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.

在此提案中，我们试图设计一个有效的工具，以大规模调查研究的遗传特征。 HERV-K和SVA元素（HKLES），都包含一个 HERV-K长期重复是插入多态性的，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，香港对周围基因组的功能，主要是通过改变顺式基因表达。这些效果表明，香港可能会导致种系原因和躯体进展疾病。确实，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，已显示出HKLES过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。当前，测量这些重要基因组特征的最有效方法是通过整个基因组测序，非常昂贵且计算繁重。以前的方法丰富插入断点的测序数据的方法可能会牺牲特异性，PCR偏置和序列误差。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。开发后，此方法将应用于未来的大规模计划多发性硬化症，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将由进行临床和全球流行病学研究。