selewis
commented
9 years ago I tend to agree - i.e. epigenetic isn't part of the genotype.
For example, methylation does indeed involve covalent links of methyl groups to the DNA and is inherited, but it's not part of what's encoded. Rather more like barnacles that is dragged along with the ship after attachment.
-S
On Wed, Apr 8, 2015 at 12:38 PM, Nicole Washington <notifications@github.com
wrote:
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
— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/GENO-ontology/issues/15.
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