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AlexandrovLab / SigProfilerSingleSample

SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
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New signatures on COSMIC website #5

Closed anishaluthra closed 3 years ago

anishaluthra commented 4 years ago

Hi,

I noticed that there were new signatures that were defined and put on the COSMIC website. I want to compute scores for one of the new signatures (SBS88), but I have exome data only. There is a signature definition that can be downloaded but I believe this is the genome signature definition; however, I believe that the exome signature definitions are different from the genome signature definitions (as the exome and genome signature text files are different). Was wondering how the genome signatures definitions are normalized to convert to exome signature definitions?

In other words, if I wanted to use SigProfilerSingleSample to find scores for SBS88 with my exome data, would I be able to use the definition that I can download from the COSMIC website or would it require some normalization?

Thanks in advance for your help!

mishugeb commented 4 years ago

@marcos-diazg, could you please help me to answer the question? I am a little confused.

mishugeb commented 4 years ago

There is no way to use genome signatures to fit in exome data. Exome signatures have to be extracted from the exome catalog.

anishaluthra commented 4 years ago

Okay, so I wouldn't be able to calculate scores for SBS88, given what's on the COSMIC website, for exome data?

anishaluthra commented 4 years ago

Will you be updating the exome and genome signature files with the new signatures from release 3.1?

mishugeb commented 4 years ago

I have to discuss this with my PI to see if he wants to update that now @lalexandrov1018

rptashkin commented 4 years ago

would also be interested in COSMIC v3.1 signatures

marcos-diazg commented 3 years ago

We are currently working on a major update of the tool that will include the option to choose among the different versions of COSMIC reference mutational signatures, including current version 3.2 (released on March 2021). We hope to have a new version in the next few months. Thanks a lot for your suggestions and interest!