Abstract 5335: A highly efficient targeted bisulfite sequencing method for accurate DNA methylation profiling

Background DNA methylation plays an important role in gene regulation. Bisulfite sequencing (BS), in which unmethylated cytosines are converted to uracil while methylated cytosines remain intact, is considered as the gold standard for DNA methylation detection with single nucleotide resolution. Due to the high cost of whole genome BS and the low throughput of amplicon BS, there remains the need for new targeted bisulfite sequencing methods with high efficiency and flexibility. Results We developed a targeted bisulfite sequencing method, by incorporating single primer enrichment (SPE) and molecular barcoding (UMI) technology. This enables flexible and scalable targeted DNA methylation analysis with high efficiency. We first studied the ability of our assay to detect CpG methylation at various levels in reference materials. We also evaluated its utility in profiling CpG methylation in different cell line DNA, and compared the results with published data from alternative technologies (WBS, RRBS and microarray). Conclusions We demonstrated the successful implementation of SPE and UMI technology on bisulfite converted DNA with high enrichment specificity and low bias. We showed that our method accurately detected CpG methylation at different levels, in concordance with expected titration mixture or published datasets. Comparing to reported amplicon BS, our technology enables much higher multiplexing scale and much simpler workflow. Comparing to probe capture based enrichment, our technology enables much lower DNA input, much higher sequencing efficiency (on-target) and shorter turnaround time. Citation Format: Quan Peng, Daniel Kim, Mohammad Nezami Ranjbar, Sascha Strauss, Scott Winter, Yexun Wang. A highly efficient targeted bisulfite sequencing method for accurate DNA methylation profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5335.