Design of a liver cancer-specific selector for the analysis of circulating tumor DNA

Circulating tumor DNA (ctDNA) has been frequently investigated to monitor tumor dynamics and measure tumor burden. This non-invasive method concerning ctDNA has been recognized as a promising biomarker. Recently, next generation sequencing has been used in ctDNA detection by researchers. However, those reports have been limited by modest sensitivity, and only a minority of patients with cancer were applicable. Additionally, a limited number of cases of liver cancer have been analyzed. A more precise method is required to be established to evaluate ctDNA noninvasively. In the present study, a novel method to design a liver cancer-associated chip region (spanning 211 kb, containing 159 genes) was performed with high specificity using International Cancer Genome Consortium datasets. Following evaluation with datasets from The Cancer Genome Atlas and data from 3 patients with liver cancer, the selected regions were demonstrated to be beneficial to locate specific somatic mutations associated with liver cancer therapy and to monitor cancer dynamics in the plasma samples of the patients. In addition to establishing performance benchmarks supporting direct clinical use, the chip designed and the high-resolution sequencing analyses pipeline would allow the development a set of patient specific markers that could monitor the process of cancer with high accuracy and low cost. Furthermore, the present study is essential to understanding the dynamics and providing insight into the basic mechanisms of liver cancer.