Comparative analysis of whole exome sequencing kits for the canine genome

Objectives As the public's interest in companion dogs grows, health issues in these animals are also emerging, necessitating the optimization of whole exome sequencing (WES) as a valuable method for disease prediction. While WES targeting the human genome is well established, WES targeting the canine genome is understudied, and there is a need to find effective analysis kits. Methods We compared and analyzed the performance of three WES kits from Twist and Agilent using the canine genome as the target to perform genetic analysis of canine diseases effectively. The levels of total reads, the duplication rate, and variant calling in canine genomic DNA samples from seven healthy dogs (three beagles, one bichon fry, one maltese, one welsh corgi, and one mixed breed) without any interventions were examined through WES via Twist and Agilent kits. Results We found that while Twist had the lowest total read number, the number of reads in the SSXT series was significantly (P<0.05) greater. Twist showed low evenness and high standard deviation, but the SSXT series showed relatively high evenness. Compared with Twist, the SSXT series from a depth of 30x presented a significantly (P<0.05) greater target ratio. Among the four kits, the significantly lowest duplicate ratio was confirmed for SSXT (O/N) (30% lower than Twist). Conclusion The most important performance of the kit, the number of variants detected, was 48,302 for Twist and 130,506 for SSXT (O/N). On the basis of the performance comparison results, SSXT (O/N) was found to have the best performance.

Dergi

PLOS ONE

Yıl

2024

Cilt

19

Sayı

11

ISSN

1932-6203

DOI

10.1371/journal.pone.0312203

WoS UID

WOS:001358284200007

Yayını aç (DOI)