HKLE-seq: an enrichment method for unbiased amplification and next-generation sequencing of all HERV-K and SVA (HKLE) insertion breakpoints genome-wide in human DNA samples

在这个建议中，我们试图设计一个有效的工具，大规模调查的一个 未充分研究的遗传特征。HERV-K和SVA元件（HKLE），两者都含有 HERV-K长末端重复序列是插入多态性的，充当启动子和增强子， 改变基因组结构和表观遗传学。因此，《香港法例》对 主要通过改变顺式基因表达来改变周围基因组的功能。这些 结果表明，HKLE可能有助于生殖系原因和体细胞进展， 疾病事实上，我们的初步研究表明，这些元素与 多发性硬化症和胶质母细胞瘤，另外HKLE已被证明过表达 包括儿童急性淋巴细胞白血病的研究。 目前，测量这些重要的基因组特征的最有效的方法是通过全 基因组测序，这是非常昂贵和计算负担。 先前用于富集插入断点的测序数据的方法受到以下因素的牺牲： 特异性、PCR偏倚和序列错误。我们建议开发一种方法，HKLE-seq， 将利用目标富集方法的效率，同时结合减少 错误和偏见。经过开发，该方法将应用于未来的大型规划 多发性硬化症、胶质母细胞瘤和儿童急性淋巴细胞白血病的研究。 此外，HKLE-seq将可供研究人员进行临床和 全球流行病学研究。

In this proposal we seek to design an efficient tool for large-scale investigation of an understudied genetic feature. HERV-K and SVA elements (HKLEs), which both contain a HERV-K long terminal repeat, are insertionally polymorphic, act as promoters and enhancers, and alter genome structure and epigenetics. As such, HKLEs have demonstrable effects on the function of the surrounding genome, primarily through altering cis-gene expression. These effects suggest HKLEs may contribute to the germ-line causes and somatic progression of disease. Indeed, our preliminary studies suggest that these elements are associated with multiple sclerosis and glioblastoma, additionally HKLEs have been shown to be overexpressed in a variety of complex diseases including our study of childhood acute lymphoblastic leukemia. Currently, the most effective method to measure these important genomic features is via whole genome sequencing, which is prohibitively expensive and computationally burdensome. Previous methods to enrich sequencing data for insertion breakpoints are subject to sacrifices of specificity, PCR bias, and sequence errors. We propose to develop a method, HKLE-seq, that will harness the efficiency of target enrichment methods while incorporating features that reduce error and bias. Upon development, this method will be applied to future large-scale planned studies of multiple sclerosis, glioblastoma, and childhood acute lymphoblastic leukemia. Furthermore, HKLE-seq will be available for use by researchers conducting clinical and epidemiological studies worldwide.