PanelCAT: an Open-Source Comparative Analysis Tool for Next-Generation Sequencing Panel Target Regions

Multi-gene next-generation sequencing (NGS) panels have become a routine diagnostic method in the contemporary practice of personalized medicine. To avoid inadequate test choice or interpretation, a detailed understanding of the precise panel target regions is required. However, the necessary bioinformatic expertise is not always available, and publicly accessible and easily interpretable analyses of target regions are scarce. To address this critical knowledge gap, we present the Panel Comparative Analysis Tool (PanelCAT) an open-source application to analyze, visualize and compare NGS panel DNA target regions. PanelCAT uses RefSeq, ClinVar and COSMIC cancer mutation census databases to quantify the exon and mutation coverage of target regions and provides interactive graphical representations and search functions to inspect the results. We demonstrate the utility of PanelCAT by analyzing two large NGS panels (Illumina TruSight Oncology 500, and Qiagen Human Pan Cancer Panel) to validate the advertised target genes, quantify targeted exons and mutations, and identify differences between panels. PanelCAT will enable institutions and researchers to catalogue and visualize NGS panel target regions independent of the manufacturer, promote transparency of panel limitations, and share this information with employees and requisitioners.