The genomic landscape of breast cancer based on ctDNA analysis: Data from the plasmaMATCH trial

Abstract

Background: Circulating tumor DNA (ctDNA) is found in the plasma of over 90% of patients with advanced breast cancer (BC). ctDNA analysis can establish the current genomic profile of an individual's cancer and identify potentially targetable mutations. The genomic landscape of advanced BC and clinical associations has yet to be fully defined. This analysis describes the genomic landscape of ctDNA in patients screened for the UK plasmaMATCH study. Methods: The plasmaMATCH trial was an open-label, multi-centre, multi-cohort platform trial, consisting of ctDNA testing in ~1000 patients with advanced BC. The trial consists of parallel treatment cohorts (Cohorts A-E) with therapies matched to mutations identified in ctDNA testing. The genomic landscape of ctDNA in advanced BC was prospectively analysed for hotspot PIK3CA,AKT1, HER2 and ESR1 mutations using digital droplet PCR (ddPCR, Bio-Rad), and using an error-corrected 73-gene targeted panel (Guardant360, Guardant Health) prospectively from part-way through the trial, and retrospectively for the remaining patients. Results: Entry into ctDNA testing for Cohorts A-D was closed on 26/Apr/2019, at which time 1044 patients had been registered and 1025 tested with ddPCR. 800 patients had targeted panel ctDNA sequencing (364 prospective, 436 retrospective) (Table 1). Targeted sequencing identified a somatic alteration in 92.9% of patients (743/800). The most frequent mutations were TP53 (44.1%), PIK3CA (34.9%), ESR1 (33.1%), GATA3 (11.0%) and ARID1A (7.8%). ESR1 (33.1%) and KRAS (4.1%) alterations occurred at higher frequency in ctDNA compared to a metastatic tissue sequencing series (q<0.0001, q<0.001, respectively). Five genes had different mutation frequency by tumor subtype. Mutations in ERBB2 were enriched in human epidermal growth factor (HER2) amplified disease (13.5%, q = 0.02), mutations in PIK3CA, ESR1 and GATA3 in hormone receptor positive (HR+) HER2 non-amplified disease (q=0.0001, q<0.0001 and q<0.0001, respectively), and TP53 in triple negative disease (q<0.0001). PIK3CA (22.6%) and ERBB2 (17.6%) frequently had multiple mutations per patient. In HR+ BC, recurrent novel second hotspot mutations occurred in PIK3CA at APOBEC mutagenesis sites. Comparison of ctDNA results with paired tissue sequencing data will be presented. Conclusions: Targeted ctDNA sequencing identified distinct genomic profiles of pre-treated advanced BC. ERBB2 mutations are common in HER2 amplified advanced BC, with recurrent second novel mutations in PIK3CA common in HR+ BC.