Certain families in the past seem to have gone out of their way to keep certain diseases amongst themselves - selfish swines.
As your answer is very unspecific, I would say you should breed your daughters with just about any auld sod that is in the radar to avoid in-breeding of any type.
If you are Royal, may I specifically nominate bucks from a sink / non-pedigree estate? A search of the Census should provide reliable information?
Gather up all your genes and stick them in the microwave for a 2 minute nuking.
First spend about 7 years studying DNA and if that doesn't put you off, you will need to specialise in genetic engineering which is probably another 7 years before you have enough nous to be able to do what you want. Then you need about 4 million quid for equipment and away you go.
You can limit some inherited diseases by preventing the women in your family from having children so that they won't pass on any dormant genes that are carried on the sex chromosmes.