Targeted sequencing of cfDNA in HR+ HER2- MBC patients. Variants in cell-free DNA of hormone receptor positive, HER2 negative metastatic breast cancer assessed by targeted sequencing show monitoring and prognostic value

Purpose: Cell-free DNA (cfDNA) is described to mirror intratumoral heterogeneity and gives insight about clonal evolution for improved therapeutic decisions. We sequenced cfDNA of a hormone receptor positive, HER2 negative metastatic breast cancer (MBC) cohort to examine the prevalence and relevance of any detected variant.Experimental design: cfDNA of 49 MBC patients was isolated (QIAamp MinElute ccfDNA Kit, QIAGEN) followed by library construction using a customized QIAseq Targeted DNA Panel (QIAGEN) with integrated unique molecular indices analyzing AKT1, AR, BRCA1, BRCA2, EGFR, ERCC4, ERBB2, ERBB3, ESR1, FGFR1, KRAS, MUC16, PIK3CA, PIK3R1, PTEN, PTGFR and TGFB1. cfDNA was sequenced on the NextSeq® 500 platform (Illumina) and variants were analyzed with Ingenuity Variant Analysis (QIAGEN).