Personalized Detection of Circulating Tumor DNA Antedates Breast Cancer Metastatic Recurrence

Abstract

Purpose: Up to 30% of patients with breast cancer relapse after primary treatment. There are no sensitive and reliable tests to monitor these patients and detect distant metastases before overt recurrence. Here, we demonstrate the use of personalized circulating tumor DNA (ctDNA) profiling for detection of recurrence in breast cancer.Experimental Design: Forty-nine primary patients with breast cancer were recruited following surgery and adjuvant therapy. Plasma samples (n ¼ 208) were collected every 6 months for up to 4 years. Personalized assays targeting 16 variants selected from primary tumor whole-exome data were tested in serial plasma for the presence of ctDNA by ultradeep sequencing (average >100,000X).Results: Plasma ctDNA was detected ahead of clinical or radiologic relapse in 16 of the 18 relapsed patients (sensitivity of 89%); metastatic relapse was predicted with a lead time of up to 2 years (median, 8.9 months; range, 0.5-24.0 months). None of the 31 nonrelapsing patients were ctDNA-positive at any time point across 156 plasma samples (specificity of 100%). Of the two relapsed patients who were not detected in the study, the first had only a local recurrence, whereas the second patient had bone recurrence and had completed chemotherapy just 13 days prior to blood sampling.Conclusions: This study demonstrates that patientspecific ctDNA analysis can be a sensitive and specific approach for disease surveillance for patients with breast cancer. More importantly, earlier detection of up to 2 years provides a possible window for therapeutic intervention. Personalized profiling detects rising ctDNA ahead of clinical relapse. A-E, Plasma levels of ctDNA across serial plasma time points for five patients with breast cancer (one per panel). Mean VAFs are denoted by a dark blue circle, and solid lines represent the average VAF profile over time. The lead time is calculated as the time interval between clinical relapse (red triangle) and molecular relapse (blue triangle). CA 15-3 levels are graphed over time (teal circle), and the baseline levels (32 U/mL) are marked in light blue. F, Summary of percent VAF and number of targets detected at molecular and clinical relapse for all ctDNA-positive samples. Data are from 13 relapsed patients, excluding three patients with only one plasma time point. Coombes et al.

A novel hotspot specific isothermal amplification method for detection of the common PIK3CA p.H1047R breast cancer mutation

“…Numerous NGS technologies such as BEAMing and Safe-SeqS have been used to detect known breast cancer mutations using ctDNA with sensitivity higher than 99% 30 . Our own studies have shown for primary patients that recurred, patient specific ctDNA profiling detected molecular relapse up to 2 years ahead of clinical relapse with 89% sensitivity and 100% specificity 31 . However, despite its high sensitivity and specificity, NGS platforms are still costly and require specialist time for data analysis and experimentation.…”

“…DNA was extracted from a healthy control tissue core as a WT control (H1047R negative) and from a tumour patient core (H1047R heterozygous sample). Patient samples used in this study were from our recent paper Coombes et al 31 with the trial protocol approved by the Riverside Research Ethics Committee REC:13/ LO/115; IRAS:126462. Methods were carried out in accordance with the relevant guidelines and regulations.…”

Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients

“…26,27 Currently, the clinical utility of ctDNA is only approved in metastatic non-small-cell lung cancer (NSCLC) by FDA as a companion diagnostic, 28,29 while studies on many other cancers have also shown good prospects. [30][31][32][33][34][35][36] The fact that even little variability in process and analysis will result in completely different results restrains the further clinical utility of ctDNA. 37 In order to solve these problems, some projects, such as the European CANCER-ID, European Liquid Biopsy Academy (ELBA) and European Liquid Biopsy Society (ELBS) networks or the US-based BloodPAC, have been initiated.…”

Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer

“…Recent studies have shown that liquid biopsies can detect minimal residual disease (MRD) in multiple cancer types (8)(9)(10)(11)(12) including breast (13)(14)(15), by tracking tumor mutations in circulating cell-free DNA (cfDNA). However, in these previous studies, clinical sensitivity has been limited at the early postoperative time points, at which treatment decisions are typically made, and the lead time prior to clinical presentation of overt metastatic disease has been relatively short.…”