Detection of two equine trisomies using SNP-CGH.

Chromosomal aberrations in the horse are known to cause congenital abnormalities, embryonic loss, and infertility. While diagnosed mainly by karyotyping and FISH in the horse, the use of SNP array comparative genome hybridization (SNP-CGH) is becoming increasingly common in human diagnostics. Normalized probe intensities and allelic ratios are used to detect changes in copy number genome-wide. Two horses with suspected chromosomal abnormalities and six horses with FISH-confirmed aberrant karyotypes were chosen for genotyping on the Equine SNP50 array. Karyotyping of the first horse indicated mosaicism for an additional small, acrocentric chromosome, although the identity of the chromosome was unclear. The second case displayed a similar phenotype to human disease caused by a gene deletion and so was chosen for SNP-CGH due to the ability to detect changes at higher resolutions than those achieved with conventional karyotyping. The results of SNP-CGH analysis for the six horses with known chromosomal aberrations agreed completely with previous karyotype and FISH analysis. The first undiagnosed case showed a pattern of altered allelic ratios without a noticeable shift in overall intensity for chromosome 27, consistent with a mosaic trisomy. The second case displayed a more drastic change in both values for chromosome 30, consistent with a complete trisomy. These results indicate that SNP-CGH is a viable method for detection of chromosomal aneuploidies in the horse.