identifying TP53 germline mutations which are also in tumor cells.

Question

[lait]

I have tumor and normal samples. When running a somatic caller, the output vcf file contains a column named 'Filter' which has two values:

1. Pass: which means that this variant is Somatic
2. Rejected.

When the Filter is 'Rejected', does this mean that the variant is Germline ? or we cannot really distinguish this?

What I need to do is, I have tumor and normal samples, and I need to check which germline TP53 variants in the normal sample are also present in the tumor cell. Is my above approach valid? i.e.

1. first identify all the germline TP53 variants in the normal sample

2. run the somatic caller on the tumor vs normal samples

3. check the output vcf of the somatic caller, and scan my germline TP53 set of variants against it, if a variant in the latter set is found in the vcf and annotated as rejected, this means that this germline mutation exists in the tumor cell

What do you think about this?

Answer 1

[Noushin N]

You are likely able to do this in a more straightforward manner as follows:

1. Identify all the germline TP53 variants in the normal sample
2. Inspect the tumor sample at those positions using samtools mpileup

Normally, one expects to see germline variants in tumor sample as well; Even in cases where the cancer cells have lost the variant due to structural changes (e.g. loss of chromosome arm where mutation is located), the normal contamination in the tumor sample will result in variant appearing in tumor sequence data at levels correlated with the extent of normal contamination.

Therefore, one has to consider tumor purity and copy number in interpreting the variant allele frequency observed in tumor.