Identifying Major Histocompatibility Complex (MHC) Alleles in Rhesus Macaques Using the Next Generation Sequencing MiSeq Platform and an Open Source Allele Identification Program.

Next generation sequencing (NGS) technology has revolutionized the ability to identify\ud important gene sets, including Major Histocompatibility Complex (MHC) alleles, the most polymorphic set of genes in the human and non-human primate genomes. The characterization of MHC class I and II alleles serves various roles in the development of resources and tools needed for vaccine development. In this study, we explored the use of the Illumina MiSeq sequencing system along with the development of software tools to identify MHC class I A and B loci in rhesus macaques. The MiSeq platform combines shotgun sequencing and bridge PCR to provide a high degree of sequence coverage through millions of short reads. The large quantity of reads allows for the statistical exclusion of sequencing errors present in the sequence data. As an\ud alternative to commercially available packages, this study presents the software code for an easily adaptable, user-friendly analysis tool that can be used to genotype rhesus macaques MHC alleles with next generation sequencing data. This tool, referred to as the ???Allele Identification Program??? (AIP), can be employed by anyone possessing basic computer programming skills. Using the AIP to analyze the MiSeq data proved effective, efficient and inexpensive, potentially making full-length MHC sequencing more accessible for nonhuman primate research.Biological Science