A genotyping method combining primer competition PCR with HRM analysis to identify point mutations in Duchenne animal models

Dystrophin-null sapje zebrafish is an excellent model for better understanding the pathological mechanisms underlying Duchenne muscular dystrophy, and it has recently arisen as a powerful tool for high-throughput screening of therapeutic candidates for this disease. While dystrophic phenotype in sapje larvae can be easily detected by birefringence, zebrafish genotyping is necessary for drug screening experiments, where the potential rescue of larvae phenotype is the primary outcome. Genotyping is also desirable during colony husbandry since heterozygous progenitors need to be selected. Currently, sapje zebrafish are genotyped through techniques involving sequencing or multi-step PCR, which are often costly, tedious, or require special equipment. Here we report a simple, precise, cost-effective, and versatile PCR genotyping method based on primer competition. Genotypes can be resolved by standard agarose gel electrophoresis and high-resolution melt assay, the latter being especially useful for genotyping a large number of samples. Our approach has shown high sensitivity, specificity, and reproducibility in detecting the A/T point mutation in sapje zebrafish and the C/T mutation in the mdx mouse model of Duchenne. Hence, this method can be applied to other single nucleotide substitutions and may be further optimized to detect small insertions and deletions. Given its robust performance with crude DNA extracts, our strategy may be particularly well-suited for detecting single nucleotide variants in poor-quality samples such as ancient DNA or DNA from formalin-fixed, paraffin-embedded material. We thank Anna Wojtalewicz and Leire Escudero for technical help, and Dr. Javier Ruiz-Ederra for helpful discussions on HRM assay. This work was supported by funding from Health Institute Carlos III (ISCIII) and the European Regional Development Fund (ERDF/ESF, "Investing in your future"), Grant PI17/00676; from Duchenne Parent Project Spain (DPPE); from the Basque Government (2016111091); and from the University of the Basque Country UPV/EHU (PPGA19/58). H.L.-F. and L.M.-M. hold predoctoral fellowships from the University of the Basque Country, J.L.-E. holds a predoctoral fellowship from the Basque Government, and A.V.-I. holds a Ramon y Cajal contract funded by the Spanish Ministry of Economy and Competitiveness