Evidence of a genomic insertion in intron 2 of SOD1 causing allelic drop‐out during routine diagnostic testing for canine degenerative myelopathy

• Published in: Animal genetics Vol. 48; no. 3; pp. 365 - 368
• Main Authors: Turba, M. E., Loechel, R., Rombolà, E., Gandini, G., Gentilini, F.
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.06.2017
• Subjects: allele drop‐out; Alleles; Animals; Breeding; Dog Diseases - genetics; Dogs; Dogs - genetics; Gene Frequency; Genes; Genotype; Genotyping Techniques; Homozygote; Introns; Laboratories; Linkage Disequilibrium; Mutagenesis, Insertional; Neurodegenerative Diseases - genetics; Neurodegenerative Diseases - veterinary; Spinal Cord Diseases - genetics; Spinal Cord Diseases - veterinary; superoxide dismutase 1; Superoxide Dismutase-1 - genetics; systematic genotyping error; dogs; allele drop-out; systematic genotyping error; superoxide dismutase 1
• ISSN: 0268-9146; 1365-2052
• DOI: 10.1111/age.12525

Summary Degenerative myelopathy is a severe and progressive neurodegenerative disease and, in the majority of breeds, is associated with the c.118G>A substitution in exon 2 of the canine superoxide dismutase 1 (SOD1) gene. Our laboratories have been engaged in determining the cause of many discordant findings between the parental and the offspring genotypes found by different laboratories. In both cases, the discordant findings refer to actual heterozygous dogs that had been typed as homozygous for the variant allele. To that aim, the genomic context of the causative variant was investigated in two Hovawart dogs. An insertion of 54 nucleotides composed of a poly‐T stretch and 15 nucleotides containing the duplication of the exon 2–intron 2 junction was found. The insertion was responsible for the partial mismatch of the reverse primer used for a direct sequencing assay. The mismatch hampered the amplification of the corresponding allele and caused an evident drop‐out effect. The insertion is in complete linkage disequilibrium with the c.118G allele. The allele containing the insertion was highly prevalent in Hovawart dogs, accounting for the 26.6% of allele frequency. The insertion was also found in other unrelated breeds such as Rough Collies and Standard Poodles. In conclusion, the study illustrates the importance of correctly designing the primers to avoid inaccurate genotyping of the degenerative myelopathy causative variant in exon 2 of the SOD1 gene.