Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques.
Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques.
复制标题
毛里求斯食蟹猴中改进的全长杀伤细胞免疫球蛋白样受体转录物发现。
DOI：
10.1007/s00251-017-0977-7
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发表时间：
2017
期刊：
影响因子：
3.2
通讯作者：
O'Connor,DavidH
中科院分区：
文献类型：
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作者：
Prall,TrentM;Graham,MichaelE;Karl,JulieA;Wiseman,RogerW;Ericsen,AdamJ;Raveendran,Muthuswamy;AlanHarris,R;Muzny,DonnaM;Gibbs,RichardA;Rogers,Jeffrey;O'Connor,DavidH
杀伤细胞免疫球蛋白样受体 (KIR) 调节包括 HIV、疟疾和丙型肝炎在内的病原体的疾病进展。食蟹猴和恒河猴被广泛用作研究人类病原体的非人类灵长类动物模型，因此，人们投入了大量精力来表征其 KIR 遗传学。然而，之前的研究依赖于 cDNA 克隆和桑格测序，缺乏当前测序平台的吞吐量。在这项研究中，我们提出了一种利用 Pacific Biosciences 循环一致性测序 (CCS) 的高通量、全长等位基因发现方法。我们还描述了一种新的猕猴外显子组测序 (MES) 方法以及 Rhexome1.0 的开发，Rhexome1.0 是一种经过改造的目标捕获试剂，其中包括猕猴特异性捕获探针组。通过使用全基因组测序 (WGS) 和 MES 生成的序列读数来指导引物设计，我们能够提高 KIR 等位基因发现的敏感性。我们通过在毛里求斯食蟹猴 (MCM) 群体中定义 9 个新等位基因来证明这种敏感性的增加，MCM 是一个地理上孤立的群体，KIR 遗传受限，被认为已完全表征。最后，我们描述了一种直接从使用 WGS/MES 读取生成的序列读取中对 KIR 进行基因分型的方法。本文提出的研究结果通过将新基因与所有八种 KIR 单倍型相关联并证明至少存在一个与每种单倍型相关的 KIR3DS 基因，扩展了我们对 MCM 中 KIR 遗传学的理解。
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS). We also describe a new approach to Macaque Exome Sequencing (MES) and the development of the Rhexome1.0, an adapted target capture reagent that includes macaque-specific capture probe sets. By using sequence reads generated by whole genome sequencing (WGS) and MES to inform primer design, we were able to increase the sensitivity of KIR allele discovery. We demonstrate this increased sensitivity by defining nine novel alleles within a cohort of Mauritian cynomolgus macaques (MCM), a geographically isolated population with restricted KIR genetics that was thought to be completely characterized. Finally, we describe an approach to genotyping KIRs directly from sequence reads generated using WGS/MES reads. The findings presented here expand our understanding of KIR genetics in MCM by associating new genes with all eight KIR haplotypes and demonstrating the existence of at least one KIR3DS gene associated with every haplotype.