Our understanding of mutations in noncoding DNA is still nascent across most cancer types. Similarly, the potential clinical utility of noncoding DNA in cancer liquid biopsy assays remains mostly unexplored. Here, we identify high-frequency noncoding mutation hotspots in whole genomes from hundreds of gastrointestinal tumors and show that these mutations can be detected in liquid biopsy samples from cancer patients. We demonstrate how profiling of noncoding mutation hotspots can significantly increase the accuracy of ctDNA burden estimation, with minimal impact on sequencing cost, when paired with existing targeted cfDNA assays. Our results suggest that targeted NGS liquid biopsy assays should target both protein-coding and noncoding mutations when estimation and monitoring of ctDNA burden is a key clinical endpoint.

Citation Format: Guo Yu, Zhong Wee Poh, Guanhua Zhu, Iain Tan, Sarah Ng, Patrick Tan, Anders Skanderup. Monitoring of ctDNA burden from noncoding DNA [abstract]. In: Proceedings of the AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; Jan 9-12, 2020; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_1):Abstract nr 44.