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A DNA sample-preparation and computational analysis pipeline called TEC-Seq may have broken new ground in detecting early stage cancers. Researchers at Aarhus University in Denmark and Johns Hopkins University in Baltimore used this deep sequencing method to detect stage I and II cancers by distinguishing between tiny amounts of circulating tumor DNA (ctDNA) from total DNA in blood.
Study findings appeared in Science Translational Medicine.“This study shows that identifying cancer early using DNA changes in the blood is feasible and that our high accuracy sequencing method is a promising approach to achieve this goal,” said senior and corresponding author Victor Velculescu, MD, PhD, professor of oncology and pathology at the Johns Hopkins Kimmel Cancer Center, in a statement.
As cells die as part of the normal turnover process, pieces of DNA release into the bloodstream as circulating, cell-free DNA. “In an individual with cancer, a portion of this circulating, cell-free DNA is tumor-derived and termed ctDNA,” first author Jillian Phallen, a graduate student at the Johns Hopkins Kimmel Cancer Center, explained to CLN Stat.
TEC-Seq, known as “targeted error correction sequencing,” reads each DNA chemical code at least 30,000 times to ensure accuracy in detecting molecular signatures of cancer in cell-free DNA.
Through this method, researchers can select and further analyze regions of DNA that correspond to gene mutations known to drive cancer, Phallen said. “These regions are assessed to identify mutations present in multiple copies of the cell free DNA. Mutations meeting these criteria are then evaluated to distinguish between cancer-related mutations, blood cell alterations, and germline alterations,” she said.
Obtaining blood samples from 200 patients in various stages of colorectal, breast, lung, or ovarian cancer, investigators used the TEC-Seq method to look for mutations within 58 cancer driver genes. From a pool of 138 stage I and II cancers, TEC-Seq identified 86, or more than 60% of these diseases.
Among the 42 colon cancer patients, the test was particularly effective in finding advanced stage cancers, although it was able to predict disease in 50% and 89% of the patients with stage I and II cancers, respectively.
In other results, TEC-Seq detected stage I and II disease in 45% and 72% of the 71 study participants with lung cancer, and a majority of the cases of advanced stage disease. In ovarian cancer patients, the results for early stage cancers were even more promising: 67% and 75% of the stage I and II cases respectively were identified among 42 patients.
For 45 breast cancer patients, 59% of stage II cancers were identified, along with 67% of the stage I cases, and 46% of the stage III cases.
Overall, the test was most successful at detecting colorectal and ovarian cancers, Phallen said. “We envision that this method will ultimately provide a pancancer approach for screening of patients with common cancers,”she said.
In a separate analysis of cancer tumors taken from half of the participants, investigators found that more than 80% had mutations that lined up with genetic changes found in blood samples.
The test also yielded promising results in a cohort of healthy study participants. In the past, technical challenges had led to false positive changes in normal DNA during analysis of mutations in the circulation, Phallen said.
“TEC-Seq was designed to overcome these technical challenges. Using this approach we did not identify any cancer-related mutations in any of the 44 healthy individuals in our study. This is significant because large-scale implementation of a liquid biopsy test for screening will require an extremely low false-positive rate to prevent overdiagnosis,” she said.