Unwanted genes are a fact of life for breeders. The point is to know as much as you can about your dog’s genetic potential for these traits so you can make informed breeding decisions. The pedigree analysis service is a way you can do that. It never was intended to be a culling mechanism for a breeding program.

Prior to the advent of DNA tests, we often had no idea what a dog's genotype for a particular trait might be. Since the tests available are still limited, this continues to be the case for most traits. The analysis searches the pedigree of a given dog for connections to traits of interest to determine relative risk of having genes for those traits which it might, in turn, pass to its offspring. The higher the score the greater the risk. However, if we eliminate from breeding all dogs of undetermined genotype that have a higher-than-average score for a serious health trait or color disqualification, we would also cause a serious depletion of the "good" genes those dogs might have. The goal is to breed dogs with problematic scores to mates with better scores, thereby reducing the level of risk for their pups.

This is essentially what breeders do when selecting away from faults in conformation or important behavioral traits. The pedigree analysis system gives breeders an objective measure for various health and disqualifying color traits that they can consider in their overall decision-making process.

History
It is helpful to know how the system developed. Shortly after the successful conclusion of the initial study of Collie Eye Anomaly (CEA) in Australian Shepherds, my first serious foray into genetic research, it occurred to me that the data I had provided for that study could be used to help breeders reduce the risk of what was then considered our major genetic health issue.

For a number of years CEA was the only trait I addressed. The process was cumbersome, with the data recorded on 3x5 cards that I had to thumb through every time I did a pedigree. Reports were typed one at a time.

Years passed; I got a PC and a good pedigree program. A home-office reorganization project reminded me that I had accumulated volumes of pedigree data on other genetic issues which could be used in a similar manner once I entered the data into my pedigree database. In 1999 I began reviewing pedigrees for about 18 different traits. Over the years I have added a few more traits and adjusted the scoring system to make it the best possible reflection I could devise of a dog’s family history for a given trait without revealing specific confidential information.

Beginning in January 2008, the program ceased to be my private project and became part of the Australian Shepherd Health & Genetics Institute's new International Directory for Australian Shepherd Health (IDASH.) At present, I am still the one doing the processing and preparation of reports, but moving the program into IDASH will guarantee that no matter what might happen to me, the data will not be lost and the program can continue.

The data is currently stored in a pedigree program but the review and calculations are done largely by hand. This is time-consuming and prone to clerical error. ASHGI has engaged a computer programmer to automate the service. A computerized system will make it possible to handle far more requests and eliminate calculation errors.

Data Sources
The information comes from multiple sources, with most of it presented to me by concerned owners and breeders who are grappling with health issues in their dogs. I supplement this with the public domain information from open health registries and listings in the United States and Europe.

The data I have gathered has been criticized because it is not complete, in that there is no mandatory reporting so not all dogs that have a given trait are listed, and because owner-submitted data may sometimes be inaccurate. These are legitimate arguments and deserve response.

It is true that I do not receive information from everyone who might have a dog affected with one of the traits I track. Frankly, the same can be said for OFA, CERF, or any voluntary health registry. Even though my data may also have gaps, it is better to make use of the information available than proceed in total ignorance.

Owner-submitted data may sometimes be in error, particularly for diseases that are not simple to diagnose. I do screen this information and ask additional questions to clarify the situation where necessary. It is extremely unlikely that someone would deliberately pump false information into the system. The owner-derived data comes from people who contact me wanting to know more about traits that have been diagnosed in their dogs or which they are trying to manage in their breeding programs. They have no motivation to give me information that would make the situation appear worse than it actually is.

Public-domain data derived from health registries is the "gold standard" for information, and I use it whenever it is available. The most useful data source, a veritable "platinum standard", is DNA screening test results. These tests reveal the actual genotype of the dog. It doesn't matter what potential risk lurks in that dog's pedigree when you know, for certain, what version(s) of a particular gene it has. We can currently test for cobalamin (Vit B12) malabsorbtion, Collie eye anomaly, yellow/gold ("E-locus") coat color, MDR1, progressive retinal atrophy and, after March 10 of this year, cataracts. There is also a non-DNA blood test that will indicate carriers for Pelger-Huet anomaly. This kind of data takes precedence over any other data I may have acquired because it reveals the actual genotype of the dog.

Traits tracked
As of this writing, I include 26 different traits in the analysis. Initially I listed only the more common health and dental issues in the breed. As time went by, I added disqualifying color traits and less-common health traits that could have serious or fatal consequences.

I also determine the coefficient of inbreeding (COI) for each pedigree analyzed. The COI is not a direct indicator of health status, but dogs with higher COIs are more likely to have inherited two copies of disease-causing gene variants from ancestors which appear on both sides of the pedigree. High COIs may also indicate a risk of inbreeding depression if they have been maintained over several generations. [For more information on how to interpret and utilize COIs, see www.ashgi.org/articles/breeding_coi.htm.]

The Process
I had to develop a reasonable and consistent scoring system that could be applied to a group of traits with varying and undetermined modes of inheritance. I settled on a modified percentage of ancestry calculation. Breeders use percentage of ancestry to determine how much a particular ancestor contributes to a pedigree. The result is expressed as a percentage. For example, if a dog’s only appearance was as grandsire of the subject, its percentage would be 25, but if it was the grandsire on both sides the percentage would be 50.

Instead of seeking repeated names in a pedigree, I look for connections to a particular trait. The resulting scores are point values, not percentages. Percentages would require that we know the exact mode of inheritance, which we usually don’t. It would also require having a different type scoring system for each trait. That would be both cumbersome and confusing, so I settled on a system that could be applied to any given trait.

Scores range from zero to 100 and indicate whether a dog has more or less background for that trait. A zero score is indicated on the report as "no known background" in recognition of the fact there may be information I do not have. Since the frequency of these traits varies considerably, I realized that the score alone might not be sufficient for breeders to make sound decisions. Starting in 2007 I began logging all the test results so I could develop averages for each trait. [See chart above.]

As I review each pedigree, I seek ancestors who had the trait or were the parents or grandparents of a dog that had it. This incorporates breadth of pedigree while working from a standard 5-generation pedigree form. Parents are given half the weight of an affected and grandparents a quarter. I also note in which generation these dogs appear. Each generation farther behind the subject dog is given half the weight of the one before. If there has been no indication of a trait in five generations, it is extremely unlikely that the dog being analyzed will have inherited genes for it. [See score chart below.]

A score of 100 is equivalent to having an affected parent, 50 to having a parent that has produced the trait, 25 a grandparent that has produced it, etc. In most cases, however, more than one dog contributes to the result. One could, using this method, have a dog that scored 200 (itself affected, two affected parents, etc.) but few dogs score more than 100. 100 already indicates a very significant level of risk, therefore I set the ceiling at 100

In 2007, I started including total scores. The average score for the 180 Aussie pedigrees analyzed in that year was 442. Average scores, both total and for individual traits, will not remain static. They will be recalculated periodically to reflect changes in the breed population and in the traits tracked.

While the method of calculation is established, the system is designed to adjust to new information. This past year the ASHGI Cancer Survey revealed that hemangiosarcoma and lymphoma are very common and often follow family lines. Therefore, they have been added to the list of traits. Another change, the discovery that the mutation causing most cataracts in Aussies is a dominant, resulted in adjustment of relationship categories for that disease where the genetic status of a dog has become known. The system will be able to adapt to future discoveries as well.

Application
Pedigree analysis results are intended to inform the breeder about potential risks in her dog’s pedigree. Even a very high score does not mean a dog will have or produce a particular disease or fault. However, the higher the score the more likely this could happen so caution is advised.

Ideally, you would like to see all individual trait scores under 25, but this is very rarely the case. A score of 25 or higher, equivalent to having a grandparent that produced the trait, is reason for concern. The higher the score, the more concerned you should be. If you plan to breed the dog, try to select mates that will lower the score in their mutual pups. A litter's score will not exceed an average between those of the parents. Avoid crosses that score in excess of 50 for any serious disease if at all possible. If your dog exceeds the average score on one or more traits, attempt to reduce those scores in its puppies below the average whenever possible.

If a dog scores 25 points or more for a trait where carrier or DNA testing is available, the dog should be tested so its genotype is known and appropriate mating decisions can be made.

A high score for a serious health trait that does not typically appear until the dog is a few years old may indicate that the breeder will want to hold off breeding that dog until it is past the typical age of onset for the trait. "High" in this context means 50 or more or at least 25 and are above average for the trait Delaying breeding will reduce the chance that the dog may become affected after it has produced offspring.

If multiple traits are a concern in any particular dog, you are unlikely to be able to reduce risk on all of them at once. Set priorities based on health impact: Epilepsy is more serious than cataracts and both are more serious than missing teeth or too much white. But if your scores for epilepsy and cataracts are low while your scores for missing teeth and excess white are high, then the higher score items should be of greater concern.

Pay attention to the current average scores. A score of 50 isn't good, but if the average the trait is high (the 2007 epilepsy average was 53,) 50 might be better than most or a significant portion of the breed. A dog may have one or two very high scores and still have a total score that is below average. The overall health risk for such a dog is better than most. You will have to be careful about those high-risk items, but the picture may not be as gloomy as it appears on first inspection.

Another point on averages: If a dog's score is 75 and the average is 10, that indicates the dog carries tremendously more risk for that trait than the majority of the breed. The good news here is that there will be plenty of potential mates with whom the dog is unlikely to produce the trait.

When looking for a stud to use with your bitch, or reviewing records on a bitch presented to your stud, you will want to seek crosses that reduce risk in the offspring wherever possible. Do not issue a blanket refusal to breed to any animal that has a higher score on something than yours does. Mate selection is a balancing act: Look at all the plusses and minuses on each side. Do the potential mates complement each other, not only for their scores but in other aspects?

Because new information flows into the database continuously, it is advisable that pedigree analysis be repeated about every three years for any breeding dog that is still living or for which semen is being stored for future use. One can consolidate analyses to some degree for full siblings. Their scores will be exactly the same unless one has produced something another has not.

Without knowledge of your dog’s genetic potential – both for good and for ill – you cannot make informed breeding decisions. If you are flying blind when it comes to health issues, you will produce them more often than if you know something could go wrong and you take steps to avoid it. The ASHGI/IDASH pedigree analysis service is one more tool you can use toward that end.