Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany.
Université Paris-Saclay, CNRS, Inria, Laboratoire de recherche en informatique, 91405, Orsay, France.
Sci Rep. 2020 Apr 30;10(1):7339. doi: 10.1038/s41598-020-64312-w.
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
高度多态性的人类白细胞抗原（HLA）在适应性免疫中发挥着关键作用，并与各种复杂疾病相关。使用古代 DNA（aDNA）数据准确分析 HLA 基因对于理解它们在人类适应病原体中的作用至关重要。在这里，我们描述了 TARGT 管道，用于从低覆盖率鸟枪法序列数据中靶向分析多态性位点。该管道已成功应用于中世纪的 aDNA 样本，并使用模拟的 aDNA 和来自 1000 基因组计划的现代经验序列数据进行了验证。因此，TARGT 管道能够在历史（和现代）人类群体中准确分析 HLA 多态性。
