User: poisonAlien
poisonAlien • 2.7k
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Cancer genomics
Posts by poisonAlien
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... If I have to explain technicalities of PCA to a biologist, [this][1] is where I would start.
[1]: https://www.youtube.com/watch?v=_UVHneBUBW0 ...
written 5 months ago by
poisonAlien • 2.7k
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... To answer your question in a simple sentence - In an ideal scenario, variants with VAF around 50% is fully clonal. Since most somatic mutations tend to be heterozygous, a clonal mutation would have an allele frequency of 50%. Anything below ~45/40% would be a sub-clonal.
But it also depends on your ...
written 5 months ago by
poisonAlien • 2.7k
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Comment:
C: TMB Tumor Mutation Burden
... I believe standard WXS capture sizes are around 50 mb. (eg; Agilent sure select) ...
written 12 months ago by
poisonAlien • 2.7k
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... I am not sure if I understand teh question correctly. But, you should look at one of those multi region WXS/WGS studies. Somatic mutation profile varies a lot within the bulk tumor based on biopsy site. So its pretty heterogeneous. ...
written 12 months ago by
poisonAlien • 2.7k
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... Its using Mutect2 under the hood for variant calling and doing LOT of filtering to remove possible FPs and gremline variants - which is GOOD. I think you should try it! ...
written 13 months ago by
poisonAlien • 2.7k
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... If you have only tumor samples, no matter how much of a sophisticated algorithm you use - there is always an uncertainty associated with the somatic status of an identified variant. Having said that, MuTect can still call somatic variants without gremline controls. But again you will have to be care ...
written 13 months ago by
poisonAlien • 2.7k
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... There are few other tools. DeconstructSigs estimates loading of known signatures for every sample in the cohort. If you are interested in de-novo you could try [EMu](http://www.sanger.ac.uk/science/tools/emu) and [Mutational Signature framework](https://www.mathworks.com/matlabcentral/fileexchange/3 ...
written 13 months ago by
poisonAlien • 2.7k
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... Try [Here](https://github.com/PoisonAlien/beadAnalyze) ...
written 13 months ago by
poisonAlien • 2.7k
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... Hi,
You're passing MAF object as an input for `SomInaClust_det` function. My guess is it requires MAF file as an input. May be try this and see...
```r
brca_Sominaclust <- SomInaClust_det(maf_brca, calculate_CDS = TRUE, convert_genenames_to_HGNC=FALSE)
``` ...
written 14 months ago by
poisonAlien • 2.7k
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... Hi,
Whether a gene is a driver or not is usually done on large cohorts based on how frequently the gene is mutated. There are algorithms to identify such genes. How many cell lines do you have in your file ?
In case if you're only interested in a particular mutation,
- you will have to look at ...
written 16 months ago by
poisonAlien • 2.7k
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