Genomewide detection of cytosine methylation by single molecule real-time sequencing

5-methylcytosine (5mC) is an important type of epigenetic modification. In this study, 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. This methodology has provided a system for simultaneous genome-wide genetic and epigenetic analyses.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 2 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001006875	In this study, 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.	NextSeq 500 Sequel II	42

Publications	Citations
Genome-wide detection of cytosine methylation by single molecule real-time sequencing. Tse OYO, Jiang P, Cheng SH, Peng W, Shang H, Wong J, Chan SL, Poon LCY, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Proc Natl Acad Sci U S A 118: 2021 e2019768118	43
Epigenetic analysis of cell-free DNA by fragmentomic profiling. Zhou Q, Kang G, Jiang P, Qiao R, Lam WKJ, Yu SCY, Ma ML, Ji L, Cheng SH, Gai W, Peng W, Shang H, Chan RWY, Chan SL, Wong GLH, Hiraki LT, Volpi S, Wong VWS, Wong J, Chiu RWK, Chan KCA, Lo YMD. Proc Natl Acad Sci U S A 119: 2022 e2209852119	26