Matched Oxford Nanopore Technologies and Bisulfite Sequencing of the GM24385 Cell Line

One of the most widespread genomic modifications is 5-methylcytosine (5mC), which most frequently occurs at CpG dinucleotides. Compared to whole-genome bisulfite sequencing, the traditional method of 5mC detection, nanopore technology can offer many advantages such as simplicity of sample prep and subsequent analysis.

In order to demonstrate the utility and convenience of Oxford Nanopore Technologies’ sequencing platform for performing detection and analysis of 5mC, we have sequenced the HG002 Genome in a Bottle Sample GM24385 with both traditional bisulfite sequencing and using nanopore sequencing. Both technologies, old and new, were applied to the same sample from a single DNA extraction.

Bisulfite sequencing

Bisulfite sequencing was performed by a commercial provider and processed with the commonly used bismark package to obtain the proportion of reads displaying methylation at CpG sites throughout the whole genome. 

Nanopore sequencing

Nanopore sequencing was performed using the same sample of GM24385 material sent for bisulfite sequencing. Sequencing was performed on the MinION platform, across multiple flowcells, as part of ongoing platform development activities. The sequencing was not performed explicitly for the analysis presented here; we are making available all sequencing runs undertaken with this sample for the benefit of the community.

Data Access

Data is available as part of the Registry of Open Data on AWS: https://registry.opendata.aws/ont-open-data/. This dataset can be accessed through the S3 prefix:

s3://ont-open-data/gm24385_mod_2021.09/

Further Information

https://labs.epi2me.io/gm24385-5mc/

https://labs.epi2me.io/gm24385-5mc-remora