**6. Conclusion**

Genotyping the polymorphisms of MHC genes using targeted NGS technologies has been developed for humans and some nonhuman species to replace the use of other more cumber‐ some and less accurate procedures. We found that targeted NGS of DNA or RNA samples is feasible, productive, and generates high-quality MHC allele information from a large number of samples not easily achievable by other genotyping methods. We used second-generation sequencing protocols to target the DNA region and RNA subsets of interest in our NGS studies. It is likely that the longer sequence reads produced by third-generation platforms such as the Pacific Biosciences single-molecule real-time sequencing or the Oxford nanopore sequencing platform will enable and improve the task of MHC sequence phasing and haplotyping, although this has yet to be demonstrated and proved to be advantageous and more economical. Continued allele data collection for different species, improvements to the reagents, protocols, and data analysis tools also are likely to simplify procedures and lower the costs of generating sequencing data in future. Most species have numerous highly polymorphic MHC loci; hence, the many benefits of using NGS technologies are likely, in the near future, to replace many of the traditional genotyping methods for the investigation of human and animal MHC genes and their role in evolutionary biology, ecology, population genetics, disease, and transplan‐ tation.
