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Susanne Tilk
Biology PhD candidate studying somatic evolution in cancer.
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Susanne Tilk proslijedio/la je tweet
Chuan Li 30. sij
Ever wonder which tumor suppressor alterations impact drug responses in vivo? Check out our recent work on using improved Tuba-seq to quantify genotype-specific treatment responses in lung cancer.
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Susanne Tilk 10. pro
Odgovor korisniku/ci @popgengoogling @GrantKinsler
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Dmitri Petrov 3. pro
Check out the paper on G3 by the amazing & and coauthors. 1/n
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Elora López 13. stu
My first study on somatic mutations in corals! We found heterogeneity among different branches of individual corals. This occurs at a similar frequency as has been reported in humans. Intriguingly, for corals the most common form of that heterogeneity is losses of heterozygosity.
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Susanne Tilk 24. lis
Odgovor korisniku/ci @auroraabuylla
Congrats!
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Dmitri Petrov 17. ruj
I am extremely excited about this work on the way natural selection succeeds and crucially fails to weed out deleterious mutations in cancer due to the constraints posed by linkage and Hill-Robertson interference. 1/n
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
How successful tumors overcome this deleterious load is an exciting, open question. Similar to constraints in germ-line evolution, we think that preventing protein mis-folding is an important first step. We’d love to hear what you think! (10/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
Thus, this allowed us to estimate that in elevated mutational burden tumors (>95% of cancers), deleterious passengers accumulate and confer an individually-weak, but collectively-substantial fitness cost of ~40% that impacts tumor progression. (9/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
Finally, we demonstrate that a simple evolutionary model incorporating HRI can explain these observed patterns of selection and allowed us to estimate the mean fitness effects of passengers (~1%) and drivers (~18%) – much larger than previously estimated. (8/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
Importantly, we see that attenuated selection on CNAs and SNVs is generic to tumor evolution. This pattern persists across broad and specific tumor sub-type categories. (7/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
We see the same trend in somatic CNAs. Using a dN/dS-style statistic called dE/dI (fractional overlap of CNAs in [E]xonic versus [I]ntergenic/[I]ntronic regions) – we similarly see that selection on CNAs attenuates as the mutational burden increases. (6/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
To test this idea, we calculated dN/dS in tumors stratified by their mutational burden and observe that negative and positive selection attenuates as more mutations accumulate in tumors. (5/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
Since linkage effects get stronger as mutation rates increase, tumors with elevated mutational burdens should be particularly inefficient at removing deleterious passengers due to genetic hitchhiking and Muller’s Ratchet. (4/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
We hypothesized that since tumors evolve asexually, under the constraints of genome-wide linkage, mutations are unable to be removed by negative selection (or favored by positive selection). (3/10)
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Susanne Tilk 16. ruj
Odgovor korisniku/ci @SusanneTilk
Here, we try to resolve why signals of negative selection are largely absent in cancer, yet pre-dominant in the human germ-line. (2/10)
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Susanne Tilk 16. ruj
Really excited to share the first chapter of my PhD on how genome-wide linkage in cancer reduces the efficacy of selection via Hill-Robertson interference (HRI), with mentors , and . (1/10)
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Ellie Armstrong 🦁🐯 25. srp
Today at petrov lab meeting we explored a very important question...which spicy Cheeto is spicier? We double blinded and controlled for Cheeto size but we’re still really confused about whos spicier. , can you help us out?
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Christina Curtis 8. velj
Excited to share our new paper on clonal replacement and heterogeneity through neoadjuvant therapy in Her2+ breast cancer: . Great work from and Katherine McNamara and the rest of the team!
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Alison Feder 14. pro 2018.
We have a new paper on bioRxiv today. It’s not a paper I was planning to write during my first semester as a postdoc. (1/n)
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KerryGeilerSamerotte 16. stu 2018.
The Geiler-Samerotte lab is recruiting graduate students and postdocs! Graduate students apply here by December 1rst: Postdocs apply here:
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