Simulated validation of intron-less transgene detection using DELLY for gene-doping control in horse sports.
horseracing
structural variant
whole genome sequencing
Journal
Animal genetics
ISSN: 1365-2052
Titre abrégé: Anim Genet
Pays: England
ID NLM: 8605704
Informations de publication
Date de publication:
Oct 2021
Oct 2021
Historique:
accepted:
22
07
2021
pubmed:
3
8
2021
medline:
24
9
2021
entrez:
2
8
2021
Statut:
ppublish
Résumé
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.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
759-761Subventions
Organisme : Japan Racing Association
ID : 2020-2021
Informations de copyright
© 2021 Stichting International Foundation for Animal Genetics.
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