epigenetic genotype (epitype?)

[nlwashington]

At some point we'll need to consider a person's epigenetic factors related to disease susceptibility, etc. This could include methylation patterns, histone modifications, etc.

Should this be another subclass of "genotype" (GENO:0000536) and/or part of the "intrinsic genotype" (GENO:0000000) ? There are some relevant classes in SO related to these kinds of modifications: http://sequenceontology.org/browser/current_svn/term/SO:0001720. We should think about how we might annotate / combine these together to create this part of an organisms' genotype. Or for a different view, perhaps the epigenetic type isn't even part of the genotype, but rather is outside of an organisms' genotype (epitype, anyone?)...considering that epigenetic markers may differ based on cell-type.

For some background reading: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3034103/ http://en.wikipedia.org/wiki/Epigenetics

Perhaps we can consider using some cancer variations and changes in their methylation pattern as a use case, as described here: http://en.wikipedia.org/wiki/Epigenetics#DNA_repair_epigenetics_in_cancer