Whether it is behaviour, an orthopedic disease or any other phenotype with a genetic background, the strength of breeding programs is that by correctly phenotyping, progress can be achieved and success rates increased. Depending on the technique that is used, this progress is however achieved at various speeds. Genomic selection is the state-of-the-art technique that has demonstrated its value in other species, but so far has not yet been used in assistance dogs. Here, we will evaluate genomic selection, based on an entirely novel targeted sequencing-based approach that allows a far more accurate assessment of the actual phenotypic value of the dog, while at the same time checking for the presence of genetic diseases.