How does parent verification work?

The November issue of the Register contained a Down to the Genes article focused on parentage testing.  Here we republished a blog post with more in depth information on how the parentage analysis works and a hands-on example where readers can work through who is the correct sire.

By Jackie Atkins, Ph.D., Director of Science and Education

Originally published on the ASA Science blog, Mar 7, 2016.

Whether you use parent verification to confirm your breeding records, distinguish between AI and pasture bred calves, or to sort through progeny from a multi-sire pasture, parental validation is an important test for breeders.  Roughly 10% of pedigrees reported across all breed associations are inaccurate.  These are frequently honest mistakes but never-the-less, vital to fix and make informed breeding decisions.  The theory behind parental validation is to determine if an animal could have inherited specific DNA markers from their reported parents.  If the animal could not inherit a specific DNA Marker from the sire or dam, then the parent is excluded.  With enough qualified markers, an animal is confirmed as the sire or dam of the offspring.

In the past, 15 microsatellite markers (also called Short Tandem Repeats or STRs) were used to confirm parentage but these were costly and not always reliable tests.  Most new parental validation is completed with single nucleotide polymorphisms or SNPs (pronounced “snips”).  The SNPs are locations in the DNA that vary from one animal to another.  The SNP parentage test uses over 100 SNP markers to either qualify or exclude an individual as a parent.  Each animal has two markers at each SNP location (one on each pair of chromosomes representing one from each parent).

Let’s work through a hypothetical example using SNPs for parental validation.  We have test results for SNPs on a calf, two possible sires, and the likely dam.  We look at each SNP and see if the calf could have inherited that SNP from the possible parents and also if the mating (the parents analyzed together) could have passed along those SNPs.  The following diagram and table show four SNP markers for the individuals and the conclusions drawn.

Slide1

Example of 4 SNP markers for a calf and his potential parents.  See the table and text for explanation of the analysis.

Slide2

Hypothetical SNP markers at 4 locations for a calf and his potential parents.  See text for further explanation for the conclusions drawn.

Working through each SNP marker, we look if the calf could have inherited his DNA markers (genotype; options are A, T, C, or G) from the potential parents.  At SNP 1, the calf has a genotype of A/T.  This means the calf inherited an “A” from one parent and a “T” from the other parent.  Both the Dam and Sire 1 are homozygous T and SNP1.  This means they could only have passed along a T at this location.  The potential dam and Sire 1 could not have conceived the calf together as neither could have passed along an “A” at this location.  However, we can’t exclude either the dam or Sire 1 based on this information, we just know that they can’t be confirmed as the parents together.

Continuing through our analysis, we cannot exclude any of the parents with SNPs 2 and 3 because the pairing of both sires with the dam could pass on the calf’s SNP markers.  Looking at SNP 4 is helpful.  The calf has two “T”s at SNP 4, one from his dam and one from his sire.  Sire 1 has two “A”s at SNP 4 so he could not have passed along a T at this location.  Sire 1 is excluded based on this comparison.  If Sire 1 is excluded, then the potential Dam and Sire 2 work for the remaining SNP locations.  The parental validation at the lab uses the same logical progression as this simple example except it uses approximately 100 SNP markers for the analysis.

 

DNA Updates: Pricing, Kits Sent FedEx, and More

DNA and genomic testing provides valuable insights to animals in a relatively short period of time.  By using genomics, breeders can have EPDs as accurate as cattle with 20 or more progeny records (depending on the trait).  All this can be accomplished while the calves are still nursing. The DNA services at the the ASA have grown and the ASA is putting in measures to continue to make our customer services more efficient and more accurate. 

Here are some recent changes to the DNA services:

    1. Billing at the time of kit or DNA test request started Sept.1.  In order to more efficiently and accurately bill for DNA tests, the ASA is now billing at the time of the kit or DNA test request. Keep in mind, this means members may be billed twice if kits are ordered twice for the same animal.  Billing up front gives members a chance to correct any mistakes prior to the test being ran. Billing up front is also more efficient allowing for more ASA staff time spent uploading results or on other customer service needs.
    2. New DNA pricing:  To cover the ASA’s cost, members will be charged $1.00 per blood card, $2.00 per sample pull, and research fees ($1/minute) associated with DNA work outside the regular procedures, for instance misidentified samples or samples showing up to the laboratory without proper paperwork.  A sample pull refers to the process where a DNA sample that was previously tested needs to be pulled from the archive for a newly requested test. Many DNA results are available as “add on” content from genomic tests (for instance coat color). These “add-on” results would not be subject to the sample pull charge.
    3. Automatic 3-day FedEx shipping for kits.  Due to delays in transit times, the ASA will now automatically ship kits via 3-day FedEx, charged to the member account.  Members can request to use US Postal service but the default will be for FedEx 3-day shipments starting Monday, October 1. 
    4. Genomic data schedule and review.  With the IGS Multi-breed Genetic Evaluation powered by BOLT, all genotypes available by Monday will enter into the evaluation which is completed and published that weekend.  If genomic data is completed on a Wednesday, the parentage results may be uploaded into Herdbook that week but the genomically enhanced EPDs will not be available until the following week’s evaluation (9 to 10 days later).  Also, the genomic data goes through a quality control process prior to entering the genetic evaluation. Some of the genotypes will be removed as they do not meet the requirements for the evaluation. If breeders notice animals that are missing genotypes, please notify the ASA (rendecott@simmgene.com) for next steps to resolve these cases. This schedule and QC process are more reasons to start testing as early as possible.   
    5. New staffing.  Robin Marston recently joined the DNA department and will help with DNA customer support.  Marston has previous experience working in another breed association’s DNA department and is very familiar with seedstock breeders, DNA services, and working with genotyping companies.  Marston joins Lilly Platts and Riley Foster to provide ASA members with timely and quality DNA services.

Please email dna@simmgene.com or call 406-587-4531 with any questions.

 

DNA Pricing – American Simmental Association

As of July 1, 2018, the DNA pricing schedule has changed. Below is an updated list of current DNA pricing:

Genomic Testing Available – DNA Enhanced EPDs
*GGP-HD
(includes PV, diluter and add-on pricing) – $90.00
   –GGP-HD is required to qualify animal as an AI sire/Donor dam
+Coat Color – $9.00
+Horned/Polled – $19.00
+Genetic Condition Panel (AM, NH, CA, DD, TH, PHA, OS) – $25.00

*GGP-LD(includes PV, diluter and add-on pricing) – $50.00
+Coat Color – $9.00
+Horned/Polled – $19.00
+Genetic Condition Panel (AM, NH, CA, DD, TH, PHA, OS) – $25.00

*GGP-uLD(includes PV, no add-ons available) – $33.00

Standalone Test Pricing
*Parent Verification(PV) – $18.00
*Horned/Polled – $33.00
*Coat Color(homozygous black) – $20.00
*Red Charlie(RC) – $15.00
*Diluter – $20.00
*Oculocutaneous Hypopigmentation(OH) – $25.00
*Bovine Arthrogyrposis Multiplex Congenita(AM) – $25.00
*Neuropathic Hydrocephalus(NH) – $25.00
*Contractural Arachnodactyly(CA) – $25.00
*Developmental Duplication(DD) – $25.00
*Tibial Hemimelia(TH) – $25.00
*Pulmonary Hypoplasia with Anasarca(PHA) – $25.00
*Osteopetrosis(OS) – $25.00

Sampling Method Choices
Allflex Tissue Sampling Units(TSUs) – $2.00/ea, boxes of 10
Allflex TSU Applicator – $35.00
Blood Cards – FREE
Hair Cards – $5.00 processing fee
-Customer pays all shipping costs associated with TSUs or cards ordered in bulk.

To view a complete pricing sheet and DNA paperwork request form, click here.
To learn more about the different tests, click here.

All hair sample submissions will be invoiced an additional $5.00/sample processing fee. Beware that hair samples take longer to process once they arrive at the lab so an increase in turnaround time should be expected.

To order a DNA kit, click here and fill out the spreadsheet. Once you have entered in the required information, email spreadsheet to dna@simmgene.com so we can get your kits in the mail.

If you have any questions email dna@simmgene.com.

Cow Herd DNA Roundup(CHR) Research Project a collaboration with GeneSeek, Inc.
CHR50K(includes PV, diluter and add-on pricing) – $20.00
+Coat Color – $9.00
+Horned/Polled – $19.00
+Genetic Condition Panel (AM, NH, CA, DD, TH, PHA, OS) – $25.00
For more specifics on participating in CHR, click here.
If you have any questions email cowdna@simmgene.com.

DNA Samples – Hair Sample Price Increase

Effective immediately all hair sample submissions will be invoiced $5.00/sample. This is a processing fee charged by our licensed lab, GeneSeek, Inc. It is a great time to explore your other DNA sampling type options.

  • Allflex Tissue Sampling Units(TSUs) are available for $2.00/ea and come in boxes of 10. The TSU applicator is $35.00.
    • Benefits of utilizing TSUs:
      • TSUs are the lab preferred sampling method since they can be processed the most efficiently by the lab, leading to optimum turnaround time for results to be reported.
      • Samples can be collected on newborn calves, no need to wait.
      • Samples can be collected on twins.
      • Decrease in samples that end in a Sample Fail (No Results) compared to blood/hair.
      • Samples can be stored at room temperature for short term and should be frozen for long-term storage.
  • Blood sample cards are available at no additional cost to the member.
    • Benefits of utilizing blood cards:
      • Samples can be processed more efficiently at the lab, leading to a decrease in turnaround time for results to be reported.
      • Samples can be collected on newborn calves, no need to wait.
      • Samples can be stored at room temperature for long length of time as long as they were collected properly.
    • Cons to utilizing blood cards:
      • Samples cannot be collected on twins since they could have shared the same blood source in-utero.
      • The sample fail rate for blood samples is at 3%.

If you would like to visit with a customer service representative about your specific herd needs please call 406.587.4531 and enter in the #4 on the automated message to be connected to the DNA department or email dna@simmgene.com and we can assist you.

Changes to DNA Notification Emails 8-2-17

Beginning today, August 2, 2017, we have updated our DNA results notification system.  We are currently working on quite a few changes to our DNA process so please bear with us as we navigate through them. We will keep you updated via this blog as the updates are implemented into Herdbook Services.

All DNA result notifications will now be emailed automatically from Herdbook Services when a DNA job is completed on a member account.  Results will be job specific, meaning only the animal/results updated in that job will be attached in the results email.  This reporting system will apply to both parentage and trait results.  Currently we upload traits individually, but very soon we will be uploading all the trait results together within one job. In the meantime, you will receive multiple emails with each individual trait result that was uploaded within that job. Please accept our apologies for the multiple emails you will receive for trait results until we are able to get it fixed in the database.

Notifications – What to Look For

The automatic emails will be sent from simmental@simmgene.com to the email listed on the account.

The subject header for parentage results will be DNA Parentage Results Job: XXXXXX and the parentage results from that job will be attached to the email. If there is an exclusion on an animal(does not qualify to a parent(s)) then please follow the exclusion protocol to submit alternate possibilities. You will be able to access DNA parentage reports in Herdbook Services on any animal you are listed as the current owner of. See the graphics below for instructions on how to view reports in Herdbook.

The email subject header for trait results will be DNA Trait Results Job: XXXXXX and the trait results from that job will be attached to the email.  Keep in mind, if the animal is having multiple traits tested then you will receive an email for each individual trait result.  If you would like to view a complete trait results report once all results have been received, follow the directions below.

How to Access Parentage or Trait Reports in Herdbook Services

There are two options: Animal Search or Herd Mgmt.
Animal Search
Log-in to Herdbook Services, go to Data Search, Animal Search, type in the ASA registration/on-file number, hit Search. It will bring up the pedigree display. At the bottom right-hand corner under Reports, select DNA Detail. Select the download button(see graphic below) and a PDF will load that you can print or save for your records.

Screenshot from 2017-08-02 15-18-19

Screenshot from 2017-08-02 15-19-15

To download results in bulk (Herd Mgmt) follow these steps:
Log-in to Herdbook Services, go to Herd Mgmt, Reports.
You can either select a default group or click on Quick Group and type/paste in the ASA registration number(s). On the right of your screen select PDF Reports. Select the report you wish to view. Click on Generate Report and PDF will load that you can print or save for your records.
Screenshot from 2017-08-02 15-21-01
Please note that you should always refer to Herdbook Services for the most up to date DNA information on an animal. If you have any questions or concerns about the above information please email dna@simmgene.com or call our office at 406.587.4531 #3 to speak to a DNA specialist.

ATTN : AJSA Regional/Classic Participants – DNA Testing

If you are planning on attending the AJSA Regionals, National Classic, or have sold an animal to a junior member who plans on attending the junior shows, please read all of the following DNA testing information.

Keep in mind that we are running short on time to get these required tests done if you have not started yet. There is no guarantee that a DNA sample submission will end with a reported result. 3% of all samples fail DNA testing or end in a No Results(NR).  Typical turnaround time for parent verification testing is about 2 weeks, however, there may be exceptions to this timeline. DNA testing is required in the following situations.

If you purchase an Embryo or a recipient dam carrying an embryo, and are not associated with the owner of the Donor Dam at the time she was flushed, you MUST parent verify your ET calf to both sire and dam prior to submitting a registration request. Contact ASA with the calf tattoo, sex, sire and dam’s registration numbers to request a DNA kit.
For Regionals: The ET calf needs to be placed on file in the database, assigned a number in parentheses and a DNA kit MUST be requested by the entry deadline of May 15, 2017. An email notification needs to be sent to elochner@simmgene.com notifying her of the status of the ET animal prior to May 15 since these will be handled on a case by case basis. The DNA kit MUST be submitted to the lab no later than May 22, 2017. Send kits via Fed Ex or UPS to be able to provide ASA with a tracking number. A registration certificate MUST be presented at cattle check-in.
For Nationals: The ET calf needs to be placed on file in the database, assigned a number in parentheses and a DNA kit MUST be requested by the entry deadline of May 22, 2017. An email notification needs to be sent to elochner@simmgene.com notifying her of the status of the ET animal prior to May 22 since these will be handled on a case by case basis. The DNA kit MUST be submitted to the lab no later than June 5, 2017. Send kits via Fed Ex or UPS to be able to provide ASA with a tracking number. A registration certificate MUST be presented at cattle check-in.

If a sire is being collected and used as an AI sire he must be approved as an AI sire with ASA. This includes all AI sires, regardless of breed.  In order to be approved as an AI sire  the following criteria must be met:
—If DNA parentage testing took place prior to May 1, 2012, we can grandfather the sire in to the database and a GGP-HD/HD50K is not required.
—If DNA parentage testing took place after May 1, 2012, the sire must have a GGP-HD/HD50K panel on file in order to be approved as an AI sire.
—If the sire is registered with another breed association please contact the other breed association and request the SNP parentage markers to be forwarded to dna@simmgene.com along with the date the DNA testing took place and confirmation of HD testing.

If a dam is being flushed and used as an donor dam she must be approved as an donor dam with ASA. This includes all donor dams, regardless of breed/registration status.  In order to be approved as an donor dam the following criteria must be met:
—If DNA parentage testing took place prior to May 1, 2012, we can grandfather the dam in to the database and a GGP-HD/HD50K is not required.
—If DNA parentage testing took place after May 1, 2012, the dam must have a GGP-HD/HD50K panel on file in order to be approved as an donor dam.
—If the dam is registered with another breed association please contact the other breed association and request the SNP parentage markers to be forwarded to dna@simmgene.com along with the date the DNA testing took place and confirmation of HD testing.

If you are hoping to show a calf out of an AI sire/Donor dam that has not been approved yet please contact ASA right away. Typically the GGP-HD testing does take 3-4 weeks to be completed so there is no time to spare in this case.

Genetic defect testing requires all sires and donors dams identified with a carrier in their lineage (CL, DL) or who come from a risk population (PR) for specified genetic defects MUST be tested for that defect before registration certificates and EPDs are available on new progeny. Please visit the TraitTrac Guide post to learn more about how to check an animal’s defect status.
***If your animal is on genetic hold that means a certificate/EPDs have not been issued. You can either test the suspect parent(s) or test the individual animal to clear the genetic hold. Contact ASA for more information and to ensure you’re testing the animal for the appropriate genetic defects. Genetic defect testing can be completed through any of the labs that commercially offer testing such as Igenity, Zoetis or Agrigenomics if you prefer to not go through ASA(time sensitive).

If you have more questions regarding DNA testing please contact the DNA department at 406.587.4531 and push the number 3 or email dna@simmgene.com.

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.