Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025This variant is typically intermixed with many wildtype EGFR ecDNAs that hitchhike on strongly positively selected variants and therefore maintaining a mixed state if ecDNA wildtype and variants in the tumour population 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025How to explain these observations? Computational modelling suggests the following scenario: First ecDNA forms and accumulates in pre-cancerous cells. Later one ecDNA copy acquires the variant and possibly starts the clonal expansion 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025We then observed a few other EGFR variants that reach high but subclonal ecDNA frequencies. 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025EGFR ecDNA showed strongest positive selection. But interestingly we found a few EGFR variants exclusively amplified on ecDNA (EGFRvIII and others) that seem under strong positive selection but were always ecDNA subclonal 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025Interestingly, we found differences depending on which oncogene is amplified on ecDNA. 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025Combining simulations and data in a Bayesian inference framework then allows to estimate the evolutionary parameters (selection, spatial constraints and initial ecDNA copy number) that describe the data best 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025We then developed a spatial framework to simulate ecDNA evolution in silico 120
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025More importantly, we could measure spatially resolved ecDNA copy number distributions in 2 to 3 samples per GBM. 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025First as we anticipated, we found the typical diverse ecDNA landscape in GBMs 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025We therefore combined whole-genome sequencing, DNA FISH analysis and RNA scope. 110
Benjamin Werner @benjaminwerner.bsky.social · 08/09/2025We had the opportunity to analyse multi-region samples of Glioblastomas taken from the core, margin and infiltrating margin. 110
Benjamin Werner @benjaminwerner.bsky.social · 22/08/2025Ruler in my daughters primary school. To make sure you never learn conversion of cm and inches 😂 000
Benjamin Werner @benjaminwerner.bsky.social · 24/04/2025Huge congratulations @francescoterenzi.bsky.social for a great thesis and viva today. Special thanks to @robjohnnoble.bsky.social and @kevinrouault.bsky.social being the examiners and a great discussion today! 3110
Benjamin Werner @benjaminwerner.bsky.social · 20/03/2025Congratulations to a successful viva Dr. @alexsteinresearch.bsky.social Many thanks to @cancerevo.org and @zaccasimo.bsky.social to be examiners! 0112
Benjamin Werner @benjaminwerner.bsky.social · 11/03/2025We added an analysis that allows to estimate innate variant fitness in the presence of clonal competition from single variant trajectories. 100
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024The complication for modular organised clonal organisms are multiple layers of possible fixation of mutations during organismal or population growth 111
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024And then we have Jessie Renton, who left us earlier this year and worked as a postdoctoral fellow in a joined project with @thorstenreusch.bsky.social and @ibaums.bsky.social on evolutionary dynamics of clonal species in the natural habitats, e.g. seagrasses and corals 110
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024Next we have Elisa Scanu, that is just finishing her PhD with Weini Huang and joined us at the beginning of October to work on ecDNA evolution. 100
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024Among many things, Alex gives a very nice formula for the size distribution of the largest resistant clone in a growing tumour 100
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024Next we have @alexsteinresearch.bsky.social , also currently finishing his PhD, working amongst other things on the population dynamics theory of treatment induced heterogeinity 100
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024Somewhat surprisingly, we found that clonal competition can quantitatively explain many of the complex observations of CH with age 110
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024The last year Nate was working very closely with Francesco Terenzi, currently finishing his PhD 100
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024Next is Nathaniel MonPere, Postdoctoral fellow mainly interested in the dynamics of human haematopoiesis with age. 100
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024We find many interesting things. One is the possible resolution of an old puzzle in GBM. We know that EGFR vIII is a GBM specific very strong driver mutation, yet almost always seems to be sub clonal. vIII is emerges on ecDNA post formation driving aggressive growth 110
Benjamin Werner @benjaminwerner.bsky.social · 19/11/2024First is Magnus Haughey, Post doctoral fellow working on spatial temporal evolution of extra-chromosomal DNAs in human cancers 120
Benjamin Werner @benjaminwerner.bsky.social · 13/10/2023I hope this time estimate is conservative 000