Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi, 320-0851, Japan.
Equine Department, Japan Racing Association, 6-11-1 Roppongi, Minato, Tokyo, 106-8401, Japan.
Anim Genet. 2021 Oct;52(5):759-761. doi: 10.1111/age.13127. Epub 2021 Aug 2.
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.
赛马比赛中禁止使用基因兴奋剂。在之前的研究中，我们开发了一种使用 DELLY 的非靶向转基因检测方法，该方法基于分割读取 (SR) 和配对末端 (PE) 算法，可在 WGS 数据上检测结构变体。在这项研究中，我们使用 12 个目标基因的人工生成序列数据验证了 DELLY 的检测灵敏度。使用 DELLY，至少一个内含子在使用 150 bp PE 读 WGS 数据的八个靶向基因中被检测为缺失，而所有靶向基因均使用 100 bp PE 读数据被 DELLY 检测到。尽管总序列覆盖率较低，但 100 bp PE 读的检测灵敏度高于 150 bp PE 读，可能是由于映射读与参考基因组之间的错配容忍度。此外，观察到仅通过 SR 单独检测到的平均内含子大小为 293 bp，通过 SR 和 PE 共同检测到的平均内含子大小为 8924 bp。因此，我们表明可以使用 DELLY 检测具有各种内含子-外显子结构的转基因，这表明其在马的基因兴奋剂控制中的应用。
