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Megaesophagus Genetic Research Update

Megaesophagus Genetic Research Update

September 21 st , 2021 The Fenway Foundation would like to take the opportunity to update the public on our progress to date regarding our research into the genetic inheritance of megaesophagus in the Friesian horse. We embarked on this project in November of 2020 at the request of the KFPS in collaboration with the University of Kentucky’s Gluck Equine Center and Wageningen University in the Netherlands. Our goal is the development of a genetic test that will assist in breeding decisions and hopefully over time eliminate this debilitating and sometimes fatal genetic flaw in our horses both young and old. As we near the one-year mark, we wanted to take the opportunity to fill you in on where the project is currently.

Research Study Structure

After discussion with the research team at UK, it was decided the project would focus its efforts on candidate horses with a very strict set of parameters, specifically Friesian horses that presented with megaesophagus as foals or young horses (<5 yrs old) with a clinical diagnosis (esophageal endoscopy or barium swallow study). By narrowing our study to just foals and young horses our goal was to investigate the inherited (congenital) form of the megaesophagus vs. the acquired form of disease which does not typically present until a horse is older. The research team determined the best approach to the study was to analyze family groups based off of DNA blood samples from a foal with megaesophagus and his/her parents and siblings.

Many months were spent identifying foals and their family groups and this initial phase of the project has undoubtably been the most challenging. Once a foal was identified and its clinical diagnosis was confirmed, it took considerable time to track down owners of the parents and siblings and secure their support for the project. While many owners were incredibly supportive of our research, some stallion owners and owners of siblings unfortunately did not wish to participate. Once support was secured, we then waited weeks, or months in many cases, for blood samples to arrive at the University of Kentucky.

When a sample arrives at the lab, the team extracts the DNA profile from each blood sample. The DNA profile is then sent off for genome sequencing, a process which identifies the order of the four chemical building blocks, called &quot;bases&quot;, that make up a DNA molecule. The resulting “sequence” reveals the type of genetic information that is carried in a particular DNA segment. Researchers then compare large stretches of DNA from different horses against a reference by running it through computer models which search for different versions of genes, called variants. By correctly identifying the unique variant (or variants) which causes megaesophagus, researchers can then work to develop a genetic test for the disease.

Progress to Date

In May of 2021, the DNA from the first family group was sequenced and aligned to the horse reference sequence (EquCab 3.0). Then, the research team ran a variant calling program on this data based on a recessive mode of inheritance (carriers heterozygous, affected animals homozygous). This first run-through resulted in the identification of approximately 65,000 possible variants which could be responsible for megaesophagus.

In July 2021, additional family groups were sequenced and aligned to the reference which further reduced the number of possible variants to 969, spanning across 135 different genes. Analysis of the potential variants is currently ongoing. However, this is still a large number of variants to sort through. Each family group we add to the study will further reduce the possible variants for megaesophagus.

Thus far, analysis has identified one variant of particular interest because it appeared to be a significant insertion that followed the predicted inheritance pattern for megaesophagus. However, because of its nature, this variant is complex to analyze so the research team is in the early stages of resequencing this region. It is premature to focus on this variant as it may simply be a variation that occurs in the Friesian breed, but this will be fully investigated.

How You Can Help Participate

To progress our research forward at a sufficient pace, we need to add additional family groups to the study. This will help us reduce the number of possible variants to investigate and it will indicate whether the current variant under study mentioned above is still of interest. Weaning will soon begin this fall, and this is the most common time foals with megaesophagus first present with symptoms of choke. If you become aware of any foals affected by megaesophagus, please encourage the owners to contact the Fenway Foundation for Friesian Horses.

Additionally, if you are contacted as a stallion owner, mare owner or sibling owner and your horse is requested to give a blood sample to help form a family group for the study- please consider participating! The identity and pedigrees of the horses involved will remain strictly confidential and will not appear in any later publication of this research. The longer it takes for us to supply adequate numbers of family groups for the study, the further we remain from developing a genetic test for megaesophagus. This means more horses may needlessly suffer from this terrible disease.


We would love to see the Friesian community come together and support this project with widespread enthusiasm. Each dollar you can contribute truly counts! Genetic research is not an inexpensive endeavor and for each horse we add to the study our costs for DNA extraction and genome sequencing are $730. To date, over 20 horses have participated in the study. Owner reimbursement fees for collection and shipment of samples and any research fees we incur are an additional cost to the project. We wish to thank FHANA for their generous donation to the project and those individuals who have donated thus far. Additionally, we are incredibly grateful for the horse owners who have participated in the study– we could not have gotten this far without your support!

To make a donation to the Friesian Megaesophagus Genetic Research Fund, please go to the following link:

More Information

To learn more about megaesophagus, please go to the following link:

For help and community support for horses with megaesophagus please join our Facebook group:



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