Detecting gene copy number alterations by comprehensive genomic profiling: a comparative study in a real-world series of FFPE tumor samples

Copy number alterations (CNAs) play a fundamental role in cancer development and constitute a potential tool for tailored treatments. The CNAs recognition in formalin fixed paraffin embedded (FFPE) material, to date, relies on fluorescence in situ hybridization, but the introduction of large-scale next-generation sequencing (NGS) has dramatically improved their discovery at genome-wide level. The detection of CNAs by NGS in FFPE material is, nonetheless, a complex issue, which still requires validation studies. Herein, the CNAs detection by a widely used NGS assay (Oncomine Comprehensive Assay plus, OCA+) were evaluated in 14 FFPE samples mirroring diagnostic daily practice and compared to a whole-genome assay. OCA+, a targeted DNA panel, showed lower CNAs detection sensitivity and equal specificity for gains and losses. According to proprietary software pipeline, OCA+ accurately identify gains characterized by CN >= 5,2. A much less robust threshold (CN <= 1.18) was identified that maximized the difference between true and false positive losses. Orthogonal FISH tests validated seven CNAs characterized by CN gain >= 6 or complete loss.Considering the CNAs growing significance in precision medicine, our findings further prompt towards a robust validation of NGS detection in FFPE materials.