Dear all. I am currently researching the mutational signatures (or patterns?) in a large cohort of targeted sequencing of tumor samples. I found that the definition of "mutational signatures" in COSMIC is like this : "The profile of each signature is displayed using the six substitution subtypes: C>A, C>G, C>T, T>A, T>C, and T>G (all substitutions are referred to by the pyrimidine of the mutated Watson–Crick base pair)". However, this is not I want.
In my study, I have identified lots of somatic mutations in different cancer patients, such as EGFR T790M, EGFR, L858R, KRAS G12D, JAK2 V617F .etc. The mutational signatures (or patterns?) I want to identify is whether some mutations more likely to appear in specific cancer types or stages. For example, EGFR T790M and EGFR, L858R have a high frequency in NSCLC patients. Thus, different cancer types or stages can have different mutation signatures. Using these mutation signatures, we can identify patients with different cancer types, tumor stages or other characteristics.
Does anyone know how to identify the mutation signatures I want?
You can use Linkedomics to correlate different omics dimensions within TCGA cancer cohorts. Disclaimer: I used to be part of the Linkedomics dev team.
as far as im concerned, thats a recommendation not a disclaimer