, Yuan, additional, Demeulemeester, Jonas, additional, Anur, Pavana, additional, Jolly, Clemency, additional, Cmero, Marek, additional, Rosebrock, Daniel, additional, Schumacher, Steve, additional, Fan, Yu, additional, Fittall, Matthew, additional, Yao, Xiaotong, additional, Lee, Juhee, additional, Schlesner, Matthias, additional, Zhu, Hongtu, additional, Adams, David, additional, Getz, Gad, additional, Boutros, Paul, additional, Imielinski, Marcin, additional, Beroukhim, Rameen, additional, Sahinalp, Cenk, additional, Peifer, Martin, additional, Martincorena, Inigo, additional, Markowetz, Florian, additional, Mustonen, Ville, additional, Yuan, Ke, additional, Gerstung, Moritz, additional, Wang, Wenyi, additional, Spellman, Paul, additional, Morris, Quaid, additional, Wedge, David, additional, and Loo, Peter Van, additional
Published: 2018
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39. Extraction of protein-protein interactions using natural language processing based pattern matching

Author: Yu, Kaixian, primary, Zhao, Tingting, additional, Zhao, Peixiang, additional, and Zhang, Jinfeng, additional
Published: 2017
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40. Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Author: Myers, Jennifer S., primary, Vallega, Karin A., additional, White, Jason, additional, Yu, Kaixian, additional, Yates, Clayton C., additional, and Sang, Qing-Xiang Amy, additional
Published: 2017
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41. Personalized chemotherapy selection for breast cancer using gene expression profiles

Author: Yu, Kaixian, primary, Sang, Qing-Xiang Amy, additional, Lung, Pei-Yau, additional, Tan, Winston, additional, Lively, Ty, additional, Sheffield, Cedric, additional, Bou-Dargham, Mayassa J., additional, Liu, Jun S., additional, and Zhang, Jinfeng, additional
Published: 2017
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42. Abstract 5275: An integrated pipeline for TCGA data analysis

Author: Yu, Kaixian, primary, Xu, Yun, additional, Tang, Ke, additional, Steppi, Albert, additional, Zhou, Jun, additional, Ouyang, Zheng, additional, and Zhang, Jinfeng, additional
Published: 2016
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43. Abstract 2034: Personalized chemotherapy regimen selection for breast cancer

Author: Zhang, Jinfeng, primary, Yu, Kaixian, additional, Sang, Qingxiang Amy, additional, Tan, Winston, additional, Dargham, Mayassa B., additional, Liu, Jun S., additional, Lively, Ty, additional, and Sheffield, Cedric, additional
Published: 2016
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44. Elevated Resistin Gene Expression in African American Estrogen and Progesterone Receptor Negative Breast Cancer

Author: Vallega, Karin A., primary, Liu, NingNing, additional, Myers, Jennifer S., additional, Yu, Kaixian, additional, and Sang, Qing-Xiang Amy, additional
Published: 2016
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45. Abstract A04: Differential DNA methylation and network analysis in African American breast cancer

Author: Yu, Kaixian, primary, Steppi, Albert, additional, Xu, Yun, additional, Tang, Ke, additional, and Zhang, Jinfeng, additional
Published: 2016
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46. Abstract A05: Biological factors associated with cancer health disparity - a high-throughput approach using big data

Author: Yu, Kaixian, primary, Xu, Yun, additional, Tang, Ke, additional, Steppi, Albert, additional, and Zhang, Jinfeng, additional
Published: 2016
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47. Personalized chemotherapy selection for breast cancer using gene expression profiles

Author: Yu, Kaixian, Sang, Qing-Xiang Amy, Lung, Pei-Yau, Tan, Winston, Lively, Ty, Sheffield, Cedric, Bou-Dargham, Mayassa J., Liu, Jun S., and Zhang, Jinfeng
Abstract: Choosing the optimal chemotherapy regimen is still an unmet medical need for breast cancer patients. In this study, we reanalyzed data from seven independent data sets with totally 1079 breast cancer patients. The patients were treated with three different types of commonly used neoadjuvant chemotherapies: anthracycline alone, anthracycline plus paclitaxel, and anthracycline plus docetaxel. We developed random forest models with variable selection using both genetic and clinical variables to predict the response of a patient using pCR (pathological complete response) as the measure of response. The models were then used to reassign an optimal regimen to each patient to maximize the chance of pCR. An independent validation was performed where each independent study was left out during model building and later used for validation. The expected pCR rates of our method are significantly higher than the rates of the best treatments for all the seven independent studies. A validation study on 21 breast cancer cell lines showed that our prediction agrees with their drug-sensitivity profiles. In conclusion, the new strategy, called PRES (Personalized REgimen Selection), may significantly increase response rates for breast cancer patients, especially those with HER2 and ER negative tumors, who will receive one of the widely-accepted chemotherapy regimens.
Published: 2017
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48. 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.

49. Inferring structural variant cancer cell fraction

Author: Cmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Corcoran, Niall M., Papenfuss, Tony, Hovens, Christopher M., Markowetz, Florian, Macintyre, Geoff, Adams, David J., Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Campbell, Peter J., Cao, Shaolong, Christie, Elizabeth L., Cun, Yupeng, Dawson, Kevin J., Demeulemeester, Jonas, Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew W., Garsed, Dale W., Gerstung, Moritz, Getz, Gad, Gonzalez, Santiago, Ha, Gavin, Haase, Kerstin, Imielinski, Marcin, Jerman, Lara, Ji, Yuan, Jolly, Clemency, Kleinheinz, Kortine, Lee, Juhee, Lee-Six, Henry, Leshchiner, Ignaty, Livitz, Dimitri, Malikic, Salem, Martincorena, Iñigo, Mitchell, Thomas J., Morris, Quaid D., Mustonen, Ville, Oesper, Layla, Peifer, Martin, Peto, Myron, Raphael, Benjamin J., Rosebrock, Daniel, Rubanova, Yulia, Sahinalp, S. Cenk, Salcedo, Adriana, Schlesner, Matthias, Schumacher, Steven E., Sengupta, Subhajit, Shi, Ruian, Shin, Seung Jun, Spellman, Paul T., Spiro, Oliver, Stein, Lincoln D., Tarabichi, Maxime, Van Loo, Peter, Vembu, Shankar, Vázquez-García, Ignacio, Wang, Wenyi, Wedge, David C., Wheeler, David A., Wintersinger, Jeffrey A., Yang, Tsun-Po, Yao, Xiaotong, Yu, Kaixian, and Zhu, Hongtu
Subjects: 631/67, 45, article, 139, 129, 631/114, 631/114/1305, 119, 3. Good health
Abstract: We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone’s performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity.

50. 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. 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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.

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