These are my personal opinions, based on research, given the information we have now.
These may change as we get more information and depending on whether breeder culture changes. They aren't simplistic, but the dog genome has over 19,000 genes and over 2.5 billion base pairs so genetics aren't simplistic either.
Choose your own path, of course. I won't judge.
- Do not cull siblings or parents of affected dogs. Do not cull dogs with risky haplotypes but do not breed them early. Do not breed without testing. Do not breed affected dogs.
- Select for health, temperament and structure as usual.
- Use pedigree information for what you know of the dogs in the recent pedigree, their health temperament and structure. Assume many close relatives with similar traits raises the possibility of those traits being in the dog, whether good or bad.
- Breed gradually or more aggressively for more rare and fewer common alleles for now, based on your comfort level. The goal will be to have fewer and fewer rare and common alleles in the population as the alleles get better distributed.
- Breed for lower IR than parents, lower than 0 as a goal, and balance lowest IR value with best type when selecting puppies, depending on your priorities.
- With SA risk but no AD risk, breed for lowest IR to a dog with low AD risk.
- With AD risk but no SA risk, breed for higher IR to a dog with no SA risk. Breed for lower IR in subsequent generations as AD risk is lowered.
- With both AD and SA risk, breed to a genetic outlier. Look for dogs with over 10 rare and under 18 common alleles and over 2007 in DLA Class II haplotypes.
- If your dog has the DLA extended haplotype 1003/2001 (frequency of 15.7%), it carries slightly higher risks of AD and SA, so check carefully for autoimmune disease in pedigree and breed as above.
- If your dog has the DLA extended haplotype 1006/2004 (frequency of 2.7%) and probably 1006/2007 (frequency of 1.6%), it has 2.8 times the risk for SA. Breed for lowest IR to a dog with low AD risk, preferably with haplotypes over 2007, and/or to a dog with over 10 rare and under 18 common alleles. Test and select best offspring without it.
- If your dog has a DLA extended haplotype of 1007/2006 (frequency of 3.2%), it has 2.4 times the risk for Addison's. Breed for higher IR to a dog with low SA risk and preferably haplotypes over 2007 and/or over 10 rare and under 18 common alleles. Test and select best offspring without it. Breed for lower IR in subsequent generations.