TEST:

Oncomine™ Breast cfDNA Assay

EV-DNA extraction and sequencing in old serum samples of patients with BC is feasible and has the potential to address clinically relevant questions in longitudinal studies.

These methods were the Oncomine Breast cell free DNA (cfDNA) NGS panel, the LINE-1 sequencing assay mFAST-SeqS, low pass shallow whole genome sequencing (WGS) and the genome-wide methylation profiling assay MeD-Seq.Results and Discussions In total 40 patients with triple negative or luminal B breast cancer were included and cell free DNA (cfDNA) from plasma before the start of NAC was analyzed with the four assays. We detected ctDNA in 3/24 (12.5%) patients with Oncomine, 5/40 (12.5%) with mFast-SeqS, 3/40 (7.7%) with low pass shallow WGS and 23/40 with MeD-Seq (57.5%).Conclusion In conclusion, we demonstrated that tumor agnostic methods, in particular MeD-Seq, can detect ctDNA in part of the patients with early breast cancer, but further optimisation is needed to reach the potential currently demonstrated by tumor-informed.

P2; Changes in ctDNA can occur rapidly and reflect changes in patients' clinical tumour responses (NCT02681523).

ctDNA was detected at baseline in almost half of the patients in the SONIA study. Compared to baseline, a decreasing number of patients had an elevation of the VAF of the tracked mutation and an increasing number of patients showed ctDNA clearance from 2 weeks to 3 months after start of treatment. There was no difference between the two arms observed regarding ctDNA dynamics.

The most prevalent mutant genes were TP53 (68.3%) and KRAS (53.5%), while the PIK3CA (39.4%), AKT1 (45.9%), and ERBB2 (17.1%) mutations constituted biomarkers for FDA-approved therapeutics. Our study showed that tumor tissue should be the source of actionable mutation detection for early breast cancers, considering that the concordance rate between tumor and liquid biopsy was only one-quarter.

Conclusion The application of NGS panels on cfDNA allowed the molecular characterization of patients with metastatic breast cancer in combination with the study of tumor tissue samples in 22 out of 26 (85%) cases. Despite the limitation of the low number of cases in our series, this work suggests that the detection of gene mutations in cfDNA correlates with cfDNA concentration.

Of the 117 patients enrolled, there were 18 patients receiving adjuvant T-DM1 and 99 receiving trastuzumab (N = 70) or trastuzumab plus pertuzumab (N = 29). The presence of ctDNA in patients with early-stage Her2-positive breast cancer after NAT was independently associated with disease recurrence; however, ctDNA(+) after NAT became inconsiderable when patients were treated with adjuvant T-DM1 therapy, which represented ctDNA(+) as an important factor determining adjuvant anti-Her2 regimen.

From breast cancer actionability, PIK3CA (39.4%) mutation is a biomarker for the FDA-approved PI3Ka inhibitor such as alpelisib, AKT1 (45.9%) mutation for agents such as capivasertib (AZD5363) and ipatasertib, and ERBB2 mutation for tyrosine kinase inhibitor such as neratinib. Table 1. Distributions of variants from common targeted genes (n=6) from cfDNA and TMO comprehensive assay.

This combined analysis of CTCs and ctDNA may offer a new approach for monitoring of disease progression and to direct therapy in patients with advanced MBC, at a time when they are coming towards the end of other treatment options.

In advanced breast cancer (BC), hormone receptor (HR) positive, HER2 negative BC cases harboring PIK3CA actionable mutations (40%) can be treated with combination of PI3K inhibitor Alpelisib and Fulvestran...DNA EVs mutational profiles were consistent with the CTCs ones, suggesting that mutated EVs are released by CTCs. Conclusion This study generated proofs of concept data on molecular content of the different circulating markers and put in evidence a new CTCs sub-population to be considered for a more comprehensive mutational characterization of the disease.

We were able detect ctDNA across the breast cancer spectrum, notably in MBC where variants in ESR1, TP53, and PIK3CA predicted poor overall survival. The assay could be used to monitor emergence of resistance mutations such as in ESR1 that herald resistance to aromatase inhibitors to tailor adjuvant therapies. However, we suggest caution is needed when interpreting results from a single plasma sample as variants were also detected in a small proportion of HCs.