The FoundationOne® assay for comprehensive genomic profiling of solid tumor cancers
Comprehensive genomic tumor profiling is the basis of precision medicine in the modern era of cancer diagnosis and treatment. The possibility to profile cancer genomes and identify driver mutations in individual tumors has changed the way how oncologists diagnose cancer, decide on therapies and identify patients for clinical trials. At the UniversityHospital Zurich and in in collaboration with Roche, Switzerland and Foundation Medicine Inc., Cambridge, USA, we have established the validated diagnostic FoundationOne® assay for solid tumors. The FoundationOne® assay is designed to detect various genomic alterations in 315 cancer related genes including single nucleotide variants, indels and copy number alterations. In addition, fusions and rearrangement events in 28 cancer associated genes are assessed. Besides these alterations, the microsatellite status (MSI) of 114 intronic homopolymer repeat loci and the tumor mutational burden (TMB) is determined as biomarkers for immun-checkpoint inhibitors. For its application in the clinical practice, the assay was designed to work with common FFPE blocks while guaranteeing a specificity of ≥ 99% and sensitivity of 90-99%. To reliably identify driver mutations in highly heterogeneous cancer samples, the assay includes targeted resequencing of exons with a median coverage of 500x. The FoundationOne® has already established itself as an essential element at tumor board meetings, where it supports oncologists in the diagnosis and decision making process for succeeding treatment options. Here, I will introduce the audience to the assay, give an overview of the first results obtained at the UniversityHopsital Zurich, will demonstrate its advantages and give statistics on its performance.