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

HKLE-seq：一种富集方法，用于人类 DNA 样本中全基因组所有 HERV-K 和 SVA (HKLE) 插入断点的无偏扩增和新一代测序

基本信息

批准号：
9442151
负责人：
So Young Ryu
金额：
$ 43.03万
依托单位：
UNIVERSITY OF NEVADA RENO
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-02-01 至 2021-01-31
项目状态：
已结题

项目摘要

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.

在本提案中，我们寻求设计一种有效的工具，用于大规模调查未充分研究的遗传特征。 HERV-K 和 SVA 元件 (HKLE)，均包含 HERV-K 长末端重复序列，具有插入多态性，充当启动子和增强子，并改变基因组结构和表观遗传学。因此，HKLEs 对主要通过改变顺式基因表达来改变周围基因组的功能。这些效应表明 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，此外 HKLE 已被证明过度表达在各种复杂疾病中，包括我们对儿童急性淋巴细胞白血病的研究。目前，测量这些重要基因组特征的最有效方法是通过整体基因组测序成本高昂且计算繁重。以前丰富插入断点测序数据的方法会牺牲特异性、PCR 偏差和序列错误。我们建议开发一种方法 HKLE-seq 将利用目标富集方法的效率，同时结合减少的功能错误和偏见。开发完成后，该方法将应用于未来大规模规划多发性硬化症、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 可供进行临床和临床研究的研究人员使用全球流行病学研究。