Accurate targeted long-read DNA methylation sequencing with TAPS.


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Yibin Liu1,Yibin Liu1,Jingfei Cheng1,Paulina Siejka-Zielinska1,Chunxiao Song1
1University of Oxford

Abstract

Background

5-methylcytosine (5mC) is the most common DNA modifications in human. Aberrant 5mC can be promising predictors for diagnosing cancer. Long-read sequencing, with its capability to characterize genetic variants, has been widely used in cancer research. Although long-read sequencing could potentially allow for epigenetic studies like allele-specific methylation in heterogeneous cancer samples and epigenetic regulation of genomic rearrangements, its application is still limited. Currently several computational methods have been proposed to detect base modifications directly from nanopore sequencing, it remains challenging to accurately determine 5mC.

Method

Here, we proposed nanopore-based TAPS (Tet-assisted pyridine borane sequencing), a novel 5mC detection method which uses the mild reaction to transit 5mC to T, followed by nanopore long-read sequencing.

Results

In contrast to harsh bisulfite treatment, we showed that our reaction can preserve the long DNA molecule, which is vital for nanopore sequencing. Remarkably, our method can accurately measure the methylation status of 5mC for long-read at single-base resolution, which outperforms the mainstream native methylation callers for nanopore sequencing.

Conclusion

We have developed a robust methylation detection method for long reads. This methylation signature, along with the genomic variants’ information, may provide further insight into epigenetic regulation of cancer genome.