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Down to the Genes Series

DNA Requirements for Foundation-Registered AI Sires and Donor Dams

SimGenetics animals are frequently cross-bred, which means members are required to navigate the DNA…

Why an Animal May Not Have GE (Genomically Enhanced) EPD

Heading into the new year and the start of bull sale preparation, one of the DNA Department’s most frequently asked questions is why an animal doesn’t have GE (genomically-enhanced) EPDs after completing a genomic test. This article explores the general process and common reasons why GE may not appear on an animal’s record in Herdbook.

The Process

After an animal is tested on a genomic panel (either GGP-uLD or GGP-100K), the information from that test goes in two directions. The first piece is parentage and any additional traits that were added to the panel. The parentage markers are visible to ASA in the lab’s system, and the results are loaded by ASA staff to Herdbook. These will look like “PQB”, signifying that the animal qualifies to both parents, for example. At this point, if there are parentage exclusions, ASA works with the member to figure out the correct parent(s). Because the parentage markers available in the lab’s system, these comparisons happen quickly and do not require a new sample. In some cases, the member will be notified that a sample has failed. In this case, an entirely new sample is required.

The second piece of this process is the genomic results. When the animal completes testing, while parentage and trait results are shared with ASA, the genomic results are sent into the genomic pipeline. The genetic evaluation runs weekly. Any new data from the past week that is available by Monday afternoon/evening is added to the system, run, and by the weekend, new EPDs are available and the GE will appear. Generally, it takes a week from the time parentage results are available for the data to be run through the evaluation, and for GE to appear.

The takeaway is that parentage results and GE will never be available on the same day, and to meet catalog deadlines, members must add that week to ensure that the genomically-enhanced EPDs will be ready. An animal cannot be rushed through the evaluation process.

What Can Prevent GE?

There are a variety of reasons why an animal may be removed from the evaluation, and consequently not have GE-EPD. While this can be frustrating, having strong, trustworthy data is critical, and the system’s ability to catch these errors should be viewed as a strength. Identifying these animals allows ASA’s team to investigate and solve the issue.

■ A failed sample will always result in no GE, in addition to no parentage information.

■ Parentage exclusions will put a hold on the GE. Once parentage is resolved, the data is released and run through the evaluation.

■ Reporting the wrong sex can put a hold on GE. For example, if a member submits a request to run a 100K panel on an animal, and a week later, notices that the animal’s sex is recorded incorrectly if the sex is also not changed in the lab’s system the mismatch will cause the animal to be thrown out of the evaluation.

■ If more than one sample enters the system for the same animal, and the genotypes do not match each other, this duplicate data will tell the system that we may not have results on the correct animal and will put a hold on GE.

■ A low call rate can cause a genomic test to be excluded. On each test conducted, there is a “confidence level” in the returned results. If this is low, it basically means the results aren’t strong enough to accept.

■ An animal MUST BE REGISTERED, with the exception of THE options, to receive EPDs, and a genomic test will not generate EPDs on an unregistered animal.

These are some of the common reasons GE may not appear on an animal’s record after a genomic test is completed. After parentage results are uploaded and members are notified, we suggest writing the date down, waiting a week, and checking to see if GE is on the record. If GE is missing on a group of animals, the group likely missed the weekly cutoff and will be run by the next. For example, if an animal’s genomic data is available the day after data is pulled to be run, it may take a few days longer. If some have GE and some don’t, contact ASA with the numbers of the animals missing GE. ASA’s team does watch the system to make sure it is working correctly, but if there is a deadline, it is best to bring our attention to any animals in question. The most efficient way to request that ASA look into missing GE is to email the registration number(s) to This email address is being protected from spambots. You need JavaScript enabled to view it..

 

 

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