A method of targeted digital sequencing (TARDIS) has been developed by a group of scientists led by Brandon McDonald from the Center for Noninvasive Diagnostics, Translational Genomics Research Institute (TGen).
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This new liquid biopsy test is set to improve the analytical sensitivity and degree of precision for circulating tumor (ctDNA) analysis by maximizing the information gleaned from the interrogation of DNA fragments derived from tumors in limited amounts of plasma DNA.
A research group achieved this by leveraging both deep sequencing of patient’s mutations and reducing the amount of template DNA lost during the preparation of DNA libraries. This technique may be particularly useful, as DNA is shed by breast cancer cells into the blood in minute quantities.
This form of tumor DNA analysis can provide a non-invasive means of reliably identifying which cancers are in remission and which are not.
Digital Sequencing from Liquid Biopsies
TARDIS, or targeted digital sequencing, could transform the way early-stage breast cancer is treated, providing sensitivity up to 100-times greater than similar liquid biopsy tests.
As it stands, the current means of tracking breast cancer cells in the blood is most successful in advanced-stage cancer patients. In this stage, cancer cells shed copious amounts of DNA as they circulate through the body during metastasis, in which new tumors are seeded at distal sites such as the bone, liver, and brain.
The research team, which included scientists at Arizona State University and the Cancer Research UK Cambridge Institute, developed an enhanced means of picking up the relatively scarce cancer DNA in patients with early-stage cancer.
To do so, the team sequenced biopsies from 33 women with stage 1, 2, or 3 breast cancer who had received chemotherapy or drug-based treatment before tumor removal. To determine the identity of mutations distinguishable only in cancer cells, scientists compared the DNA sequences of normal cells.
This comparison revealed ‘founder mutations.’ Founder mutations are genetic alterations found at high frequency in a group of distinct cells, in which the mutation can be traced back to one or more individuals that gave rise to the group.
The average number of founder mutations was 66 for each patient. By combining the founding mutations to existing personalized assays, the group could then detect signs of breast cancer DNA in blood samples.
The combination of several mutations was found to be more sensitive relative to the implementation of a single or small number of mutations, which are derived from an already small number of tumor DNA fragments.
Combining TARDIS with Amplification Methods to Improve Results
The team combined this detection method with a new strategy of amplification. This amplification preserves the size of the DNA fragments obtained from patients by attaching unique molecular identifiers that enhance detection.
TARDIS is unique in that it takes advantage of PCR-based methods, which minimize the loss of template DNA, and ligation-based methods, which minimizes errors in sequencing and enriches the target region.
Typically, sequencing results in the loss of the majority of starting DNA material. In the context of ctDNA analysis, this is a significant problem, as plasma DNA concentrations are low.
A Move Towards Personalized Medicine
This study represents an important advance in the field of breast cancer detection and treatment. This technology may be able to identify individuals with early-stage breast cancer who may still have undetected residual cancer in the body.
The direction of therapy is therefore guided, as the assay enables highly personalized means of detection and subsequent monitoring. Most notably, TARDIS avoids unnecessary operational intervention as a simple non-invasive blood test, confirming whether or not residual tumor DNA remains.
Conversely, in patients with residual disease, TARDIS facilitates the determination of the next most effective therapy -- delivering a degree of personalization that cannot be afforded otherwise. As such, this novel detection method makes an important advancement towards the ultimate goal of personalized medicine.
Muhammed Murtaza, co-director at TGen, Notes that TARDIS must be tested in larger groups of patients and undergo validation in clinical and randomized trials before finding its place in the clinical setting.
Also, future studies may involve treatment design to determine whether the magnitude of decreased ctDNA concentration during pre-surgical treatment (chemotherapy and other medications) can be used to identify the therapeutic benefit of treatment options.
By using blood-based residual disease testing, it is hoped that under- and over-treatment of patients with early-stage cancer can be avoided. This could set an encouraging precedent for the use of liquid biopsy in the detection of other forms of cancer -- a new frontier in cancer therapy.
The study comes from the Translational Genomics Research Institute (TGen) and Mayo Clinic (Arizona) campus and was published in the journal Science Translational Medicine on August 7, 2019.
- Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer, Bradon R. McDonald, Tania Contente-Cuomo, Stephen-John Sammut, Ahuva Odenheimer-Bergman, Brenda Ernst, Nieves Perdigones, Suet-Feung Chin, Maria Farooq, Rosa Mejia, Patricia A. Cronin, Karen S. Anderson, Heidi E. Kosiorek, Donald W. Northfelt, Ann E. McCullough, Bhavika K. Patel, Jeffrey N. Weitzel, Thomas P. Slavin, Carlos Caldas, Barbara A. Pockaj, and Muhammed Murtaza1, Science Translational Medicine 07 Aug 2019: Vol. 11, Issue 504, eaax7392 DOI:10.1126/scitranslmed.aax7392, https://stm.sciencemag.org/content/11/504/eaax7392