The IGS Feeder Profit Calculator (FPC)

Thursday, 08 March 2018 11:57


Seedstock and commercial producers share their firsthand experience with ASA’s new and innovative feeder calf value prediction.       |

By Emme Troendle and Lilly Platts        |

What is it?  Historically, the primary limitation of valuing feeder calves has been accurately gauging the profit potential of the largest genetic group within the industry — the crossbred calf. International Genetic Solutions (IGS), a collaborative effort of numerous breed associations, has developed a tool to assist in determining feeder calf value, called the Feeder Profit CalculatorTM (FPC).  

“The FPC offers an objective way of describing the genetic merit on a set of calves,” comments John Irvine of Irvine Ranch, owner and manager of a 225-head operation of registered Simmental located outside of Manhattan, Kansas. “To date, there has not been a more accurate way to quantify calf value. Many producers try to do the right things in terms of management such as weaning and using sound vaccination practices, to prepare calves for the challenges they will face in the feedlot. The FPC offers a common language to bridge communication between those selling and purchasing feeder cattle.”

The FPC incorporates genetic knowledge of mainstream sires, regardless of breed, preconditioning and vaccination information, and weaning management and responsible health programs to evaluate the value on a set of calves. “As this tool gains traction and becomes commonplace for cattle buyers to use, producers will be better rewarded for their efforts, in respect to their investments in better genetics as well as improved efforts in preconditioning calves to offer a better product for the next link in the industry chain,” says Mike Forman, owner and operator of Trinity Farms, a 700-head ranch of registered SimAngusTM cows in Ellensburg, WA.

The finished product is a certificate that highlights the genetic and management predictions on calves along with certain carcass and growth traits. All producer-provided information is highlighted on the official certificate, and an additional page is included, indicating all the genetic information provided. “Our hope is that with a certificate in hand, our customers who are already making investments in quality genetics, making further commitments to provide better health and management of their calves, will be rewarded,” Forman continues.

As seedstock producers, Irvine and Forman share their insight on the FPC:

Q: Why is having this information valuable to those supplying feeder calves?

Forman: FPC is a well-designed third-party validation that helps to provide structured reasoning to establish value relative to the average feeder calf price dependent upon the producer inputs in regard to genetic selection, health and management. It helps to reinforce what our position has been for years – producers have three things to sell – genetics, health and the management the cattle are under. 

 Irvine: The FPC provides a great metric to gauge value for producers that have routinely invested in quality genetics as well as practice good management. Additionally, by scoring their calves, FPC provides the cow-calf producer a benchmark to make measurable progress moving forward, whether it be on the management or genetics side. 


Q: What would you say to someone hesitant about using the Feeder Profit Calculator?

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Bar CK Cattle, Culver, OR, hosts an IGS Feeder Profit Calculator Session with Chip Kemp. Watch it here and get in on the Q and A segment.

by Chip Kemp                   

In the March Issue of SimTalk, we introduced the revolutionary IGS Feeder Profit Calculator™ and its role in providing true awareness of feeder calf profit potential. In this article, we are going to walk through the simple and straightforward process of getting an IGS Feeder Profit Calculator certificate generated on a specific set of calves.

The first step is to get to the IGS website. You can either use the IGS link at the top of Simmental.org or you can go directly to InternationalGeneticSolutions.com. The IGS Feeder Profit Calculator link can be found in the upper right-hand corner.

The second step will take you to the input form. Complete the form and submit that information for certification. You will provide contact and location information, weaning and herd health specifics, marketing weights and timelines, and of course registration numbers on sires.

It is possible that staff will reach out seeking additional information, but roughly three business days following your submission you will receive an email providing you a digital copy of your IGS Feeder Profit Calculator certificate.

Now it is time to interpret the information on your certificate. On the left side of the certificate will be all information provided by the producer. This gives confidence and knowledge to a potential buyer, knowing you are hanging your credibility on the details you provided. The buyer is able to quickly gauge your management and health practices that built value into this set of calves.

The lower right-hand-side of the certificate focuses in on five categories that are crucial to feedlot and carcass success. The star metrics reflect the ranking of your calf genetics versus the IGS database.

The upper right portion of the certificate is the true foundation and core of the IGS Feeder Profit Calculator. Using the largest genetic database in the industry and some of the elite minds in the business we have leveraged known genetics, herd health, current economic conditions, and basic accounting principles to provide the most robust indicator of feedlot profit potential to date. It breaks it down to a language we all understand — dollars and cents. Frankly, feedlot buyers want to know if a set of calves has a reasonable chance to turn a profit.

Three measures are highlighted on the certificate:

Relative Genetic Value: Predicted difference in value due to genetics between the calves being evaluated and the average Angus calves of the same sex, starting weight and management conditions.

Relative Management Value: Predicted difference in value due to management between the calves being evaluated and those same calves under the assumption of an industry average of 60% of calves being vaccinated against BRD and 60% of calves being weaned for 30 days or more.

Total Relative Value: A combination of Relative Genetic Value and Relative Management Value.

When evaluating each of the relative value categories it is important to be aware that the average in each category is zero.  A $0.00/cwt means these calves reflect the breakeven potential of the average calf.  There is no artificial adjustment to the base just for marketing advantage or to provide a feel-good effect.  You expect the truth and the facts. So do your customers and your buyers.

On the example certificate provided, we predict a breakeven price (at the time they are sold as feeder calves) based on their predicted feedlot performance of an additional $9.84/cwt.  In laymen’s terms, that means the buyer at your local auction market or through your online platform could afford to pay an extra $9.84/cwt over the average animal on that day and still come out breaking even.  To be clear, the buyer isn’t looking at these calves to break even.  Like you, the buyer has an eye on profit.  But in this example, the buyer has true awareness, through IGS, that leads him to believe these calves are a safer bet. So is he looking to pay an additional $9.84/cwt? No. Is he willing to give $2, $3 or $4 more on a safe bet rather than risking everything? We think he is.

Additionally, a second page highlighting all registration numbers and known genetics accompanies each certificate.

It is really that simple. And you won’t pay a thing. Roughly 20 minutes of work will provide you with the most credible and trusted information available on the potential feedlot performance of your calves. Trust is the Gold Standard.

Your success is wrapped up in the value of each year’s calf crop. You’ve invested years, significant dollars, and countless hours of sweat to get the calves to this point. Why leave calf knowledge to chance? You can either Know or Guess. Choose Know.

DNA profiles provide additional information about the genetic merit of a DNA tested animal and increase the accuracy of EPDs, which are called Genomic Enhanced EPD or GE-EPDs. In the IGS Single-step process, the DNA marker genotypes are directly incorporated into the genetic evaluation along with the phenotypes (performance data) and the pedigree. As a result, the DNA information has an impact not only on the genotyped individual but also on all the relatives of that genotyped individual. This allows for the DNA information to improve the accuracy of non-genotyped relatives. To measure the impact of DNA information on accuracies of GE-EPDs in the IGS Singlestep genetic evaluations, we compared the average BIF accuracies of GE-EPDs of DNA tested young animals (born in 2016 with no progeny) to the average BIF accuracies of nongenotyped sires born in 2010-2014. Only sires with non-genotyped calves were used for this comparison. We found that the average BIF accuracy of GE-EPD for a DNA tested young animal is equivalent to the average BIF accuracy of a non-genotyped sire with 21, 22 and 24 calves with observed phenotypes for birth, weaning and yearling weights, respectively (Figure 1, where a horizontal line cross a curve for a specific trait (e.g. red line and blue curve cross each other at the data point correspond to y(accuracy)=0.46) and x(progeny)=21 for birth weight)). The progeny equivalent (PE) for direct calving ease was 15 and it was only 3 for total maternal calving ease due to limited genotypes on cows. The PE for milk and stayability were 18 and 25, respectively (Figure 1). 


The IGS Multi-breed Single-step powered by BOLT is a breakthrough in GE-EPD accuracy improvement. Enabling technologies such as BOLT software allow for even faster genetic progress with more accurate EPDs earlier in an animal’s life. We (IGS) are dedicated to using the best available technology to deliver more accurate GE-EPDs to our members so they have the best tools available for their selection decisions. 

By Mahdi Saatchi, Rohan L. Fernando, Lauren Hyde, Jackie Atkins, Steve McGuire, Wade Shafer,  Matt L. Spangler, and Bruce Golden, IGS Genetic Evaluation Team, and Consultants.

The ASA and International Genetic Solution (IGS) partners invested in a new and improved genetic evaluation software called BOLT to replace the Cornell EPD evaluation system. Among other benefits, this enables the use of Single-step methods for incorporating genomic information into the National Cattle Evaluation instead of the blending approach. In the Single-step process, the DNA marker genotypes are directly incorporated into the genetic evaluation along with the phenotypes (performance data) and the pedigree. As a result, the genomic data has an impact not only on the genotyped individual but also on all the relatives of that genotyped individual. This allows for the genomic information to improve the accuracy of non-genotyped relatives.

The IGS Multi-breed Single-step powered by BOLT squeezes more information from the DNA markers by allowing for certain DNA markers to have a larger influence on predicting the genetic merit of an animal than other DNA markers while some DNA markers to have no effects on trait(s) of interest (for progeny equivalents of select traits, see page 46). This model is closer to what we expect based on biology where some parts of an animal’s genome (or genes) play more important roles than other parts of its genome (or genes). This is unique to the IGS Single-step method compared to other organizations where the DNA marker information is used to adjust relationships among the individuals.

Many ASA members and IGS partners wonder if the BOLT EPDs are more accurate than the Cornell derived EPDs in the real world? To answer this question, we performed a validation study where we ran a data set (pedigree, performance, genomics) through both genetic evaluation software (BOLT and Cornell) to compare the accuracies of the EPDs produced. To enable a fair comparison, we removed the performance records of animals born in 2015 and later from the evaluation in both systems to be used as progeny performance records for validation purposes. Table 1 shows the correlations between EPDs and progeny performance of non-genotyped sires evaluated in both systems that have progeny born in 2015 or later with recorded birth, weaning, and yearling weights. As shown, the BOLT EPDs are more accurate than Cornell EPDs as the correlations are higher for BOLT EPDs with sires’ progeny performances.

Table 1- The correlations between BOLT vs. Cornell EPDs with progeny performance of non-genotyped sires for birth, weaning and yearling weights. 

Trait 1 N of Sires BOLT Cornell
Birth weight 29,154   0.34   0.27 
Weaning weight   21,571   0.29   0.19 
Yearling weight  10,849  0.26  0.20

To have a better sense of improvement in accuracies, we ranked sires based on either BOLT or Cornell EPDs for birth, weaning and yearling weights. Then, we compared the progeny performance of the top 1% vs bottom 1% ranked sires for each trait in each evaluation system. The results are shown in Table 2.


Table 2 – The average progeny performance of non-genotyped sires ranked based on either BOLT or Cornell EPDs



      Cornell   BOLT vs Cornell
Trait N of sires  Top 1%

Bottom 1%

Difference   Top 1% Bottom 1% Difference   Top 1%
 BW   29,151   74.2   95.9  +21.7     76.0   92.8   +16.8  +3.1 
 WW   21,571   655.3   546.2  +109.1     638.5   558.6  +79.9   +16.8 
 YW  10,849  1,151.5   915.8   +235.7     1,111.3   895.6 +215.7    +40.2


 As you can see, the BOLT EPDs ranked sires more accurately than EPDs from the Cornell software, where progenies of top 1% ranked sires based on the BOLT EPDs are +3.1, +16.8 and +40.2 lb heavier at birth, weaning and yearling. These results are exciting and show that our investment in new technology will lead to more accurate EPDs. 


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Change can be a scary concept to some yet sought after by others. Many ASA members and International Genetic Solution (IGS) partners wonder about the changes on the horizon once the new evaluation, IGS Multi-breed Single-step powered by BOLT, is fully implemented. That change may be nerve-racking but in reality, things should change. Why invest in new and improved methods if you get the same answers? Here are key changes to expect with the new genetic evaluation:

1. Movement of EPDs and reranking. EPDs will change especially in younger, lower accuracy cattle. Members should expect movement in lower accuracy cattle, as seen in the existing evaluations, because they may have new progeny data reported. Some cattle will move in a favorable direction while others will do the opposite. Keep in mind even if the EPDs get worse, the prediction of them is more accurate. With IGS Single-step, we will have more accurate EPDs earlier in an animal’s life.

2. More accurate accuracy. This idea takes a little time to sink in. The accuracy reported for each EPD will be more directly calculated and thus closer to the “real” accuracy. The methods to solve accuracy directly are extremely difficult and take a lot of computer power. With the previous Cornell software, it was not possible to solve for accuracy directly so an approximation method was used to estimate accuracy for each EPD. There were inherent flaws with approximating the accuracy of the previous method. Now with BOLT software, the accuracy reported with the EPD will be more reliable.

3. Reported accuracies will tend to be lower. One of the inherent flaws in the approximation methods used to find accuracy in the previous evaluation, and in all evaluations not produced through BOLT, was they frequently overestimated accuracy, especially for younger animals. This was known for a long time, but there was no way to calculate the accuracies directly. With BOLT, having accuracy more directly solved results in a more reliable accuracy but that accuracy will often be numerically lower than the previous evaluation would predict. However, the newly reported accuracies with BOLT should better represent the possible changes for the EPDs.

4. DNA testing will have a larger impact. With the switch to BOLT software, IGS will use Single-step genomic evaluation on all EPDs (currently using Single Step for Stayability EPDs). Single-step uses the DNA markers, pedigree information, and phenotypic data simultaneously in the prediction of the EPDs. Previously molecular breeding values (MBVs) were calculated from the genomic information and those MBVs were blended separately into the EPD prediction. The Single-step method squeezes more information from the DNA markers than the previous approach allowed. Also, there are biases inherent in the blending process that aren’t a problem with the Single-step approach. Additionally, with Single-step, the genomic information will not only enhance EPDs for the genotyped animal but also will be used in the EPD estimates of relatives.

5. Weekly genetic evaluation runs. With the horsepower behind BOLT, IGS can run genetic evaluations weekly. This has many benefits. It allows members to get more immediate feedback after submitting their records. If members miss a deadline, they can catch the next evaluation run the following week. It allows for more accurate EPDs throughout the year and faster incorporation of the genomics. This also means the EPDs put in print will quickly be outdated.


Genetic evaluation is not stagnant. There will always be improvements as new research in animal breeding, genomics, and statistics advance.  BOLT software is revolutionary in the innate flexibility, the computational power, and the statistical methods made possible using this software. IGS Multi-breed Single-step powered by BOLT promises more accurate EPDs, accuracies, and better use of genomics all delivered to you on a weekly basis. 


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Know. Or Guess. You decide.

Monday, 03 July 2017 10:08

Welcome to the IGS Feeder Profit CalculatorTM.  

Finally, you have a powerful, no-nonsense tool to highlight the true profit potential in your calf crop.  It is time to leverage the investment you’ve made in your bull battery and the expense you’ve put into your health program to receive a third-party validation of the predicted feedlot success of your feeder calves.  The IGS Feeder Profit CalculatorTM incorporates the genetic knowledge of most mainstream sires, regardless of breed, by referencing their EPD profile.  At the same time, the extra time and serious effort you’ve put into your preconditioning and vaccination program are also considered as a fundamental part of feeder calf value.  Weaning management and a responsible health program set your calves up for success.  When superior calf management combines with profit focused genetics you’ve done your job.  Now it is time to make your buyers aware.

What is IGS?  IGS, or International Genetic Solutions, is a collaborative effort of numerous breed associations working together to generate the largest beef genetic evaluation on the planet.  The IGS evaluation has the substantial benefit of being multi-breed, thus providing a much more accurate genetic picture of crossbred and composite cattle.  

The member associations of IGS, and the seedstock producers, involved are invested in the future and sustainability of commercial producers by providing profit focused solutions and tools.  The IGS Feeder Profit CalculatorTM is a highlight.  And as such, it is offered at no cost to you.  

That is correct, you can receive a third-party validation of your feeder calves at NO COST to you!

So what is the process?  Simple.  Here is a link to the IGS Feeder Profit CalculatorTM Input form.  You need to compile the requested information and fill out the form.  You must know the registration numbers on your bull battery and the Association in which they are registered.  Likely, your seedstock provider(s) can help fill in any gaps.  Also, if you know the sires represented in your cowherd, that will add tremendous awareness.  For those who don’t know maternal grandsires, you will need to provide the approximate breed composition of your cowherd.  These requirements form the basis of the genetic predictions of your calves.  

Additionally, you will provide health and weaning information along with other specifics about your calf crop.  This builds the foundation for the management predictions of your calves.  The more thorough the information you provide the more accurate the IGS Feeder Profit CalculatorTM will be at reflecting the profit potential in your calves.  Also, the more thorough you are the faster you will receive your official certification.  Should you have questions feel free to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it. or 406-205-3033.

Once your form is completed, submit the form electronically, by email, to This email address is being protected from spambots. You need JavaScript enabled to view it..  You will be contacted within in two business days about the processing of your form.  At the completion of the validation, typically three business days or less, you will receive an electronic certificate that highlights the genetic and management predictions on your calves along with individual awareness of certain carcass and growth traits.  Along with the certificate, you will receive a detailed page indicating all the genetic information you provided.  

This provides you with an IGS Feeder Profit CalculatorTM Certificate to share with potential buyers and marketers of your feeder calves.

All producer provided information will be highlighted on the official certificate.  Buyers will be able to view and evaluate all information given.  This allows a transparent process whereby you highlight your efforts and the buyer has the confidence of knowing the background of your calves.  

It’s that simple.  Finally, a streamlined process for progressive commercial producers to validate their hard work and focus on producing a quality product.

Know.  Or Guess.  Choose Know.

Article by Wes Ishmael   |   Beef Magazine

As the art and science of genomics becomes more accurate, cow-calf producers benefit. While cow-calf producers won’t directly participate in genomic evaluation now that single-step evaluation is a reality, they’ll be able to buy bulls with more accurate and reliable EPDs from their seedstock suppliers.


“If you’re a breeder doing a lot of genotyping and phenotyping — you’re measuring all of the data in all of the traits — single-step genomic evaluation lets you leverage the accuracy from that immediately,” says Stephen Miller, director of genetic research for Angus Genetics Inc. (AGI). “I think that’s a strong component of why breeders may become even more active in genotyping than they have been so far.”

Miller is describing what he believes will be one of the results of the single-step beef cattle genetic evaluation currently being refined and tested by organizations with massive databases, including AGI and International Genetic Solutions (IGS), which is a collaboration of 12 breed associations.

For the American Angus Association (AAA), AGI conducts a single-breed genetic evaluation. AAA’s registry grows by about 300,000 annually. The AAA database for genetic evaluation includes weaning weights for 8.3 million animals and birth weights for 7.6 million, among a host of various phenotypes.

Conversely, Mahdi Saatchi, lead genomicist at IGS, explains the organization’s database includes more than 16 million animals — the largest multibreed beef cattle genetic evaluation system in the world — adding more than 400,000 each year.

Single-step genetic evaluation is meant to replace what is currently and usually a multistep process used to incorporate genomic information into the calculation of expected progeny differences (EPDs).

As Alison Van Eenennaam, University of California, Davis, Extension beef geneticist, explains in the report titled “Recent Developments in Genetic Evalua-tions and Genomic Testing” (available at ebeef.org), “Currently, the incorporation of genomic information into genetic evaluations is statistically complex, and often involves a multistep approach that requires 1) traditional genetic evaluation with an animal model, 2) estimation of the marker effects and development of the prediction equation, and 3) a blending of those two pieces of information using a variety of approaches to develop a genome-enhanced EPD [GE-EPD].”

With this multistep approach, GE-EPDs are available only for genotyped animals. Including their information in genetic evaluation requires what’s termed a “training population” used to recalibrate prediction equations periodically. Suffice it to say, this is an added step that requires lots of time.

A shortcoming of the multistep approach is that selection bias can creep into the evaluation, since animals superior in genetic merit are the most likely ones to be genotyped. Saatchi adds that weighting estimates for the information included can be a primary source of biases.

Keep in mind that EPDs were already the gold standard of genetic prediction, even before genomic data was included in genetic evaluation.

Continue reading

by Will Townsend and Chip Kemp

The Problem

Imagine you had to find bulls for your operation but you didn’t know any breeders, nobody used EPDs, or even shared actual data. It’s obvious to anyone interested in building quality cattle and maximizing profit this would be a major blow to the bottom line.

Yet, this is how the feeder calf business exists today. Frequently, when purchasing quality feeder calves, we can receive crucial information regarding environmental factors such as management and health protocols, weights, etc. However, when it comes to genetic awareness, color and polled status are often asked to substitute for true knowledge. A common scenario, and at times the best-case scenario, is that the calf buyer has a previous relationship with the seller and has owned and experienced the performance of the seller’s calves before. In more rare cases, we may have some information on the seller’s bull purchases. Again, this is a powerful step forward. It provides at least some insight into a portion of the genetics within the program.  However, in a data-driven world, this level of genetic awareness is woefully inadequate.  Especially since the financial stakes for feeder calf procurement are even higher than the stakes for bull procurement. Understandably, most large cattle buyers have technology to estimate genetic and environmental performance on feeder cattle but that information is not public and, for obvious reasons, is kept to those companies. Therefore, price discovery as we know it today, most often does not take account the actual performance potential of a producer’s feeder cattle.

The Solution

Attempts to determine relative value of feeder cattle have been made for a long-time; however, certain issues have made it difficult.  The foremost limitation has been accurately gauging the profit potential in the largest genetic group within the beef industry — the crossbred calf. It is a known scientific fact that commercial beef producers wishing to maximize cowherd fertility and longevity must crossbreed. This not only provides them a sustainable and profitable cow base, but fortunately generates an end product that is known to be the best combination of growth potential and carcass merit — the crossbred calf.  The history of the Feeder Profit Calculator (FPC) has its roots in ASA’s Terminal Index ($TI). The $TI was developed over a decade ago by ASA in collaboration with Dr. Michael MacNeil, who was a USDA research geneticist at the time. The $TI is an economic selection index designed for selecting terminal sires.  Though $TI could do a reasonable job valuing feeder calves, it was determined that evolving $TI into a tool that could account for such things as a current accounting of prices/costs, heterosis, and non-genetic factors (e.g., vaccination status), would improve the accuracy of predicting feeder calf values. Dr. MacNeil, now with Delta G Genetics, was tapped to evolve $TI into that tool — the FPC. Many of the FPC’s non-genetic components were sourced by Dr. David Lalman of Oklahoma State University.  Providing the most robust genetic awareness of crossbred calves requires the most robust multi-breed genetic evaluation.  Fortunately, International Genetic Solutions (IGS) provides the ideal platform to generate unparalleled information on crossbred and composite feeder calves. IGS, along with its’ member associations, the science team at Theta Solutions, and scientific contributions by Dr. Matt Spangler of the University of Nebraska is ideally suited to provide the industry’s benchmark in gauging feeder calf value. The IGS Feeder Profit Calculator empowers producers to market with confidence and allows feeders to maximize their purchasing dollars.

The Future

Capitalizing on novel technology usually requires a tremendous learning curve and a major outlay of dollars.  Not this time! The IGS Feeder Profit Calculator is unique. It will offer a level of genetic awareness of crossbred feeder calves that has not been previously possible in the beef business.  The IGS science team, the IGS partner associations, and the world’s largest beef genetic evaluation database allows the IGS FPC to be delivered at no cost to producers. That is correct. No Cost!

Beef producers looking for a transparent and straightforward assessment of their calves will harness the power of IGS by simply making a call, sending an email, or visiting the IGS website.  IGS and/or breed association personnel will request information on herd health, basic management protocols, the bull battery used in previous years, and insight into the makeup of the cowherd. The more thorough the inputs from the producer, the better the predictive ability of the FPC.  While individual sire identification isn’t required, identification of the bulls used in the operation is required.  Producers will be asked to share preconditioning information and the health program in place.  The IGS FPC will be demonstrated at the 2017 NCBA Convention in Nashville, TN, and be made available to the public shortly thereafter. Three short demos will be held at the IGS booth each day of the convention.  For producers who have interest in having their calves evaluated through the IGS FPC please contact one of the IGS breed partners or contact beef@internationalgeneticsolutions.  com. Cattle feeders who are interested in integrating the capabilities of the IGS FPC into their purchasing decisions please use the same email. Additional information and highlights will be provided in the coming months.

The IGS Implementation of BOLT

Tuesday, 14 June 2016 15:58

Bruce Golden
Theta Solutions

Over the last 50 years we have had evolution of the statistical methods used to calculate genetic predictions, EPDs, for livestock. What drove the evolution of these methods? Knowledge of statistical models? New methods? Data? Enabling computer technology? Golden states that he believes the drive for better models has been a desire to increase the accuracy of prediction.

Golden and Garrick had written grants to write genetic prediction software in the past. This avenue appears to have dried up, so they decided to start a company, Theta Solutions, in order to fund the development of genetic prediction. The latest genetic prediction runs contained 46,000 animals with genomic data.

Theta Solutions uses graphical processing units, originally built for video gaming, to have a high performance computer at a relatively low cost. The BOLT software focuses on custom turnkey analyses, once the system is set up all one needs to do is feed it data.

Using non-GPU computing, Golden can solve 51 million equations in 1649 seconds. The fastest GPU implementation took 78 seconds.

Why do we use a Bayesian sampler for solving mixed models?

  • No accuracy approximation bias 
  • Can get PE covariance
  • Can apply marker selection methods
  • Can include prior information

With traditional methods, it took 23 seconds per sample, with new implementation can do a sample in 2 seconds. (Gibbs sampling is kind of like turning a statistical crank over and over to solve very complex equations, each sample is one turn of the crank.) They also parallelized the sampling, further speeding up the process. This parallelized processing is like working cattle with 100s of chutes rather than a single cute.

There are three ways to combine genomics with traditional EPDs,

  • blending Genomic BLUP (combine pedigree prediction with genomic prediction, two separate analyses)
  • single-step Genomic BLUP (combine pedigree relationships and genomic relationships, one analysis)
  • hybrid model (single step with marker effects)

Single-step genomic models outperform traditional EPDs. But, the hybrid model outperforms both models, especially for unproven animals. The purpose of the hybrid model is to squeeze more information out of the data.

Currently looking at a data set with 6 million pedigree records, 4.8 million birth weight records, and 1.9 million post weaning gain records, 46,402 genotyped animals and used 44,414 SNP markers.


Read the full article here

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