4.0 years ago by
Washington University in St. Louis, MO
To rehash/expand on what Dan said, if you're sequencing normal tissue, you generally expect to see single-nucleotide variant sites fall into one of three bins: 0%, 50%, or 100%, depending on whether they're heterozygous or homozygous.
With tumors, you have to deal with a whole host of other factors:
- Normal admixture in the tumor sample: lowers variant allele fraction (VAF)
- Tumor admixture in the normal - this occurs when adjacent normals are used, or in hematological cancers, when there is some blood in the skin normal sample
- Subclonal variants, which may occur in any fraction of the cells, meaning that your het-site VAF might be anywhere from 50% down to sub-1%, depending on the tumor's clonal architecture and the sensitivity of your method
- Copy number variants, cn-neutral loss of heterozygosity, or ploidy changes, all of which again shift the expected distribution of variant fractions
These, and other factors, make calling somatic variants difficult and still an area that is being heavily researched. If someone tells you that somatic variant calling is a solved problem, they probably have never tried to call somatic variants.