Hi, I am seeing recurrent technical artifacts and germline mutations in my set of tumor samples. I do not have a matched normal for the tumor sample to be able to do a robust somatic variant call. To help clean up the artifacts, I am looking to create a panel of normals (PoN) for somatic variant calling using Mutect2.
Related to that I have a few questions:
- I realize that the minimum recommended number of samples is 40 according to the document for Panel of Normals by GATK team. Do the 40 samples need to be of same cancer type? Is there any heterogeneity okay in the panel of normals. For instance, can we have 20 endometrial cancer, 20 colorectal cancer, 20 brain tumor samples in our panel of normal? (Note that we will have sample library prep, sequencing protocols for these, but just cancer type might differ)
- The document recommends blood as the typical sample type. Is FFPE acceptable? Our assay will be using solid tumors and samples are typically FFPE type here.
- The document also recommends healthy/young samples, and this might not always be the case in solid tumor samples. I am wondering if this is okay. In some cases, the normals are normal tissue cuts right next to the tumor, are there specific red flags about using such samples?
Please let me know. Thanks in advance for your help and looking forward to hearing from the GATK team.
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