Proposal SVD-WG005 (gom/lom)#
- Status: accepted: proposal SVD-WG005 opened for Community Consultation on October 20 (2016), and closed on Dec.31 (2016). Since no major objections were received the SVD-WG decided to accept the proposal.
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).
g.12345678_12345901|gom: compared to the reference (normal situation), the region between nucleotides g.12345678 and 12345901 showed general gain in methylation (increased methylation, hypermethylated)
g.23456789_23456901|lom: compared to the reference (normal situation), the region between nucleotides g.23456789 and 23456901 showed general loss in methylation (reduced methylation, hypomethylated)
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.