Background Human endogenous retroviruses (HERVs), suspected to be transposition-defective, may reshape the transcriptional network of the human genome by regulatory elements distributed in their long terminal repeats (LTRs). HERV-K (HML-2), the most preserved group with the least number of accumulated of mutations, has been associated with aberrant gene expression in tumorigenesis and autoimmune diseases. Because of the high sequence similarity between different HERV-Ks, current methods have limitations in providing genome-wide mapping specific for individual HERV-K (HML-2) members, a major barrier in delineating HERV-K (HML-2) function. Results In an attempt to obtain detailed distribution information of HERV-K (HML-2), we utilized a PCR-based target enrichment sequencing protocol for HERV-K (HML-2) (PTESHK) loci, which not only maps the presence of reference loci, but also identifies non-reference loci, enabling determination of the genome-wide distribution of HERV-K (HML-2) loci. Here we report on the genomic data obtained from three individuals. We identified a total of 978 loci using this method, including 30 new reference loci and 5 non-reference loci. Among the 3 individuals in our study, 14 polymorphic HERV-K (HML-2) loci were identified, and solo-LTR330 and N6p21.32 were identified as polymorphic for the first time. Conclusions Interestingly, PTESHK provides an approach for the identification of the genome-wide distribution of HERV-K (HML-2) and can be used for the identification of polymorphic loci. Since polymorphic HERV-K (HML-2) integrations are suspected to be related to various diseases, PTESHK can supplement other emerging techniques in accessing polymorphic HERV-K (HML-2) elements in cancer and autoimmune diseases.

中文翻译：

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基于 PCR 的目标富集测序鉴定人内源性逆转录病毒 K (HML-2) 的分布

背景 人类内源性逆转录病毒（HERV）被怀疑存在转座缺陷，可能通过分布在其长末端重复序列（LTR）中的调控元件重塑人类基因组的转录网络。HERV-K (HML-2) 是保存最完好、累积突变数量最少的群体，与肿瘤发生和自身免疫性疾病中的异常基因表达有关。由于不同 HERV-K 之间的高度序列相似性，目前的方法在提供针对个体 HERV-K (HML-2) 成员的全基因组图谱方面存在局限性，这是描绘 HERV-K (HML-2) 功能的主要障碍。结果 为了获得 HERV-K (HML-2) 的详细分布信息，我们对 HERV-K (HML-2) (PTESHK) 位点采用了基于 PCR 的目标富集测序方案，该方案不仅映射了 HERV-K (HML-2) 基因座的存在不仅可以识别参考位点，还可以识别非参考位点，从而能够确定 HERV-K (HML-2) 位点的全基因组分布。在这里，我们报告从三个个体获得的基因组数据。我们使用该方法总共鉴定了 978 个位点，其中包括 30 个新参考位点和 5 个非参考位点。在我们研究的3个个体中，鉴定出14个多态性HERV-K（HML-2）位点，其中solo-LTR330和N6p21.32首次被鉴定为多态性。结论 有趣的是，PTESHK 提供了一种鉴定 HERV-K（HML-2）全基因组分布的方法，并可用于多态性位点的鉴定。由于多态性 HERV-K (HML-2) 整合被怀疑与多种疾病有关，PTESHK 可以补充其他新兴技术，以获取癌症和自身免疫性疾病中的多态性 HERV-K (HML-2) 元件。