Segmental Copy Number Variant Detection Using an Amplicon-Based Next-Generation Sequencing Panel for Integrated Glioma Classification

Next-generation sequencing is a first-tier test in molecular oncology, capable of detecting sequence variants and copy number variants (CNVs). Although most amplicon-based gene panels are not designed to detect segmental chromosomal CNVs, they can still be inferred. This study describes a custom analysis for CNV detection using the amplicon-based Oncomine Comprehensive Assay version 3, for critical glioma biomarker 1p/19q codeletion, +7/–10, EGFR amplification, and CDKN2A/B homozygous deletion. The segmental CNV calling algorithm leverages vendor-normalized gene-level CNV data with intersample normalization to control regions.