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.

 

Top Tips for Taking Blood and TSU Samples

Sample failure can often be prevented by ensuring the sample collection process is correct.

With mail time, DNA testing can take around 2 months. FedEx’ing kits from ASA to members, and from members to the lab, can cut down this time. However, if a sample fails this time is doubled.

Below are tips for taking blood and TSU samples.

Please find the Down to the Genes article, “Common Reasons for Delays in DNA testing”, in the October issue of the Register for more information.

 

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 Timeline, Requirements, and Top Tips

By Lilly Platts, Jackie Atkins, Riley Foster, and Leoma Wells

Everything you need to know about ASA’s DNA Services & more. This is an extended version of the first installment of ‘Down to the Genes’ published in the September 2018 issue of the Register.  This article covers frequently asked questions and offers tips for a smooth DNA process. For additional FAQ’s and information, see the September issue of the Register.

When do I have to DNA test an animal?

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I purchased semen, are those selling semen monitored by ASA to ensure HD/150K testing?

No. Breeders are responsible for completing ASA’s testing requirements. It is strongly suggested that buyers of semen ensure a bull has all required testing prior to purchasing semen and breeding cows.

Do ASA’s genetic defect testing requirements match those put in place by sales management and bull tests?

Not always. Sales managers and bull tests may require additional testing depending on their requirements. It is always best to follow up with the specific sales manager or bull test on the testing requirements prior to ordering DNA kits from ASA to ensure the animal can be sold through that venue.

Do other associations require the same testing?

Each association has different requirements. If a sire/dam is registered with ASA from another breed certificate, additional testing may be required to register progeny. Make sure to contact ASA with any questions prior to progeny being born to avoid delays at registration time.

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Take home message:  Do not delay your DNA testing – order your kits today!

Ten things you can do to ensure a smooth DNA testing process:

  1. Familiarize yourself with ASA’s DNA testing requirements.
  2. First contact the sale, bull test, show, etc., you may participate in to be clear of their DNA requirements.
  3. Order kits early (at least two months before you need results) by contacting the ASA – DNA@simmgene.com or 406-587-4531. Please follow instructions and have all required information before calling.
  4. Use a blood card, TSU, or hair card for collection. NEVER send vials of blood, bags of hair, etc. to the lab.
  5. Follow the instructions for collection included with your kits. Failure to collect the samples properly may result in samples failing testing – watch for more information in the October issue.
  6. If you make a mistake, i.e. collect sample from the wrong animal, etc., do NOT send the sample to the lab. If you do, contact ASA immediately.
  7. Never send kits to the lab without either ordering them for specific animals, or if you have blank kits, always complete paperwork with the DNA department first.
  8. Send samples to the lab as soon as they are ready. Getting them out the door ensures faster processing and less time for paperwork to get mixed up.
  9. Check your email for results.
  10. If you have a question, ASA is happy to help. Please have your membership number and information on the animal you are inquiring about (ASA number, tattoo, etc.).

 

DNA Results – Realistic Expectations

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.

Once GeneSeek receives the sample it is expected to enter processing within 3-5 business days as long as proper paperwork has been filed with ASA. Hair samples will see a longer turnaround time since they are only processed one time per week. Allflex TSUs and blood are the preferred sampling methods.

If samples arrive without official ASA paperwork/2D barcode stickers, they will NOT be placed in to test until the appropriate requests have been filed. This can add anywhere from 7-14 days to the turnaround time, depending on communication between ASA and the submitting member. Please do not mail samples without proper ASA documentation.

It will take approximately 4 weeks for results to be reported to ASA. This time can vary depending on the time of year or type of testing requested. Keep in mind, December through March are the highest volume months and samples may be in test longer than other months.

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 address is listed on the account) or by mail. At this time testing fees will be invoiced to the ASA member’s account.

If the animal is registered/on-file in the database, all results are viewable if the owner is logged into Herdbook Services by searching the animal record and clicking on DNA details. Click here for more information on how to view DNA reports.

If you have additional questions please email dna@simmgene.com or call our office at 406.587.4531 and choose 4 to be connected to the DNA department.

Posted in DNA

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.