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Versatile for a number of clinical uses, liquid biopsy is making headway as a personalized cancer screening device. In a study published in Science Translational Medicine (STM), a highly sensitive liquid biopsy test known as targeted digital sequencing (TARDIS) identified fragments of circulating tumor DNA (ctDNA) as low as 2 parts per 100,000 in the blood of breast cancer patients, showing promise as a tool for detecting residual cancer following treatment. To achieve such high accuracy, “assays like TARDIS are using a personalized patient-specific testing approach. This is in contrast from standardized clinical testing where the same assay is used across multiple patients and samples,” Muhammed Murtaza, MBBS, PhD, the study’s corresponding author, told CLN Stat.

Logistics, analytical validation and quantitative thresholds for such assays do present new challenges for clinical labs that will require further study and development, he acknowledged.

Liquid biopsy application extends to four major clinical uses for identifying mutations: at initial diagnosis; after surgery; after additional therapies; and cancer screening. The latter category “is by far the most difficult application, but it also has the greatest potential to reduce morbidity and mortality from cancer,” according to an STM Focus article, co-authored by highly regarded biomedical scientists Kenneth W. Kinzler, PhD, Bert Vogelstein, MD, and colleagues.

Most longitudinal ctDNA methods fall short in adequately tracking residual disease following treatment in nonmetastatic cancer patients. Responding to this gap, the investigators developed the TARDIS method, a liquid biopsy assay that conducts multiplex analyses of patient-specific tumors. According to Murtaza, an assistant professor and co-director at the Center for Noninvasive Diagnostics at TGen, the method improves sensitivity over other ctDNA assays in three ways:

  • Simultaneously measures a large number of patient-specific somatic founder mutations;
  • Improves reaction efficiency so that a smaller fraction of input DNA is lost during sequencing library preparation;
  • Leverages a combination of fragment size and unique molecular identifiers to computationally suppress background errors.

The researchers used TARDIS to analyze blood samples from 33 breast cancer patients, most of whom presented with stage II disease and invasive ductal carcinoma. Of the 33 patients, 17 had ER+ HER2− cancer, 7 had HER2+ cancer, and 9 had triple negative cancer. Twenty-two ended up receiving neoadjuvant therapy. Compared with patients with residual disease following neoadjuvant therapy, ctDNA concentrations were lower in those who achieved complete pathological response. Overall, the method was 100 times more sensitive in measuring ctDNA than other cancer monitoring blood tests.

“The results from our current study suggest an ability to distinguish breast cancer patients with residual disease after neoadjuvant therapy from those who achieved complete response. If these are validated, TARDIS could be used to monitor treatment response to neoadjuvant therapy in breast cancer and other cancer subtypes,” according to Murtaza.

TARDIS may also be able to help individualize decisions about the extent, duration, and timing of different treatment modalities for cancer patients treated with curative intent, following additional research, he added.

In a Clinical Chemistry interview Kinzler and Vogelstein touched on liquid biopsy as an important diagnostic tool for early cancer detection, and in the STM article discussed with their colleagues the many ways in which this technology could be applied. “With advances in mass spectrometry, we expect that a new generation of protein biomarkers for cancer will soon be available,” they wrote of one approach. Multi-analyte tests that evaluate DNA, proteins, metabolites, and RNA show promise as a highly sensitive tool. “Practically, however, there are challenges associated with using several platforms within a single test while maintaining sufficient specificity, throughput, and cost-effectiveness,” they indicated.

More than half a million patients in the United States die of cancer annually due to late detection and diagnosis of disease. “How to balance the current, intolerable underdiagnosis with potential overdiagnosis is a challenge that further research will hopefully solve. However, a solution to this problem will only be possible if reliable early diagnostic tests for major cancers are developed and used,” they summarized.