New ‘liquid biopsy’ blood test improves breast cancer diagnostics

A new type of blood test for breast cancer could help avoid thousands of unnecessary surgeries and otherwise precisely monitor disease progression, according to a study led by the Translational Genomics Research Institute (TGen), Mayo Clinic in Arizona and the Biodesign Institute at Arizona State University.

TGen is an affiliate of City of Hope, which contributed to this study along with Cambridge University.

Published in the premier journal Science Translational Medicine, the study suggests that the test called TARDIS — TARgeted DIgital Sequencing — is as much as 100 times more sensitive than other blood-based cancer monitoring tests.

TARDIS is a “liquid biopsy” that specifically identifies and quantifies small fragments of cancer DNA circulating in the patient’s bloodstream, known as circulating tumor DNA (ctDNA). According to the study, TARDIS detected ctDNA in as low as 2 parts per 100,000 in patient blood.

“By precisely measuring ctDNA, this test can detect the presence of residual cancer, and inform physicians if cancer has been successfully eradicated by treatment,” said Muhammed Murtaza, assistant professor and co-director of TGen’s Center for Noninvasive Diagnostics. He also holds a joint appointment on the Research Faculty at Mayo Clinic Arizona and is one of the study’s senior authors. 

“This data represents an exciting strategy to improve the sensitivities of liquid biopsies, which have been challenging for breast cancer,” said Karen Anderson, a researcher at the Biodesign Institute, a medical oncologist at Mayo Clinic Arizona and one of the study’s contributing authors. “This work represents highly collaborative efforts across multiple institutions, and with the generosity and foresight of our patients who have contributed to this study.”

Anderson actively recruits patients and conducts clinical cancer trials. Her focus areas include postoperative therapies to reduce breast cancer relapse risk; treatments for metastatic breast cancer, especially targeted therapies and immunotherapies; genomic factors that may guide treatment decisions in breast cancer, new diagnostics for early detection for a broad range of cancer indications and new vaccines for cancers.

As Murtaza explained, TARDIS is precise enough to tell if early stage breast cancer patients have responded well to pre-operative drug therapy. It is more sensitive than the current method of determining response to drug therapy using imaging.

“This has enormous implications for women with breast cancer. This test could help plan the timing and extent of surgical resection and radiation therapy after patients have received pre-operative therapy,” said Barbara A. Pockaj, a surgical oncologist who specializes in breast and melanoma cancer patients at Mayo Clinic in Arizona and is the study’s other senior author. Pockaj is the Michael M. Eisenberg Professor of Surgery and the chair of the Breast Cancer Interest Group, a collaboration between researchers at Mayo, TGen and ASU.

Unlike traditional biopsies, which only produce results from one place at one time, liquid biopsies use a simple blood draw, and so could safely be performed repeatedly, as often as needed, to detect a patient’s disease status.

This study was performed in collaboration with Carlos Caldas, professor of cancer medicine at the University of Cambridge and director of the Breast Cancer Programme at Cambridge Cancer Centre.

“TARDIS is a game changer for response monitoring and residual disease detection in early breast cancer treated with curative intent. The sensitivity and specificity of patient-specific TARDIS panels will allow us to tell very early, probably after one cycle, whether neo-adjuvant (before surgery) therapy is working and will also enable detecting micro-metastatic disease and risk-adapted treatment after completing neo-adjuvant therapy,” said Caldas, who also is senior group leader at CRUK Cambridge Institute and one of the study’s contributing authors.

Following further clinical testing and trials, TARDIS could someday be routinely used for monitoring patients during cancer treatment and discovering when patients are essentially cured and cancer-free.

“The results of these tests could be used to individualize cancer therapy avoiding overtreatment in some cases and undertreatment in others,” Murtaza said. “The central premise of our research is whether we can develop a blood test that can tell patients who have been completely cured apart from patients who have residual disease. We wondered whether we can see clearance of ctDNA from blood in patients who respond well to pre-surgical treatment.”

Current tests and imaging lack the sensitivity needed to make this determination.

“Fragments of ctDNA shed into blood by tumors carry the same cancer-specific mutations as the tumor cells, giving us a way to measure the tumor,” said Bradon McDonald, a computational scientist in Murtaza’s lab and the study’s first author.

“The problem is that ctDNA levels can be so low in nonmetastatic cancer patients, there are often just not enough fragments of ctDNA in a single blood sample to reliably detect any one mutation. This is especially true in the residual disease setting, when there is no obvious tumor left during or after treatment,” McDonald said. “So, instead of focusing on a single mutation from every patient, we decided to integrate the results of dozens of mutations from each patient.”

The study results suggest that tumor-guided personalized ctDNA analysis, using TARDIS, is a promising approach to identifying patients with pathological complete response following presurgical drug therapy.

“Together with imaging and tissue-based predictive biomarkers, ctDNA could become a useful diagnostic test to determine individualized decisions about additional treatment,” Murtaza said.

Pockaj affirmed: “We are excited that TARDIS has the potential to really individualize clinical management of patients with nonmetastatic cancer.”

Thomas Slavin, assistant clinical professor at City of Hope National Medical Center, and a contributing author of the study, noted that “reliably identifying, often multiple, circulating tumor mutations in the plasma of patients with nonmetastatic breast cancer also holds promise that ctDNA may one day be a great tool for early breast cancer detection.”

TGen is now focused on evaluating the best partners to work with to automate and scale TARDIS, so it can be made available broadly to benefit patients in need.

Patient samples for this study were collected at Mayo Clinic, at Addenbrookes Hospital at the University of Cambridge and at City of Hope.

This research was funded by the National Cancer Institute, Mayo Clinic Center for Individualized Medicine, the V Foundation for Cancer Research, Science Foundation Arizona, the Ben and Catherine Ivy Foundation, SmartPractice, City of Hope and TGen.

Written by Steve Yozwiak, TGen senior science writer, 602-343-8704, syozwiak@tgen.org