To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

How should I select samples for a Panel of Normals for somatic analysis?

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

The Panel of Normals (PoN) plays two important roles in somatic variant analysis:

  1. Exclude germline variant sites that are found in the normals to avoid calling them as potential somatic variants in the tumor;
  2. Exclude technical artifacts that arise from particular techniques (eg sample preservation) and technologies (eg library capture, sequencing chemistry).

Given these roles, the most important selection criteria are the technical properties of how the normal data was generated. It's very important to use normals that are as technically similar as possible to the tumor. Also, 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).

If possible it is better to use normals generated from the same type of tissue because if the tissues were preserved differently, the artifact patterns may be different.


  • I read from Broad's presentation that PoN is preferable to matched normal. I wonder those samples you have used for PoN validation are sequenced technically consistently. (e.g. Tumor/Normal samples were sequenced using same sequencing machine and chemistry?)
    I would like to try PoN for Mutect and CNV calling, but it is challenging to get many sequencing samples for PoN due to the curse of dimensionality. (e.g. sequencing machine, chemistry version, technician, etc.)

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    The point of the PoN is to eliminate technical bias, so yes you should try to get normal samples sequenced in the same way as your tumor samples. Have a look at this thread for more information.


Sign In or Register to comment.