dnil
commented
8 months ago Hm, we had a tool for this way back when that would avoid you going into the R deconstruction jungle, and as an additional benefit also includes SV profiles: https://github.com/jessada/pyCancerSig. It hasn't been maintained for a good few years though, and I feel pretty confident others have improved on that elsewhere (e.g. there was at least another out that used SVs in profiling: https://github.com/dermasugita/Viola-SV). It does seem we now have python components from the Cosmic associated group: https://github.com/alexandrovlab/SigProfilerAssignment.
Need
As a clinical geneticist I would like to be able to use COSMIC signatures, which can identify signatures of for instance DNA-repair mutations, which would lend confidence to the impact of mutations in genes involved in such processes.
They can also be used to assist in classifying cancer sub-types where the histological slides are difficult to interpret.
In addition to this, these signatures could also be used in internal QC-checks to look for issues in the prep of the samples -- such as an abundance of sequencing artefacts, etc. Such as this signature: https://cancer.sanger.ac.uk/signatures/sbs/sbs45/ mentioned here: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=63385
Cosmic signatures: https://cancer.sanger.ac.uk/signatures/
Examples from https://sigven.github.io/pcgr/:
https://insilico.hpc.uio.no/pcgr/example_reports/latest/breast_tumor_only.grch37.flexdb.html#mutational-signatures https://insilico.hpc.uio.no/pcgr/example_reports/latest/esophagus_stomach_tumor_control.grch37.flexdb.html#mutational-signatures
In terms of priority, MSI and TMB is likely more highly prioritised!
Suggested approach
It might be possible to use an R-package (deconstructSigs, see article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0893-4)
Considered alternatives
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Deviation
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System requirements assessed
Requirements affected by this story
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Risk assessment needed
Risk assessment
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SOUPs
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Can be closed when
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Blockers
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Anything else?
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