I'm working on calling somatic variants from solid tissue tumors. I have one normal and one tumor sample for each patient. I plan to use Mutect2 to call somatic variants after preprocessing the data with the GATK Best Practices pipeline. Mutect2 recommends the use of a Panel of Normals (PON), but I can't figure out what samples should be used to built the PON. The guide says
Additionally, the samples should come from subjects that were young and healthy to minimize the chance of using as normal a sample from someone who has an undiagnosed tumor. Normals are typically derived from blood samples.
My normal samples are from solid tissue, not blood. Can I use the normal samples from each patient to build the panel of normals? Or would this cause problems because I'm using reusing the same normals for both the PON and as the normal sample for somatic variant calling? My first thought is that most somatic variants in individual normal samples should be filtered out by pooling all the normals together to build the PON but I wasn't sure if there are other reasons to avoid using non-blood based normal samples to build the PON