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The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils.
Maximilian R Stammnitz, Tim HH Coorens, Kevin C Gori, Dane Hayes, Beiyuan Fu, Jinhong Wang, Daniel E Martin-Herranz, Ludmil B Alexandrov, Adrian Baez-Ortega, Syd Barthorpe, Alexandra Beck, Francesca Giordano, Graeme W Knowles, Young Mi Kwon, George Hall, Stacey Price, Ruth J Pye, Jose MC Tubio, Hannah VT Siddle, Sukhwinder Singh Sohal, Gregory M Woods, Ultan McDermott, Fengtang Yang, Mathew J Garnett, Zemin Ning, Elizabeth P Murchison
Mar 13, 2018
Transmissible cancers are clonal lineages that spread through populations via contagious cancer cells. Although rare in nature, two facial tumor clones affect Tasmanian devils. Here we perform comparative genetic and functional...
DFTD Tasmanian devils Cancer Cancer evolution Cancer genomics CONSERVATION contagious cancer drug screening marsupials transmissible cancer Animals Cell Line Tumor Chromosomes Mammalian Clone Cells Facial Neoplasms Female Gene Dosage Gene Editing Immunity Male Marsupialia Mutation Receptors Platelet-Derived Growth Factor
Evolutionary dynamics in pre-invasive neoplasia.
Christopher Abbosh, Subramanian Venkatesan, Samuel M Janes, Rebecca C Fitzgerald, Charles Swanton
Sep 21, 2018
Mutational processes occur in normal tissues from conception throughout life. Field cancerization describes the preconditioning of an area of epithelium to tumor growth. Pre-invasive lesions may arise in these fields, however...
OncoNEM
Cancer evolution Phylogenetic tree Single-cell sequencing Tumor evolution Tumor heterogeneity Algorithms Clonal Evolution Computational Biology evolution Molecular Genotype High-Throughput Nucleotide Sequencing Humans Models Statistical Phylogeny Polymorphism Single Nucleotide Single-Cell Analysis Thrombocytopenia Urinary Bladder Neoplasms
Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer
Clear cell renal cell carcinoma is characterized by near-universal loss of the short arm of chromosome 3, deleting several tumor suppressor genes. We analyzed whole genomes from 95 biopsies across 33 patients with clear cell...
Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer
Thomas J Mitchell, Samra Turajlic, Andrew Rowan, David Nicol, James HR Farmery, Tim O'Brien, Inigo Martincorena, Patrick Tarpey, Nicos Angelopoulos, Lucy R Yates, Adam P Butler, Keiran Raine, Grant D Stewart, Ben Challacombe, Archana Fernando, Jose I Lopez, Steve Hazell, Ashish Chandra, Simon Chowdhury, Sarah Rudman, Aspasia Soultati, Gordon Stamp, Nicos Fotiadis, Lisa Pickering, Lewis Au, Lavinia Spain, Joanna Lynch, Mark Stares, Jon Teague, Francesco Maura, David C Wedge, Stuart Horswell, Tim Chambers, Kevin Litchfield, Hang Xu, Aengus Stewart, Reza Elaidi, Stéphane Oudard, Nicholas McGranahan, Istvan Csabai, Martin Gore, P Andrew Futreal, James Larkin, Andy G Lynch, Zoltan Szallasi, Charles Swanton, Peter J Campbell, TRACERx Renal Consortium
Jul 16, 2018
Clear cell renal cell carcinoma (ccRCC) is characterized by near-universal loss of the short arm of chromosome 3, deleting several tumor suppressor genes. We analyzed whole genomes from 95 biopsies across 33 patients with clear...
Cancer evolution Chromothripsis clear cell renal cell carcinoma 5' Untranslated Regions Adult Aged Aged 80 and over Carcinoma Renal Cell Chromosomes Human Pair 3 Chromosomes Human Pair 5 Disease Progression Female Gene Dosage Genome Human Humans Kidney Neoplasms Male Middle Aged Mutation Prospective Studies Telomerase Von Hippel-Lindau Tumor Suppressor Protein
The Promising Connection Between Data Science and Evolutionary Theory in Oncology.
Theoretical and empirical work over the past several decades suggests that oncogenesis and disease progression represents an evolutionary story. Despite this knowledge, current anti-resistance strategies to drugs are often...
Deterministic Evolutionary Trajectories Influence Primary Tumor Growth
Samra Turajlic, Hang Xu, Kevin Litchfield, Andrew Rowan, Stuart Horswell, Tim Chambers, Tim O'Brien, Jose I Lopez, Thomas BK Watkins, David Nicol, Mark Stares, Ben Challacombe, Steve Hazell, Ashish Chandra, Thomas J Mitchell, Lewis Au, Claudia Eichler-Jonsson, Faiz Jabbar, Aspasia Soultati, Simon Chowdhury, Sarah Rudman, Joanna Lynch, Archana Fernando, Gordon Stamp, Emma Nye, Aengus Stewart, Wei Xing, Jonathan C Smith, Mickael Escudero, Adam Huffman, Nik Matthews, Greg Elgar, Ben Phillimore, Marta Costa, Sharmin Begum, Sophia Ward, Max Salm, Stefan Boeing, Rosalie Fisher, Lavinia Spain, Carolina Navas, Eva Grönroos, Sebastijan Hobor, Sarkhara Sharma, Ismaeel Aurangzeb, Sharanpreet Lall, Alexander Polson, Mary Varia, Catherine Horsfield, Nicos Fotiadis, Lisa Pickering, Roland F Schwarz, Bruno Silva, Javier Herrero, Nick M Luscombe, Mariam Jamal-Hanjani, Rachel Rosenthal, Nicolai J Birkbak, Gareth A Wilson, Orsolya Pipek, Dezso Ribli, Marcin Krzystanek, Istvan Csabai, Zoltan Szallasi, Martin Gore, Nicholas McGranahan, Peter Van Loo, Peter Campbell, James Larkin, Charles Swanton, TRACERx Renal Consortium
Jul 17, 2018
The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study...
branched evolution Cancer evolution chromosome instability deterministic evolution intratumor heterogeneity linear evolution metastasis punctuated evolution renal cell cancer tumor diversity Adult Aged Aged 80 and over Alleles Biomarkers Tumor Carcinoma Renal Cell Chromosomes Clonal Evolution Disease Progression evolution Molecular Female Genetic Heterogeneity genetic variation Humans Kidney Neoplasms Longitudinal Studies Male Middle Aged Models Statistical Mutation Neoplasm Metastasis Phenotype Phylogeny Prognosis Prospective Studies Sequence Analysis DNA
In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution.
Anja Fischer, Robert Lersch, Niklas de Andrade Krätzig, Alexander Strong, Mathias J Friedrich, Julia Weber, Thomas Engleitner, Rupert Öllinger, Hsi-Yu Yen, Ursula Kohlhofer, Irene Gonzalez-Menendez, David Sailer, Liz Kogan, Mari Lahnalampi, Saara Laukkanen, Thorsten Kaltenbacher, Christine Klement, Majdaddin Rezaei, Tim Ammon, Juan J Montero, Günter Schneider, Julia Mayerle, Mathias Heikenwälder, Marc Schmidt-Supprian, Leticia Quintanilla-Martinez, Katja Steiger, Pentao Liu, Juan Cadiñanos, George S Vassiliou, Dieter Saur, Olli Lohi, Merja Heinäniemi, Nathalie Conte, Allan Bradley, Lena Rad, Roland Rad
Apr 17, 2023
In contrast to mono- or biallelic loss of tumor-suppressor function, effects of discrete gene dysregulations, as caused by non-coding (epi)genome alterations, are poorly understood. Here, by perturbing the regulatory genome in...