What to Expect When You’re Expecting…DNA Results!

Once you have collected a DNA sample either utilizing an ASA provided kit or a lab provided sample card you are responsible for mailing the sample along with official ASA 2D barcode/paperwork to the GeneSeek lab.

GeneSeek places samples into test on Mondays, Wednesdays and Fridays for ASA. Once GeneSeek receives the sample it is expected to enter processing within 3-5 business days.

It will take 3-4 weeks for results to be reported to ASA. This time can vary depending on the time of year or type of testing requested.

There is NO WAY TO EXPEDITE DNA testing at GeneSeek.

Once results are reported to ASA from Geneseek, members will receive reports of testing either via email(if email is listed on the account) or by mail and at this time testing fees will be invoiced to the ASA member’s account.

Almost all results are viewable in Herdbook Services by searching the animal record and clicking on TraitTrac.

If you have additional questions please email dna@simmgene.com or call our office at 406.587.4531 and hit the number 3 to be connected to the DNA department.

 

New DNA Sampling Method – AllFlex TSUs

Allflex Tissue Sampling Units for DNA Testing

AllFlex has a method for collecting DNA Samples that ASA has recently embraced. This new form of sampling is being offered as another way to collect DNA and submit for all the tests we offer through ASA. The Tissue Sampling Unit (TSU) kit offers another way for producers to properly and successfully collect and submit DNA samples, even on newborn calves. To order your TSU kit please contact the DNA Department and we can mail you a kit. The start up costs are $35 for the TSU applicator and $2 per TSU ordered (increments of 10). The TSUs come in a box of 10 ($20) and Allflex recommends that you store them at room temperature prior to use (for a maximum period of 12 months). Member will also be responsible for shipping charges via UPS for the applicator and TSUs.
For more information on ordering these kits please contact the DNA department by phone 406-587-4531 or email dna@simmgene.com and we will be happy to answer any questions you might have.

Box of TSU $20 (includes 10 TSU)
tsu_box_set__24587-1390449859-220-220
Applicator $35
tsu-applicator
Mailing TSU Samples to GeneSeek
When you have successfully collected your sample, please contact the DNA department at dna@simmgene.com and provide the following information: Account Number, Animal ID/Registration Number, TSU Bar code(displayed on the side of the TSU), and the tests you would like to have done. We will then process your DNA request and email you paperwork with instructions to send to the lab. The new DNA paperwork will have 2D barcode(s) and all you have to do is print and mail with the sample(s) to the lab. We recommend mailing your samples UPS ground since the samples may pop open if flown due to the pressure.

DNA Testing – Lab and ASA Holiday Schedule

If you are planning on submitting DNA samples for testing in the next few weeks please review GeneSeek’s holiday schedule listed below.  The lab will be closed on the following dates, so that means samples will not be received or logged in to test until the following business day they are open.

Friday, December 23
Monday, December 26
Friday, December 30
Monday, January 2

If you are shipping blood tubes or raw tissue you will need to make sure it does not arrive at the lab any of the above dates.  DNA testing and results may experience delays during the holiday season.

The ASA offices will be closed the following days in observance of the Holidays.

Friday, December 23
Monday, December 26
Monday, January 2

If you have any questions on the above schedules please contact ASA via email dna@simmgene.com or call 406.587.4531 and press #3 to be connected to the DNA department.

holidays-card

New DNA Pricing – Effective November 1

New DNA pricing has went in to effect as of November 1, 2016.  To a view the new pricing, click here.  The DNA paperwork request form has also been updated.  If you have any questions please contact ASA.  Email dna@simmgene.com or call 406.587.4531 and hit the number 3 to be connected to the DNA department.

DNA Parentage Results – What if animal doesn’t qualify to the Parent(s)?

For some breeders the DNA process is similar to waiting for a present to arrive.  The DNA sample is submitted to the lab and from that moment forward, the anticipation starts to build.  Will the animal submitted qualify to the parents? Will it test homo polled? Homo black? Free of genetic defects?  The not knowing, it’s absolutely heart wrenching, stressful and can just about drive you crazy during the 3-4 week wait.  However, whether the results leave you feeling excited or let down, it’s important to understand the process so lets take a moment and walk through how DNA parentage results are reported from the lab to ASA, uploaded and then emailed/mailed to the member.

Lab Reports Results to ASA

Every business day the lab uploads results that are ready to their online information system named LIMS.  Each day ASA checks LIMS and downloads any results that are available.  Results are uploaded to Herdbook Services and the membership account is invoiced for the testing.  If the sire/dam of the animal being tested has DNA on file with ASA, the lab will run a comparison to the parent(s) and determine whether the animal verifies to sire/dam. There are three critical pieces on the parentage report: sire qualify, dam qualify and sire/dam qualify as a mated pair.

There are 4 possible outcomes if both the sire and the dam have DNA on file with ASA

  • the animal qualifies to both sire/dam
  • the animal does not qualify to sire/dam (result is an exclusion)
  • the animal qualifies to dam but does not qualify to sire – (result is an exclusion)
  • the animal qualifies to sire but does not qualify to dam – (result is an exclusion)

Once the records are uploaded/submitted, an animal that is registered/on file and marked as an exclusion, is automatically suspended pending DNA verification or a pedigree update.

If only one or the other(sire/dam) has DNA on file, the animal is only compared to that parent. If the parent animal does not qualify, the exclusion procedure is followed as described above.

If neither parent has DNA on file, the animal’s DNA parentage is simply placed on file and uploaded.

Member notification

If the member has an email address on the account, an automated email is sent out displaying the invoicing information. These automated notifications do not contain any parentage result information, they simply display the amount invoiced to the account.  If your animal is registered/on file in the database you can go in to Herdbook Services, view the animal pedigree and look for the results designation on the animal record.  For an explanation on what to look for, please view the blog post on DNA results.

DNA parentage reports are then generated and emailed to members as attachments or mailed out the following business day.

What happens if the parentage report says the animal did not qualify to the parent(s)?

  1. If it’s an ET animal, we’re going to ask for other mating possibilities.
  2. If it’s a single birth animal we’re going to ask if there are any other sire/dam possibilities.

If you’re the breeder on this animal, go back and double check your records and if your response is, “no, there are no other possibilities” then you do have the option to submit a *second sample on the animal.  If you submitted a blood sample the first time, we recommend sending in a hair collector card for the second submission or vice-versa.

If there are other sire/dam possibilities, those will be forwarded to the lab for comparison, this process is called a re-check.  Re-checks typically take 24-48 hours to complete, depending on lab workload. If animal qualifies to the sire/dam on the re-check, the pedigree is updated and unsuspended.

If the animal/ET was purchased, you will need to check with the seller/breeder/sales management team and ask them if there are other possible matings.  If they respond as mentioned above, you have the option to submit a *second sample on the animal.

*Please note – If you submit a second sample and the animal tests the same way it did the first time, i.e. does not qualify to parent(s), you will be invoiced for both DNA parentage tests.  If the second sample qualifies to parent(s) as originally stated we will refund the amount invoiced for the second set of results.

Keep in mind, each exclusion case is unique and in certain cases, forces us to leave our comfort zones and consider even the most remote of possibilities.  For some people it’s helpful to think of DNA as a giant puzzle and with that in mind, it often takes more than one person to sort out how all the pieces fit together. Take a moment and consider all the people involved in the process of flushing a donor dam or AI breeding a dam.  The wrong semen straw gets pulled for the flush, the petri dishes on the flushed donors get switched, the ET straws get mis-labeled, the dam gets bred with two straws and it doesn’t get written down, the wrong dam loads in the chute first and it doesn’t get written down or caught.  The list goes on and on. None of us ever like to admit that we are all human and mistakes do happen(me least of all) but I can make you a promise that as issues arise,  ASA will work diligently with you each step of the way  to resolve and try to make real world sense of the situation.

If you have any questions/concerns on a particular DNA case please do not hesitate to email dna@simmgene.com or call 406.587.4531.

Red Charlie – FAQs

In order to understand Red Charlie, a new red coat variant, breeders must first understand the inheritance and DNA testing for the main coat color gene. The following is a brief summary.

Coat Color inheritance: The main gene that controls the base coat color in cattle is called the extension gene. Historically, it was believed there were three alleles (variations) for this gene in cattle: black (ED), wild type (E+), or red (e). Black coat color is a dominant trait and will mask the presence of other coat color alleles. The wild type allele is dominant to red. Each animal will have two copies of the extension gene (one from each parent) and it can be any combination of the three alleles.

Since Black is dominant, a black animal could have three different pairing of the coat color alleles. A black animal can be homozygous black (ED/ED) or heterozygous black (ED/E+ or ED/e). An animal that is truly homozygous black should always pass a black gene to the progeny. Therefore, an animal that tests homozygous black should always have black progeny. Heterozygous black animals can pass on the wild type or red allele to the next generation and have wild type or red calves. Conversely, as red is a recessive trait, red animals are typically homozygous for the e allele (e/e) and would always pass the red allele to their calves. Sometimes red animals can carry the wild type allele so the example is a little over simplified.

DNA testing for coat color: The DNA marker for the red allele is a mutation in the extension gene that makes the gene unable to make a protein product. Without this protein, an animal will have a red coat. The DNA marker associated with the black allele makes the protein always active and the animal then has a black coat color. Wild type animals have the ability to either have black or red hair and are therefore can be affected by other genes for different coat color patterning (tiger striping or darker hair on the extremities).

There are an infinite number of possibilities that could result in the loss of function of the coat color gene, resulting in a new red coat variant. Red Charlie is a prime example.

FAQs

Q : What is Red Charlie?
A : Red Charlie is a newly discovered red coat color variant (allele). It works exactly like the existing red coat color allele except it wasn’t being detected by the DNA test for Coat Color. Like the red allele, Red Charlie causes a loss of function of the extension gene. Until recently, we did not know about this mutation so existing coat color test was unable to detect the Red Charlie mutation. Therefore, some animals were testing homozygous black but having red progeny.

Q : What does it mean if my animal is a Red Charlie carrier?
A : Being a Red Charlie carrier is equivalent to being a red carrier. Red Charlie carrier should be viewed just like an animal that tests heterozygous black (carries the red allele).

Q : How can I tell if an animal is a potential Red Charlie carrier?
A : Log-in to Herdbook Services, go to Data Search, Animal Search, enter in the ASA registration number, hit search. Click on TraitTrac.  Look under Genetic Traits, Red Charlie is abbreviated as RC.  Verify your animal’s status by using the legend key on the left and look to see if there are Red Charlie test results or carriers in the lineage.

Q : How can I order Red Charlie testing?
A : As of 5/12, Red Charlie is not available as a commercial test. However, GeneSeek is working on the final stages of making Red Charlie a publicly available test. Once available, tests can be ordered through the usual DNA test procedure – either call the office at 406-587-4531 or email the DNA department at DNA@simmgene.com.

Q : Will ASA be able to use the sample that was submitted for coat color testing to run Red Charlie?
A : Yes, the ASA can use any viable DNA sample to test for Red Charlie. Please contact ASA by emailing dna@simmgene.com or calling our office and providing us with the ASA registration number of the animal you would like to test. We will have the lab pull the sample and see if there is enough sample left to run the RC test.

Q : Does this mean all coat color testing done up to now is wrong?
A : No, animals without Red Charlie carriers in the lineage are likely okay (although this is not a guarantee).

Q : Should I be worried about the validity of my animals homozygous black coat color results?
A : Using TraitTrac will help identify animals that have the possibility of carrying Red Charlie. If an animal has coat color test results already and has a carrier in the lineage for Red Charlie, then there is a possibility that this animal carries Red Charlie as well. If there is no indication of Red Charlie in the TraitTrac system then the odds are low that the animal would carry this allele. However, there may be carriers that the ASA doesn’t know about so no known risk in the pedigree is not a guarantee of being free of Red Charlie.

Q : Is Red Charlie the same as Wild Type?
A : No, Red Charlie has nothing to do with the wild type coat color allele.

Q : Are red or wild type coat color test results affected by Red Charlie?
A : No, Red Charlie is linked only to the Black coat color allele so will only change black coat color test results.

Q : How do we know the Red Charlie coat color variant isn’t present in other pedigrees?
A : It isn’t likely to show up in other pedigrees but this is not a certainty.

Q : Will this affect animals that are tested heterozygous?
A : Animals that tested heterozygous black should be unaffected by Red Charlie. Red Charlie is only linked to the black allele and makes that black allele function like a red allele. So, if an animal tested heterozygous black and appears black, then this animals black allele must be functional and therefore does not carry the Red Charlie variant.

Q : What are the implications of breeding with a Red Charlie Carrier?
A : A Red Charlie carrier has a 50% chance of passing the Red Charlie allele to its progeny and a 50% chance of passing the black allele. See the punnett square below for a more detailed explanation. A Red Charlie carrier has a 50% chance of passing the Red Charlie allele to its progeny and a 50% chance of passing the black allele. See the punnett square below for a more detailed explanation.

Punnett Square showing the progeny outcomes when mating two heterozygous black animals

Screenshot from 2016-05-16 08:54:48e can represent either the traditional red coat color variant or the Red Charlie variant

  • ¼ of the calves will be homozygous black: These will appear black and always have black calves.
  • ½ of the calves will be heterozygous black: These will appear black and half of their calves will inherit the black allele.
  • ¼ of the calves will be homozygous red: These will appear red and always pass on the red allele.

To read more about Red Charlie and to view a list of tested Red Charlie carriers as of 5/12/16, click here.

If you have additional questions not answered above, please email dna@simmgene.com or call our office at 406.587.4531 and push number 3 for assistance.

 

 

DNA – Your Insurance Policy

We are continuously asked the following questions in the DNA department.
“How many more genetic defect tests will be developed?”
“How can I best protect my herd if something comes up down the road?”
“If my sire/dam has a clear TraitTrac, will that always be the case?”

The answer to all of these questions is simple.  Protect and insure your herd.  No, I do not mean that you need to call your local insurance representative and take out a policy, but what I do mean is you do need to start taking the necessary steps to properly protect your genetic investments. There will always be new DNA testing that is constantly coming about and being introduced in to the industry, that is a fact.  Whether it is a few months down the road, a year or even ten years, it’s coming.  What is important to remember is each animal, including you, has genetic defects.  It is up to you, as the breeder, to evaluate each animal/defect, determine the economic impact and decide whether they will be retained in the herd as a breeding animal.

Naturally, your next question is, “what’s the best way to start collecting DNA insurance on my herd?” The answer is once again, a fairly easy one.  After you have finished calving or prior to weaning, or if you’re planning on working the entire herd through the chute any time soon, call ASA and order blank DNA cards.  Blood cards are supplied free of charge and you can order any amount you wish.  Keep in mind, if an animal is a twin, you’ll need to pull a hair sample instead of a blood sample since twins can share the same blood source in-utero so oftentimes a blood sample will end in a No Results(NR). When the animal comes through the chute, collect a blood sample on the card.  Label the card and place it in a secure location, out of the elements, such as a safe or desk drawer.  Every animal that steps foot or is born on your ranch, should have a DNA sample collected and stored.  Whether you ever have to submit the sample for testing or not, it’s better to have it and not need it, than to not have it.  By collecting a sample on each animal, you’re insuring that if a DNA test becomes available somewhere down the road, you can submit that one sample for testing and depending on the result, further testing may not be necessary on any other animals.  You can potentially save yourself hundreds or even thousands of dollars worth of testing by taking the time to secure a DNA sample on each animal and store it. Yes, this includes your AI sires and donor dams which are required to have a DNA sample submitted through the Association.  Go ahead, take an extra sample, or two, especially on the high impact animals.  It never hurts to have extra samples stored for use at a later date if it becomes necessary.

As the spring calving season is coming to a close, herd bulls are being turned out, AI sires are going to stud and donor dams are being flushed, take a moment, order some blank cards and start stockpiling a DNA sample on every animal. I can guarantee you, it’s the best way to prepare for the future of DNA technology and at the same time, insure your genetic investments.

If you have questions on the above information or would like more information, email dna@simmgene.com or call our office at 406.587.4531 and select #3 from the menu options.