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Animal genetics2025; 56(5); e70047; doi: 10.1111/age.70047

Evaluation of a targeted enrichment panel for gene editing detection and assessment of population variation in Thoroughbred horses.

Abstract: Gene editing and genome manipulation offer great promise for treating diseases in both humans and animals. There is a danger, however, that this technology could be used for other purposes such as performance enhancement. To detect such 'gene doping' events, we evaluated a targeted enrichment panel and next-generation sequencing to assess its reproducibility, sensitivity, and capability of variant detection on a wide variety of samples and biological matrices. The panel was verified against existing data for the myostatin gene, a PCR-based SNP panel, and whole genome sequencing in a subset of samples. As successful detection of seamless edits will rely on a detailed understanding of the natural population, we also screened over 170 Thoroughbreds and catalogued numerous novel variants. These included several resulting in coding alterations, and a structural variant. Samples spiked with transgenic cDNA-based material to simulate gene doping events were detected down to 3.2% mosaicism, giving confidence that mosaic mutations resulting from embryonic introduction of gene editing reagents can be detected using these methods. The ability of software packages to detect gene doping events was also assessed, including multiple genome alignment tools, variant callers, and structural variant callers. Freebayes performed strongest at SNP-based editing detection, and Delly and Manta had complementary advantages depending on the mutation type. For routine testing, a multi-faceted approach to calling should be taken to maximise the detection capabilities.
© 2025 Stichting International Foundation for Animal Genetics.
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Publication Date: 2025-10-13 PubMed ID: 41081551DOI: 10.1111/age.70047Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Plain Language Overview

  • This study evaluated a specialized genetic testing method to detect gene editing in Thoroughbred horses, focusing on identifying both natural genetic variation and artificially introduced changes that could be used for performance enhancement (“gene doping”).
  • The research demonstrated the effectiveness of the method in detecting small levels of edited genetic material and assessed various software tools to optimize reliable detection of gene edits in horse populations.

Introduction to the Research

  • Gene editing and genome manipulation have potential applications for treating diseases in humans and animals, but there is concern about misuse for non-therapeutic purposes such as enhancing athletic performance in horses.
  • Detecting unauthorized gene editing or “gene doping” in animals presents challenges because edits can be subtle and difficult to differentiate from natural genetic variation.
  • This research aimed to evaluate a targeted enrichment panel combined with next-generation sequencing (NGS) technology for reliably detecting gene editing in Thoroughbred horses.

Methods and Testing Approach

  • The targeted enrichment panel was designed to focus on specific gene regions, including the myostatin gene, which affects muscle growth and is often targeted for performance enhancement.
  • The panel’s performance was benchmarked against:
    • Existing genetic data for the myostatin gene
    • A PCR-based single nucleotide polymorphism (SNP) panel
    • Whole genome sequencing data from a subset of samples
  • The study included over 170 Thoroughbred horses to build a comprehensive catalog of natural genetic variation, including novel variants and structural variants—key for differentiating spontaneous from artificial edits.
  • To simulate gene doping events, horse DNA samples were spiked with transgenic cDNA to test the method’s sensitivity in detecting edited sequences, even when present at low levels (mosaicism as low as 3.2%).
  • Various bioinformatic tools were evaluated for their ability to detect gene editing from sequencing data, including:
    • Multiple genome alignment tools
    • Variant callers such as Freebayes
    • Structural variant callers like Delly and Manta

Key Findings

  • The targeted enrichment panel showed high reproducibility and sensitivity, effectively detecting gene edits in a variety of biological samples and matrices.
  • The extensive cataloging of variants in Thoroughbreds revealed numerous novel SNPs and at least one structural variant, highlighting the complexity of natural genetic diversity.
  • The detection limit for introduced gene edits was as low as 3.2% mosaicism, indicating that even minor edited cell populations (such as those arising from early embryonic gene editing) can be identified.
  • Freebayes outperformed other variant callers in detecting SNP-based gene edits, while Delly and Manta had complementary strengths in identifying structural variants, depending on mutation type.
  • For routine surveillance or testing, using a combination of variant calling software improves the probability of detecting different types of edits, suggesting a multi-faceted bioinformatics approach is optimal.

Implications and Conclusions

  • This research demonstrates the feasibility of detecting gene doping in horses using targeted sequencing panels combined with advanced computational analyses.
  • The comprehensive understanding of natural population genetics is critical to confidently identify artificial edits versus naturally occurring variants.
  • Multi-tool software pipelines enhance detection capabilities and should be implemented in monitoring programs for gene editing in animals involved in sports or breeding.
  • The approaches validated here can serve as a model for developing gene doping detection frameworks in other species or contexts where gene editing may be misused.

Cite This Article

APA
Maniego J, Swinburne J, Hincks P, Habershon-Butcher J, Given J, Ryder E. (2025). Evaluation of a targeted enrichment panel for gene editing detection and assessment of population variation in Thoroughbred horses. Anim Genet, 56(5), e70047. https://doi.org/10.1111/age.70047

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 56
Issue: 5
Pages: e70047

Researcher Affiliations

Maniego, Jillian
  • LGC Ltd, Cambridgeshire, UK.
Swinburne, June
  • LGC Ltd, Cambridgeshire, UK.
Hincks, Pamela
  • LGC Ltd, Cambridgeshire, UK.
Habershon-Butcher, Jocelyn
  • British Horseracing Authority, London, UK.
Given, James
  • British Horseracing Authority, London, UK.
Ryder, Edward
  • LGC Ltd, Cambridgeshire, UK.

MeSH Terms

  • Animals
  • Horses / genetics
  • Gene Editing / veterinary
  • Gene Editing / methods
  • Polymorphism, Single Nucleotide
  • High-Throughput Nucleotide Sequencing / veterinary
  • Myostatin / genetics
  • Reproducibility of Results

Grant Funding

  • British Horseracing Authority

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