Study Evaluates Clinical Utility of Novel Liquid Biopsy-Breast Cancer Methylation Prototype Assay

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A novel, automated liquid biopsy test—the Liquid Biopsy for Breast Cancer Methylation assay—may be effective at predicting early disease progression and potential survival outcomes in patients with metastatic breast cancer after as little as 1 month of treatment, according to a study published by Visvanathan et al in Clinical Cancer Research. Researchers explained that although the novel test is currently just a prototype, it was able to identify the presence of cancer DNA in up to nine genes commonly associated with breast cancer after analyzing blood samples from patients actively undergoing breast cancer treatment.


Methylation, a type of chemical tag associated with cancer development and progression, is known for its ability to turn off tumor suppressor genes.

The researchers stressed that predictive clinical biomarkers to identify early disease progression are needed for patients with metastatic breast cancer given how heterogeneous the condition is. These biomarkers could help physicians minimize the negative impacts of drug combinations on patients’ quality of life by optimizing the use of available and effective therapies.

Study Methods and Results

In the new study, the researchers evaluated the novel Liquid Biopsy for Breast Cancer Methylation assay using plasma samples collected from 144 patients with a median age of 56 years who had metastatic breast cancer prior to treatment and at 4 and 8 weeks into treatment.

The novel Liquid Biopsy for Breast Cancer Methylation assay was compatible with a commercially available molecular testing platform called GeneXpert and was capable of detecting methylation in the AKR1B1, TM6SF1, ZNF671, TMEFF2, COL6A2, HIST1H3C, RASGRF2, HOXB4, and RASSF1 genes altered in the four subtypes of breast cancers in under 5 hours. The assay required less than 15 minutes of hands-on time by a laboratory technician.

Further, the researchers also looked for methylation in the ZNF671 gene—associated with estrogen receptor–negative breast cancer.

The researchers used methylation levels measured after 4 weeks of treatment to develop the new model to predict the risk of early disease progression in patients with metastatic breast cancer.

After a follow-up of 6 years, the researchers discovered that patients with high cumulative methylation after 4 weeks had a median progression-free survival of 2.88 months and a median overall survival of 14.5 months vs 6.66 months and 22.4 months, respectively, for those with low methylation.

Additionally, the researchers sought to better understand the association between cumulative methylation and disease status at the first cancer restaging, approximately 3 months later. In 77% of patients, cumulative methylation levels decreased in the first 4 weeks and then remained stable until the first restaging. In 18% of patients with stable disease and 37% of patients with progressive disease, an increase in cumulative methylation was observed from baseline to 4 weeks. There was no further increase in cumulative methylation among those who responded to treatment—with levels remaining stable from 4 to 8 weeks.

The researchers noted that high vs low cumulative methylation at 4 weeks was associated with progressive disease at first restaging. The association between week 4 cumulative methylation levels at first restaging and progressive disease remained significant despite the presence of other circulating markers used to monitor disease progression such as circulating tumor cells.

“It looks promising that we can detect methylation in the first 4 weeks of treatment,” highlighted co–lead study author Kala Visvanathan, MD, MHS, Professor of Epidemiology in the Division of Cancer Epidemiology at the School of Medicine, Director of the Cancer Epidemiology Track in the Department of Epidemiology at the Bloomberg School of Public Health, and Director of the Clinical Cancer Genetics and Prevention Service at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University. “Currently, we wait until we see symptomatic or clinical changes, usually within 3 months, before adjusting treatments. If we could detect changes earlier, we could adjust treatments earlier—if necessary—with the goal of achieving better clinical outcomes and prolonging survival,” she underscored.


“To our knowledge, this is the first methylation-based prediction model focused on early disease progression in patients with metastatic breast cancer,” emphasized co–senior study author Saraswati Sukumar, PhD, Professor of Oncology in the Division of Women’s Malignancies and Professor of Pathology at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University.

“The model was robust when tested under many different statistical assumptions,” added co–lead study author Leslie Cope, PhD, Associate Professor of Oncology in the Division of Oncology–Quantitative Sciences and Co–Director of the Experimental and Computational Genomics Core at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University.

In future studies, the researchers hope to examine patterns of methylation seen each week after starting treatment to identify the optimum time to measure cumulative methylation, and to validate and refine the model in similar patient populations as well as in patients with early-stage breast cancer.          

Disclosure: The research in this study was supported by a grant from the Department of Defense and in part by a research agreement from Cepheid, as well as by funding from The Breast Cancer Research Foundation and Susan G. Komen for the Translational Breast Cancer Research Consortium. For full disclosures of the study authors, visit

The content in this post has not been reviewed by the American Society of Clinical Oncology, Inc. (ASCO®) and does not necessarily reflect the ideas and opinions of ASCO®.