The proposal suggests to extend the HGVS recommendations to allow description of changes in general methylation status. The abbreviation gom to indicate a general gain of methylation (hypermethylation), the abbreviation lom to indicate a general loss of methylation (hypomethylation). The “|” character (“pipe”) is introduced to indicate that not a direct change of the sequence is described but a modification (change of state, here methylation).
The proposal (“lom” and “gom”) follows the current standard to use three-letter abbreviations. The “|” character (“pipe”) is used to indicate a modification of the sequence is reported, a change in state (here methylation), not a change in the sequence itself. Introduction of the “|” facilitates future additions when recommendations would be requested to describe other types of modification, e.g. of protein sequences (phosphorylation). In addition introduction of the “|” facilitates backward compatibility, modifications can be easily stripped from the description. The current proposal does not include recommendations to add a numerical description of the amount of methylation detected. The SVD-WG is interested to learn whether such an extension is desired and, when yes, how to add it.