Genome-wide detection of cytosine methylation by single molecule real-time sequencing
O. Y. Olivia Tse, Peiyong Jiang, Suk Hang Cheng, Wenlei Peng, Huimin Shang, John Wong, Stephen L. Chan, Liona C. Poon, Tak Yeung Leung, K.C. Allen Chan, Rossa W. K. Chiu, Yuk Ming Dennis Lo
Abstract
Significance Single molecule real-time (SMRT) sequencing theoretically offers the opportunity to directly assess certain base modifications of native DNA molecules without any prior chemical/enzymatic conversions and PCR amplification, using kinetic signals of a DNA polymerase. However, the kinetic signal changes caused by 5mC modification are extremely subtle. Hence, the robust genome-wide measurement of 5mC modification has not been achieved. We enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model, leading to genome-wide 5mC detection. The sensitivity and specificity reached 90% and 94%, with a 99% correlation of overall methylation level with bisulfite sequencing.