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Home / Equine Research Bank / Anim Genet / Simulated validation of intron-less transgene detection usin...
Animal genetics2021; 52(5); 759-761; doi: 10.1111/age.13127

Simulated validation of intron-less transgene detection using DELLY for gene-doping control in horse sports.

Abstract: Gene doping is prohibited in horseracing. In a previous study, we developed a method for non-targeted transgene detection using DELLY, which is based on split-read (SR) and paired-end (PE) algorithms to detect structural variants, on WGS data. In this study, we validated the detection sensitivity of DELLY using artificially generated sequence data of 12 target genes. With DELLY, at least one intron was detected as a deletion in eight targeted genes using the 150 bp PE read WGS data, whereas all targeted genes were detected by DELLY using the 100 bp PE read data. The detection sensitivity was higher in 100 bp PE reads than in 150 bp PE reads, despite a lower total sequence coverage, probably because of mismatch tolerance between the mapped reads and reference genome. In addition, it was observed that the average intron size detected by SR alone was 293 bp and that that detected by both SR and PE was 8924 bp. Thus, we showed that transgenes with various intron-exon structures could be detected using DELLY, suggesting its application in gene-doping control in horses.
© 2021 Stichting International Foundation for Animal Genetics.
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Publication Date: 2021-08-02 PubMed ID: 34339052DOI: 10.1111/age.13127Google Scholar: Lookup
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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.

The study involves validating a computational method called DELLY for the non-targeted detection of illegal transgenes (artificially inserted genes) performance-enhancing doping in horses. The study uses artificially generated sequence data and reveals a higher detection sensitivity with 100 bp paired-end reads data as compared to 150 bp despite lower total sequence coverage.

Understanding Gene-Doping

  • Gene doping is a subset of genetic modification that athletes might utilize to enhance their performance, including horseracing. This is generally seen as unethical and is typically banned in competitive sports.

Detection of Gene Doping with DELLY

  • To combat gene doping, the study looks at a method called DELLY that uses split-read and paired-end algorithms to discover structural variations within the genome.
  • The DELLY method was developed in a previous study and this current study serves as a validation of its detection sensitivity.

Data Generation and Findings

  • The researchers validated DELLY using artificially generated sequence data for 12 target genes relevant to horseracing performance enhancement.
  • The detection sensitivity of DELLY was found to be higher with 100 base pair (bp) paired-end (PE) reads as compared to 150 bp PE reads despite lower total sequence coverage.
  • With DELLY, at least one intron (noncoding sections of a gene) was detected as a deletion in eight targeted genes using 150 bp PE read data, whereas all targeted genes were detected by DELLY with the 100 bp PE read data.

Significance of the Study

  • The discovery implies that DELLY can be a useful tool to detect gene doping within horse sports, even when the total sequence coverage is relatively low.
  • The researchers suggest that the difference in detection sensitivity can be attributed to the mismatch tolerance between the mapped reads and the reference genome.

Intron Detection

  • The study also evaluated the intron size detection by split-read (SR) and paired-end (PE) algorithms. The average intron size detected by SR alone was 293 bp, and that detected by both SR and PE was 8924 bp.
  • The ability to detect transgenes with varying intron-exon structures demonstrates the versatility of DELLY as a tool for gene-doping detection.

Cite This Article

APA
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota K, Kusano K, Nagata S. (2021). Simulated validation of intron-less transgene detection using DELLY for gene-doping control in horse sports. Anim Genet, 52(5), 759-761. https://doi.org/10.1111/age.13127

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 52
Issue: 5
Pages: 759-761

Researcher Affiliations

Tozaki, T
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.
Ohnuma, A
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.
Kikuchi, M
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.
Ishige, T
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.
Kakoi, H
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.
Hirota, K
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.
Kusano, K
  • Equine Department, Japan Racing Association, 6-11-1 Roppongi, Minato, Tokyo, 106-8401, Japan.
Nagata, S
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.

MeSH Terms

  • Algorithms
  • Animals
  • Animals, Genetically Modified
  • Doping in Sports
  • Exons
  • Horses / genetics
  • Introns
  • Sports
  • Transgenes

Grant Funding

  • 2020-2021 / Japan Racing Association

References

This article includes 10 references
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Citations

This article has been cited 1 times.
  1. Tozaki T, Ohnuma A, Nakamura K, Hano K, Takasu M, Takahashi Y, Tamura N, Sato F, Shimizu K, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Hamilton NA, Nagata SI. Detection of Indiscriminate Genetic Manipulation in Thoroughbred Racehorses by Targeted Resequencing for Gene-Doping Control.. Genes (Basel) 2022 Sep 4;13(9).
    doi: 10.3390/genes13091589pubmed: 36140757google scholar: lookup
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