Design guidelines for CNV detection in Ion AmpliSeq™ and Ion AmpliSeq™ HD custom panels

For any genomic region for which you want to detect CNVs, it is recommended that samples include at least 10 amplicons. That is, if the goal is to detect CNVs in a gene, at least 10 amplicons should be in or next to that gene, ideally 12 amplicons or more. If fewer than 10 amplicons are present, only CNVs with greater copy numbers may be detectable.

For robust detection of CNVs, most amplicons in a panel should be in normal diploid regions. If more than 30 percent of the amplicons are in a CNV region, it may be difficult to detect the CNV. In practice, if a panel contains at least 5 genes widely spread across the genome, the panel typically meets these criteria.