I am working on cancer heterogeneity NGS data derived from patients (primary) solid tumors, and generations of mice that carry the cancer patient's primary tumors. I did exome-seq analysis and have identified SNPs/Indels on many genes in the cohort.
The passage from primary patient's sample to the third generation (F3) of mice shows that the tumor accumulates more mutations, but the mutational patterns are also heterogeneous among the same generation of mice. I am wondering about an effective way for presenting the heterogeneity results. Some methods I was thinking about include:
Get the ratio of the variant allele frequency (VAF, each mutation identified) in each mice vs the primary tumor (patient), then calculate the correction coefficient between the mice and the primary sample; plot the VAF vs sample lineages (?)
Sum up the number of SNPS/Indels in each sample, and divide the number by the total number of mutations. This will give a mutation rate in each sample, then plot this numbers against each sample name. I would expect this to show a linear accumulation.
I am not sure these two presentations will make any sense, so I am looking for suggestions for presenting the heterogeneity results. If you know some methods or have seen some good way of presentation, please reply. I appreciate it.