Panel of normals (PON)

Panel of Normals (PON) is a a set of matched normal samples to determine a baseline coverage pattern and account for recurrent technical artifacts that are specific to your workflow. Depth of coverage per each sequenced region is averaged across PON samples; if a significant increase or decrease from this baseline is detected in a test sample, a CNV is called.

A PON linked to a coverage BED kit is used by DRAGEN to increase accuracy of copy number variation (CNV) calling in targeted panel and exome cases.

A PON file is typically a text file listing absolute paths to 'target counts' files of individual matched normal samples. However, a PON can also be in the form of a combined counts file, which is a column-wise concatenation of individual target counts files (either GC-corrected or not).

The Illumina BaseSpace Baseline Builder App can generate this combined counts file (see "Creating a PON for Emedgene using BaseSpace Baseline Builder").

Recommendations for creating a PON to call CNVs from exome data:

1. Samples for a PON should be derived from healthy individuals.

2. In our experience, a PON of at least 40-50 samples yields the best results. A smaller PON is better than nothing, but keep in mind that you may encounter more false positives.

3. You should aim at preparing samples for a PON in a unified manner to avoid the batch effect. Please log differences in library preparation (if any).