This article presents the strategy to evaluate candidate mutations underlying QTL or responsible for genetic defects, based upon the design and large-scale use of the Eurogenomics custom SNP chip set up for bovine genomic selection. Some variants under study originated from mapping genetic defects, embryonic lethals, or QTL by GWAS. Other variants originated from a reverse genetics approach and were selected according to their annotation. Because of the limitation in chip size, these variants were severely selected. For instance, structural variants were required to affect a gene. Loss-of-function variants were preferred to deleterious non synonymous variants. An incremental process was used, with one or two chip versions each year, the less informative variants being replaced by new candidates. Many examples are presented. Expected results are: confirmation of effects in large independent populations; estimation of allelic frequencies in different breeds; accumulation of individual genotypes. When confirmed, a variant can be used in a straightforward way by the industry in breeding programs by switching its status on the chip. Keywords: bovine, custom chip, causal variant, genetic defect, GWAS analysis