@article{01JPF63QZ6Y8NQ82R0G1R45ZM8,
  abstract     = {{Background: Whole-exome sequencing (WES) is used to selectively sequence all exons of protein-coding genes. WES is considered as a cost-effective and direct approach for identifying phenotype-associated variants in protein-coding regions and is as such situated between the traditional Sanger sequencing and whole genome sequencing (WGS). While WES is already widely used as a clinical tool in human and medical genetics, its use in veterinary medicine is currently restricted to research purposes. In this article, we aimed to provide baseline performance characteristics of a WES design to assess its suitability with future applications in veterinary clinical genetics in mind. Methods: To assess the potential of WES in a clinical setting for dogs, 49 canine samples underwent capture, sequencing and analysis for the presence of 352 known phenotype-associated variants. The sequencing performance was compared for three types of variants, based on their size and location: single nucleotide variants (SNVs) inside exons, larger indel variants (<= 20 bp) inside exons and intronic variants. Results: On average, 85 % and 82 % of the exonic SNPs and larger variants were sequenced at a sequencing depth of >= 10x in the 49 samples, respectively. In the best performing sample, 94 % of the exonic SNPs were covered at least 10x, whereas in the worst performing sample, still 71 % of the exonic SNPs had an average sequencing depth of more than 10x. Conclusion: To our knowledge, this is the first report that describes the performance of a research-intended WES design if it would be used in clinical genetics. This study found that WES demonstrated high efficacy in detecting variants located within target regions, including those that were not initially included in the design. However, the performance varied across different variants. The next steps would be the development of improved designs and settings to ameliorate the results.}},
  author       = {{Boeykens, Fréderique and Bogaerts, Evelien and Vossaert, Liesbeth and Peelman, Luc and Van Nieuwerburgh, Filip and Saunders, Jimmy and Broeckx, Bart}},
  issn         = {{2001-0370}},
  journal      = {{COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}},
  keywords     = {{Whole Exome Sequencing (WES),Canine genetics,Veterinary diagnostics,Genetic,Screening,Variant detection,Veterinary clinical genetics,Diagnostic tool,SPLICE DONOR,COAT COLOR,MUTATION,GENE,GUIDELINES,VARIANTS,ABSENCE,TIME,SNP}},
  language     = {{eng}},
  pages        = {{960--968}},
  title        = {{Whole exome sequencing as a screening tool in dogs : a pilot study}},
  url          = {{http://doi.org/10.1016/j.csbj.2025.03.008}},
  volume       = {{27}},
  year         = {{2025}},
}

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