I realize that this is an old thread. It is of particular interest to me as a member of this extremely under-analyzed demographic.
There are many comments that I would love to address here, but the original question is the focus of this post.
We at Trio health are using the OMOP CDM and Atlas tool-set for the study of multiple diseases. Where those diseases are not apparently related to persons who have multiple recorded genders or do not map to ‘M’ or ‘F’ we exclude them.
I have not had the chance to design a study related to conditions arising from hormone replacement therapy and/or sexual reassignment surgery although I have thought extensively about how to approach this within the OMOP & OHDSI ecosystem.
On a personal note: I would love to design a study on mental health-related condition improvements after transgender indicated procedures such as Facial Feminization Surgery, Mastectomy, Sexual Reassignment Surgery, and Laryngeal Surgical Treatment.
For a study such as this, I would follow an approach similar to that recommended in the comments by @ericaVoss and @hripcsa . Although I am not thrilled with the THEMIS verbiage and give extra points to @hripcsa for the use of the term real gender
I would use a dedicated CDM and, probably inadvizably, expand the OHDSI Gender concept to include Assigned at birth designations with a combination F-AMAB or M-AFAB (at a minimum) for those that have changed gender prior to the observation_period.
For those that changed gender during the study, I would record this as an observation.