Clinical tumor specimens are routinely formalin-fixed and paraffin-embedded (FFPE) in Pathology departments worldwide. FFPE blocks are convenient, long-term stable, and easy to archive and manipulate. However, nucleic acids extracted from FFPE tissues generally show a high degree of fragmentation as well as chemical modifications, mainly due to the fixation process. Methods to determine copy number alterations (CNAs) from FFPE clinical samples have proven challenging, in the fact that they are low-plex, only able to profile single genes or gene clusters (such as in situ hybridization-based methods), and/or show a low degree of robustness with partially degraded samples (array-based, NGS-based) as well as being time-consuming, costly, and with limitations in resolution. The NanoString nCounter® System is a medium-plex, extremely FFPE-robust system, that overcomes several of the frequent issues when dealing with clinical samples. The technique is based on hybridization of molecular barcoded probes directly to FFPE-derived DNA, followed by single molecule imaging to detect hundreds of unique molecules in a single reaction without any amplification steps that might introduce undesired biases. Here we describe nCounter v2 Cancer Copy Number Assay, a robust and highly reproducible method for detecting the copy number status of 87 genes commonly amplified or deleted in cancer, including the MYC proto-oncogene.
Keywords: Amplification; Copy number alterations; Deletion; Gain; Loss; NanoString.