What I understand is Tumor mutation burden (TMB) is
number of unique mutation in a sample/
the size of the capture
and variant allele fraction (VAF) is
tumour allele count /
coverage and can be infer as the size of the mutant clone. correct?
Let say I am sequencing normal tissue to compare the somatic mutation load between 2 samples and the maf file is as follow for sample A and B with capture size of 10Mb:
ID refcount altcount coverage TumorVAF A 1268 1088 2356 0.46179966 A 1260 1237 2497 0.495394473 B 2113 20 2133 0.009376465 B 793 625 1418 0.440761636
Tumor mutation burden for both A and B would be
10Mb = 0.4/Mb
But if I want to find the
mutation load or
fraction of mutant cells in the normal tissue, can it be calculated as
sum of tumour allele count/
sum of coverage
2356+2497= 0.47 for sample A
2133+1418= 0.181 for sample B?
Or it can't because we cannot assume all cells and regions were sequenced evenly?
I know TMB is usually reported but wouldn't TMB under-estimate or over-estimate in this case the mutation burden in sample B? when actually only a small fraction of cells are mutated?