Base Modification Detection with Pacific BioSciences

After having launched the new C2 chemistry for PacBio RS sequencing with longer read length it has been quiet for a while with Pacific BioSciences. However, a few days ago they have again attracted attention by launching a new analysis software that indicates base-modifications in the sequencing data. And from what I hear and read about these techniques, the epigenetics market could really be a great success story for Pacific Biosciences.

As PacBio’s SMRT sequencing is observing the DNA polymerization in real time it allows not only to decode the sequence, but also to study kinetic characteristics of the process. The kinetics of a base incorporation is characteristically changed by the presence of a modified base in the template strand and therefore can be used to distinguish between different base modifications. Different modifications result in different signatures (or fingerprints) that vary in signal magnitude and the length of the region over which the kinetics are altered.

I think that the study of base-modifications with PacBio RS has several advantages compared to experiments like methyl-Seq or bisulfite sequencing. On the one hand side PacBio RS sequencing is a direct detection, where no enzymatic restriction or bisulfite conversion has to be applied upfront. On the other hand – and this is the most important advantage for me – the PacBio RS system allows to distinguish a wide spectrum of base modifications, which has not been possible so far.

Unfortunately, the recently launched software is not yet ready to distinguish the different types of modifications, it only flags positions where modifications are present. However the company has shown proof of principle data and has already stated that the information to discriminate between modifications will be incorporated into future releases of the software. Moreover a Technical Note is provided from the company regarding their motif identification tool for bacterial methylomes.