BPG: Seamless, automated and interactive visualization of scientific data by Christine P’ng, Jeffrey Green, Lauren C. Chong, Daryl Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Denise Y. F. Mak, Felix Lam, Marco A. Albuquerque, Ying Wu, Esther H. Jung, Maud H. W. Starmans, Michelle A. Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang, Emilie Lalonde, Syed Haider, Nicole A. Simone, Dorota Sendorek, Kenneth C. Chu, Nathalie C. Moon, Natalie S. Fox, Michal R. Grzadkowski, Nicholas J. Harding, Clement Fung, Amanda R. Murdoch, Kathleen E. Houlahan, Jianxin Wang, David R. Garcia, Richard de Borja, Ren X. Sun, Xihui Lin, Gregory M. Chen, Aileen Lu, Yu-Jia Shiah, Amin Zia, Ryan Kearns, Paul C. Boutros

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Pathway-based subnetworks enable cross-disease biomarker discovery by Syed Haider, Cindy Q. Yao, Vicky S. Sabine, Michal Grzadkowski, Vincent Stimper, Maud H. W. Starmans, Jianxin Wang, Francis Nguyen, Nathalie C. Moon, Xihui Lin, Camilla Drake, Cheryl A. Crozier, Cassandra L. Brookes, Cornelis J. H. van de Velde, Annette Hasenburg, Dirk G. Kieback, Christos J. Markopoulos, Luc Y. Dirix, Caroline Seynaeve, Daniel W. Rea, Arek Kasprzyk, Philippe Lambin, Pietro Lio’, John M. S. Bartlett, Paul C. Boutros

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Author Correction: Integrative pathway enrichment analysis of multivariate omics data by Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S. Fox, Helen Zhu, Diala Abd-Rabbo, Miles W. Mee, Paul C. Boutros, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, PCAWG Consortium

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Gene-by-environment interactions in urban populations modulate risk phenotypes by Marie-Julie Favé, Fabien C. Lamaze, David Soave, Alan Hodgkinson, Héloïse Gauvin, Vanessa Bruat, Jean-Christophe Grenier, Elias Gbeha, Kimberly Skead, Audrey Smargiassi, Markey Johnson, Youssef Idaghdour, Philip Awadalla

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Molecular stratification of early breast cancer identifies drug targets to drive stratified medicine by Jane Bayani, Cindy Q. Yao, Mary Anne Quintayo, Fu Yan, Syed Haider, Alister D’Costa, Cassandra L. Brookes, Cornelis J. H. van de Velde, Annette Hasenburg, Dirk G. Kieback, Christos Markopoulos, Luc Dirix, Caroline Seynaeve, Daniel Rea, Paul C. Boutros, John M. S. Bartlett

“…A team led by John Bartlett and Paul Boutros from the Ontario Institute for Cancer Research in Toronto, Canada, measured the activity levels of 165 genes known to be involved in breast cancer development in tumor samples from 3825 patients with early estrogen receptor-positive disease. …”
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P097: Validation of a clinical test for genome-wide homologous recombination deficiency signatures in solid tumors by Felix Beaudry, Aqsa Alam, Iain Bancarz, Alexander Fortuna, Trevor Pugh

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Valection: design optimization for validation and verification studies by Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P’ng, Kathleen E Houlahan, Cristian Caloian, Michael Fraser, SMC-DNA Challenge Participants, Kyle Ellrott, Adam A Margolin, Robert G Bristow, Joshua M Stuart, Paul C Boutros

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P054: Creation of the Ontario Hereditary Cancer Research Network (OHCRN) by Lauren Hughes, Kirsten Farncombe, Michelle Brazas, Melyssa Aronson, Kathleen Bell, Brandon Chan, Andrea Eisen, Harriet Feilotter, Bailey Gallinger, Jordan Lerner-Ellis, David Malkin, Ellen MacDougall, Steven Narod, Karen Panabaker, Trevor Pugh, Sarah Sawyer, Alison Rusnak, Andrea Vaags, Laszlo Radvanyi, Lincoln Stein, Raymond Kim

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Sex differences in oncogenic mutational processes by Constance H. Li, Stephenie D. Prokopec, Ren X. Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes and Clinical Translation, Paul C. Boutros, PCAWG Consortium

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The telomere length landscape of prostate cancer by Julie Livingstone, Yu-Jia Shiah, Takafumi N. Yamaguchi, Lawrence E. Heisler, Vincent Huang, Robert Lesurf, Tsumugi Gebo, Benjamin Carlin, Stefan Eng, Erik Drysdale, Jeffrey Green, Theodorus van der Kwast, Robert G. Bristow, Michael Fraser, Paul C. Boutros

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Deregulation of the spindle assembly checkpoint is associated with paclitaxel resistance in ovarian cancer by Taryne Chong, Amila Sarac, Cindy Q. Yao, Linda Liao, Nicola Lyttle, Paul C. Boutros, John M. S. Bartlett, Melanie Spears

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Pan-cancer classification of single cells in the tumour microenvironment by Ido Nofech-Mozes, David Soave, Philip Awadalla, Sagi Abelson

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JBrowse 2: a modular genome browser with views of synteny and structural variation by Colin Diesh, Garrett J Stevens, Peter Xie, Teresa De Jesus Martinez, Elliot A. Hershberg, Angel Leung, Emma Guo, Shihab Dider, Junjun Zhang, Caroline Bridge, Gregory Hogue, Andrew Duncan, Matthew Morgan, Tia Flores, Benjamin N. Bimber, Robin Haw, Scott Cain, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes

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Landscape of transcriptomic interactions between breast cancer and its microenvironment by Natalie S. Fox, Syed Haider, Adrian L. Harris, Paul C. Boutros

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A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns by Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, PCAWG Tumor Subtypes and Clinical Translation Working Group, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P. Lolkema, Neeltje Steeghs, Gad Getz, Quaid Morris, Lincoln D. Stein, PCAWG Consortium

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The value of GATA6 immunohistochemistry and computer-assisted diagnosis to predict clinical outcome in advanced pancreatic cancer by Kai Duan, Gun-Ho Jang, Robert C. Grant, Julie M. Wilson, Faiyaz Notta, Grainne M. O’Kane, Jennifer J. Knox, Steven Gallinger, Sandra Fischer

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ISOWN: accurate somatic mutation identification in the absence of normal tissue controls by Irina Kalatskaya, Quang M. Trinh, Melanie Spears, John D. McPherson, John M. S. Bartlett, Lincoln Stein

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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection by Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros

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Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma by James T. Topham, Erica S. Tsang, Joanna M. Karasinska, Andrew Metcalfe, Hassan Ali, Steve E. Kalloger, Veronika Csizmok, Laura M. Williamson, Emma Titmuss, Karina Nielsen, Gian Luca Negri, Sandra E. Spencer Miko, Gun Ho Jang, Robert E. Denroche, Hui-li Wong, Grainne M. O’Kane, Richard A. Moore, Andrew J. Mungall, Jonathan M. Loree, Faiyaz Notta, Julie M. Wilson, Oliver F. Bathe, Patricia A. Tang, Rachel Goodwin, Gregg B. Morin, Jennifer J. Knox, Steven Gallinger, Janessa Laskin, Marco A. Marra, Steven J. M. Jones, David F. Schaeffer, Daniel J. Renouf

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Antioxidant Supplementation Reduces Genomic Aberrations in Human Induced Pluripotent Stem Cells by Junfeng Ji, Vivek Sharma, Suxia Qi, Meritxell Espino Guarch, Ping Zhao, Zhiwei Luo, Wenxia Fan, Yu Wang, Faridah Mbabaali, Dante Neculai, Miguel Angel Esteban, John D. McPherson, Nizar N. Batada

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