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With the availability of the horse genome reference sequence for the past 10 years, several new cutting edge technologies have emerged for horse genome and chromosome analysis. Single nucleotide polymorphism (SNP) arrays can detect aneuploidies and small sub‐chromosomal deletions and duplications at a resolution not achieved by conventional karyotyping or FISH. An even more powerful approach is next generation sequencing (NGS), which allows the analysis of the whole genome sequence of an individual horse. Although SNP arrays and NGS are widely used in horse disease genetics, their application in clinical cytogenetics has been limited, likely because of the relatively high cost and demanding bioinformatics. Also, neither platform is able to ascertain cell to cell variations or accurately resolve mosaic/chimeric cytogenetic patterns.

Perhaps the most promising technology for next generation cytogenetics is the BioNano Genomics Irys® System, which utilizes nanochannel technology and high resolution imaging of high molecular weight DNA. The platform can detect almost any structural or numeric changes in the genome, including balanced translocations and inversions. It is anticipated that the BioNano Irys® System will fill a role between cytogenetics and NGS, given that the estimated price per sample will get close to that of conventional clinical cytogenetic analysis.

Table 22.1 Horse clinical cytogenetics service laboratories in different countries.

Country, City	Laboratory	Director/Principal Investigator	Contact
Poland, Krakow	Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture	Monika Bugno Poniewierska	monika.bugno.poniewierska@gmail.com
Spain, Cordoba	Department of Genetics, University of Cordoba	Miguel Moreno‐Millán	Ge1momim@uco.es
Canada, Guelph	KARYOTEKK, University of Guelph	Allan W. King	info@karyotekk.com; http://www.karyotekk.com/home
USA, Texas, College Station	Molecular Cytogenetics, Texas A&M University	Terje Raudsepp	http://vetmed.tamu.edu/labs/cytogenics‐genomics

Despite the promises of novel technology, it is unlikely that it will entirely replace conventional and FISH‐based chromosome analysis in horses. Traditional cytogenetics is still the most straightforward and cost‐effective approach and will remain the gold standard for the initial evaluation of breeding animals and individuals with reproductive or developmental disorders.