Parentage Verification Under the Microscope

[zephyrhillsusan]

Since PV is so much in the forefront of ADCA news right now, here are several posts I've done about it.  Hopefully, they will be thought-provoking and helpful to those who are new to the breed.

Parentage Verification:  Our Whole Herd is "Sire and Dam Qualified!"

Parentage Verification: Why Is It Important?

Parentage Verification Questions & Answers

Parentage Verification: Some Interesting Statistics  -- If you spend some time searching the ADCA online database, you'll come up with some interesting findings!  This kept me up till all hours of the night, but I kept finding more stuff!  

[Dahdo]

Susan, I just wanted to say thanks, and let you know I am working on these. I started with the last one for some reason and was surprised at how few breeders are doing full PV. Judging from some of the discussion on FB, I think part of the reason that many breeders don't know how easy and cheap it is and much it improves the accuracy and value of our pedigrees. It's why I think the ADCA's new education committee should make DNA testing a priority. And by the way, I would highly encourage YOU to apply for membership on that committee. You have a knack for producing very helpful information on complex issues. Please think about it!

[legendrockranch]

Sorry Dave I have already suggested to Sue that she run for director one of these days Oh wait, I think she can do both

Barb

[kansasdexters]

Great job Susan! Thank you for taking the time to put this altogether. It will be a wonderful reference for ADCA current and future members!


Patti

[zephyrhillsusan]

Thanks for the encouragement, Dahdo, legendrockranch and kansasdexters. I would actually love to work with the education committee, because I love helping people learn things.  As far as the rest, Barb, we have a super Regional Director right now, and I'm glad to let him keep on keeping on.   Hopefully for now I can serve in a small way here and through my blog/website.

Dave, I'm glad you're getting your herd PV'd. You are so right that it improves the value of your pedigrees.  Good luck, as it can be a time-consuming task if your animals' parents aren't genotyped yet. That's the first step--once that is viewed as "entry level" for registration, it will become an easy task to PV.  I hope that once people realize the benefit to them in not having to test every calf for PHA and chondro, it will be done more frequently.

[midhilldexters]

Such a nice job, well done. I liked reading the stats part, very interesting.

Carol K

[lonecowhand]

Wow, Susan, that's really concise and understandable! You do have a knack for organization, and explanation.

And the photo of the concerned cow is great, too.

[Cascade Meadows Farm - Kirk]

Since the parentage tests are only 99% accurate, would you trust an obligate negative chondro status from any farm that breeds mixed chondro and non-chondo? I believe that farms that host the chondro gene, should directly chondro-test ALL calves for chondro to be 100% certain of their status instead of only 99% certain. Am I missing something here?

[kansasdexters]

Kirk,

It is necessary to Chondro-test the offspring of a Chondro-carrier, to positively determine if the offspring is a Chondro-carrier or a non-carrier; same goes for the offspring of a PHA-carrier. So even with parentage verification, the offspring of a Chondro and/or PHA carriers does have to be tested and reported in order for their Chondro and/or PHA status to be shown on the ADCA Online Pedigree and on the animal's pedigree certificate.

Anyone that is breeding to a Chondro-carrier herd sire, already has to test their progeny for Chondro and report it, in order for anything to show up in regards to the offspring's Chondro status. Same goes for calves born to cows that are Chondro-carriers. The offspring can be parentage verified, but if they aren't tested for what either their sire or dam carries (PHA or Chondro or both), then the field is left blank where PHA status and/or Chondro status is shown.

If that same herd is doing parentage verification and using a tested PHA non-carrier, Chondro non-carrier herdsire on cows that have not been tested and reported as to their PHA and Chondro status, then the offspring have no information shown for PHA status and/or Chondro status. They will just have "Sire and Dam Qualified" indicated for the appropriate field on the Online pedigree, and have "G5" on the pedigree certificate.

If all of the breeding stock is genotyped and is also tested to determine each individual animal's PHA status and Chondro status, and it is reported and recorded in the registry, then the offspring can be parentage verified (Sire and Dam Qualified) and the offspring of any carriers must still have the relevant test (PHA or Chondro) in order for their Chondro or PHA status to be indicated on their pedigrees. If the offspring of a carrier isn't tested, their status is left blank.

The offspring of tested non-carriers, that are parentage verified (Sire and Dam Qualified) to tested non-carriers (Sire and Dam), can be considered obligate non-carriers and their status can be shown as "non-carrier" without testing. While "Obligate" non-carrier status doesn't provide the same level of assurance as "Tested" non-carrier status does, there is the remote chance that the lab made a mistake (in sampling, testing, recording, or in reporting) in determining non-carrier status of the tested animals, in the first place!


Patti

[RedRidge]

To summarize... if I have a chondro and a non-chondro bull on my farm and I do PV on a calf out of two non-chondro... then the obligate non-chondro status is just as accurate as the PV test. Adding the actual chondro test does not give you more accuracy for the PV.
In theory the PV would have determined a non match on the sire if, in fact, the chondro bull was the sire.
IOW... We can't make it any more accurate than the human error element.

[kansasdexters]

Sheri,

You said it well. The human error element is always a factor in any of these tests, it doesn't matter if you are parentage testing or chondro testing or PHA testing, there will be errors made. There is no such thing as "perfect" or 100% accuracy in any of these tests done by human beings. Human beings are just not "perfect". Darn!


Patti

[RedRidge]

As a former software engineer I repeatedly had to remind clients that their computer could never be any smarter than the person who programmed it. ;-) we are all only human. That's never an excuse for errors but simply a reality

[Cascade Meadows Farm - Kirk]

Dec 10, 2014 19:19:45 GMT -5 RedRidge said:

To summarize... if I have a chondro and a non-chondro bull on my farm and I do PV on a calf out of two non-chondro... then the obligate non-chondro status is just as accurate as the PV test. Adding the actual chondro test does not give you more accuracy for the PV.
In theory the PV would have determined a non match on the sire if, in fact, the chondro bull was the sire.
IOW... We can't make it any more accurate than the human error element.

If you have closely related line-bred cattle on your farm and you have a non-chondro bull and his 6 month old chondro son that you assumed was too young to breed, it's possible that this chondro-son has a VERY similar DNA genotype to the non-chondro sire. It's very possible that when you do a parentage verification on your calves, your non-chondro herd-sire bull will verify as the parent even though the chondro son (sneaker bull) is actually the sire of some of the calves.

This is NOT human error or computer error. You should get this same result if you redid the parentage verification 100 times. This is due to the way the parentage verification works. If the two bulls aren't related, then the accuracy is pretty good. But if the two bulls are very closely related, then the accuracy falls off a considerable amount. In the case of the sneaker bull, he's often going to be the son of the presumed herd sire, so that alone drops the accuracy of the parentage verification and accuracy drops much further if there is a lot of other interrelatedness.

The Chondro test itself is very accurate, but it is prone to a tiny degree of human or computer error. If you got such a human error, and you retested, you would almost certainly get the correct result on the next re-test.

The parentage verification test (like the chondro test) is also subject to a small chance of human error BUT it may also only be 90% accurate in the case of very closely related bulls.

90% accuracy may be good-enough for the purpose of pedigrees (the two closely related bulls are very similar in pedigrees anyway), but 90% is probably NOT good enough for the purpose of making certain an animal isn't a carrier of a lethal gene to unknowingly be spread to other herds.

[zephyrhillsusan]

Since the parentage tests are only 99% accurate, would you trust an obligate negative chondro status from any farm that breeds mixed chondro and non-chondo?

Read more: dextercattle.proboards.com/post/new/4384#ixzz3LYdfnr9R

Cascade Meadows Farm - Kirk, why would you NOT trust "Chondro non-carrier - obligate by PV" just because there were other Chondro carriers on the farm, but you would trust it when there weren't other carriers on the farm?  Who knows, maybe on the non-chondro farm a neighbor's chondro carrier jumped a fence and bred a cow, then jumped back out again.  PV is just as accurate whether there are carriers on the farm or not.

To summarize... if I have a chondro and a non-chondro bull on my farm and I do PV on a calf out of two non-chondro... then the obligate non-chondro status is just as accurate as the PV test. Adding the actual chondro test does not give you more accuracy for the PV.
In theory the PV would have determined a non match on the sire if, in fact, the chondro bull was the sire.
IOW... We can't make it any more accurate than the human error element.

Read more: dextercattle.proboards.com/post/new/4384#ixzz3LYgsybja

Sheri explained it very well.  If you're trying to say, Kirk, that because the PV tests are stated to be "only" 99% effective when both parents are included--that an obligate by PV non-chondro "Sire and Dam Qualified" calf could actually be a carrier, then you must also be saying that you don't actually trust the pedigree of any "Sire and Dam Qualified" calf.  You can't logically hold that "Sire and Dam Qualified" is legitimate for pedigree verification, but not for non-chondro status.  

 

[Cascade Meadows Farm - Kirk]

ZephyrhillSusan,

We must have been typing at the same time, I think I answered your questions in my above post just prior to yours (let me know if I didn't).