Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we determine MHC class I and class II genotypes using target-capture probes enriched for MHC sequences, a method we term macaque exome sequence (MES) genotyping. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.

中文翻译：

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恒河猴外显子组序列的 MHC 基因分型。


印度恒河猴主要组织相容性复合体 (MHC) 变异会影响移植和传染病研究的结果。通常，会对恒河猴进行 MHC 基因分型，以识别可能导致意外结果的变异。由于 MHC 只是基因组中变异可能影响实验结果的一个区域，因此同时分析猕猴 MHC 和蛋白质编码基因组其余部分变异的策略将是有用的。在这里，我们使用富含 MHC 序列的目标捕获探针来确定 MHC I 类和 II 类基因型，我们将这种方法称为猕猴外显子组序列 (MES) 基因分型。对于 27 只印度恒河猴队列，我们​​描述了从 MES 数据获取 MHC 基因型的两种方法，并证明用这些方法获得的 MHC I 类和 II 类基因分型结果分别与预期 MHC 基因型的一致性为 98.1% 和 98.7% 。相比之下，通过短多重 PCR 扩增子深度测序获得的传统 MHC 基因分型结果与该队列的预期只有 92.6% 的一致性。