MHC haplotype for rhesus macaques.

Summary of comprehensive MHC class I genotypes of Chinese-origin rhesus macaques as determined by Sanger-based and Roche/454 pyrosequence-based typing. MHC class I sequences from each animal were compared to an in-house database of all known Mamu sequences using BLASTN. Total numbers of sequences evaluated and unique MHC-I alleles detected for each animal are listed. Pyrosequencing provided significantly greater depth of coverage, but the method used was still being established at the time the genotyping was performed and as such, most animals were typed using Sanger-based methods. Animals observed with MHC-I alleles or haplotypes associated with control of SIV replication (Mamu-B*003 and Mamu-B*017) are indicated by shading. The percentage of sequence reads corresponding to a given protective allele lineage in each animal are shown in burgundy. Other alleles associated with control, such as the Indian-origin rhesus macaque alleles Mamu-A1*001, Mamu-B*008 or Mamu-B*047, were not observed in this cohort. Only alleles with known positive association to SIV control are displayed here; there is always the potential that positive associations to control will be identified for other alleles observed in this cohort in the future, since most alleles expressed by Chinese-origin rhesus macaques have not been studied for correlations to SIV disease outcome.

本数据集为基于桑格测序法（Sanger-based）与罗氏454焦磷酸测序法（Roche/454 pyrosequence-based）分型的中国来源恒河猴完整主要组织相容性复合体I类（MHC class I）基因型汇总。本研究借助BLASTN工具，将每只受试动物的MHC I类序列与自建的全部已知Mamu序列数据库进行比对，本数据集汇总列出了每只受试动物的评估序列总数与检测到的独特MHC-I等位基因数量。焦磷酸测序法的测序覆盖深度显著更高，但在本次基因分型实验开展时，该方法仍处于优化完善阶段，因此多数受试动物采用桑格测序法完成分型。携带与猴免疫缺陷病毒（SIV）复制控制相关的MHC-I等位基因或单倍型（包括Mamu-B*003与Mamu-B*017）的受试动物，已通过阴影标注予以区分。每只受试动物中对应特定保护性等位基因谱系的序列读段（sequence reads）占比，以酒红色标注展示。其他与病毒控制相关的等位基因，例如印度来源恒河猴的Mamu-A1*001、Mamu-B*008及Mamu-B*047等位基因，在本次受试队列中未被检测到。本次仅展示已被证实与SIV控制存在正相关的等位基因；由于中国来源恒河猴表达的多数等位基因尚未开展与SIV疾病结局相关性的研究，因此未来仍有可能在本队列检测到的其他等位基因中发现具备病毒控制相关功能的等位基因。