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AlexandrovLab / SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
BSD 2-Clause "Simplified" License
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Pentanucleotide context mutational signature reference matrix #60

Closed sjin09 closed 3 years ago

sjin09 commented 3 years ago

Hello,

I am writing to inquire whether it is possible to know where I could potentially find pentanucleotide context mutational signature matrix describing the probabilities of each mutation in pentanucleotide context for all the mutational signatures.

Employing the single base substitution classification of 1536 mutation types, which uses the pentanucleotide sequence context two bases 5’ and two bases 3’ to each mutated base, yielded a set of signatures largely consistent with that based on substitutions in trinucleotide context alone. Notably, however, the pentanucleotide context enabled the extraction of two forms of both SBS2 and SBS13, one with mainly a pyrimidine (C or T) and the other with a purine (A or G) at the -2 base (the second base 5’ to the mutated cytosine). These may represent the activities of the cytidine deaminases APOBEC3A and APOBEC3B, respectively44. described in the paper The Repertoire of Mutational Signatures in Human Cancer

I wasn't able to find the matrix on the website https://www.synapse.org/#!Synapse:syn11726601/files or on the paper https://www.nature.com/articles/s41586-020-1943-3#Sec18

If the matrix is confidential, I was wondering if it could be shared through email at sl17@sanger.ac.uk.

Many thanks for the help!

Regards, Sangjin

mishugeb commented 3 years ago

@lalexandrov1018 could you please answer the question?

lalexandrov1018 commented 3 years ago

Unfortunately, we do not have a 1536 reference set of COSMIC signatures. While PCAWG performed a number of 1536 analyses, we did not release any of these as official COSMIC signatures due to a number of issues with the results. We are currently in the process of updating the set of reference signatures but we do not anticipate to have a stable version before the summer.