Novel approaches to identify tandem repeat expansions in neurodegenerative disease

阿尔茨海默病(AD)是最常见的神经退行性疾病之一，具有较高的全球发病率 健康负担。虽然已经确定了几个AD遗传风险基因座，但这些基因组上的因果变异- 尽管进行了密集的测序工作，但广谱关联研究(GWAS)的位置仍然未知。重要的是 然而，大多数全基因组测序方法无法准确地解析串联重复序列，超过40% 它们是神经性疾病的关键驱动因素。我们假设有很大一部分基因 AD的贡献来自数量可变的串联重复序列(VnTRs)，这些重复序列通常包含内部重复序列 单位20个核苷酸或更多，到目前为止还没有在全基因组范围内进行系统评估。我们 通过建立最先进的长读测序，克服了关键的测序障碍 扩增和表征串联重复序列中的准确核苷酸序列的技术。我们最近 WDR7基因与肌萎缩侧索硬化症相关的串联重复序列的发现 硬化症(ALS)。使用我们为串联重复序列长度估计和验证建立的管道， 我们建议在AD中描述人类特有的串联重复序列的扩展。我们激动人心的预赛 分析揭示了AD中许多长度增加或减少的重复序列的例子。其中的几个 显著差异扩增的重复序列位于先前与AD有关的GWA基因座。值得注意的是， 在杂合子个体中，这些基因座上的先导SNP与重复长度的逐步改变有关 或者是风险等位基因的纯合，这表明VNTRs甚至可能在这些基因座上发挥因果作用。我们 还可以确定大规模扩展的罕见实例，和/或依赖于 疾病状态。我们的目标是评估易于扩展的串联重复序列，以估计VNTR长度的基因组- 在AD中广泛存在，以确定新的重复扩展在疾病中的作用。我们利用大量的 来自阿尔茨海默病测序项目的全基因组序列数据。成千上万的人 可用的基因组意味着我们可以在西班牙裔、非裔美国人和非 西班牙裔白人个体以及VNTR扩大对性别的特定影响。然后我们将表演 对AD DNA样本进行靶向长读测序以解析串联重复序列的完整序列 并定义了AD的内部序列变异的后果。最后，我们将努力建立 AD中新的串联重复序列扩增的发病机制。我们建议的研究将 建立一种新的范式来询问重复扩展的机制，并将揭示 导致或调节AD风险的新的遗传因素。

Alzheimer’s disease (AD) is one of the most common neurodegenerative diseases and has a high global health burden. While several AD genetic risk loci have been identified, the causal variant at these genome- wide association study (GWAS) sites is still unknown despite intensive sequencing efforts. Importantly, however, most genome-wide sequencing methods fail to accurately resolve tandem repeats, over 40 of which are key drivers of neurological disorders. We hypothesize that a substantial fraction of genetic contributions to AD come from variable number tandem repeats (VNTRs) that often contain internal repeat units 20 nucleotides or more and that until now have not been systematically assessed genome-wide. We have surmounted critical sequencing barriers by establishing state-of-the-art long-read sequencing techniques to amplify and characterize the exact nucleotide sequence across tandem repeats. We recently reported the identification of a tandem repeat in WDR7 that is associated with Amyotrophic Lateral Sclerosis (ALS). Using the pipeline that we established for tandem repeat length estimation and validation, we propose to characterize human-specific tandem repeat expansions in AD. Our exciting preliminary analysis reveals many examples of repeats with increased or decreased length in AD. Several of these significantly differentially expanded repeats are in GWAS loci previously implicated in AD. Remarkably, the lead SNP at these loci is associated with stepwise changes in repeat length in individuals heterozygous or homozygous for the risk allele, suggesting that VNTRs may even play a causal role at these loci. We also identify rare instances of massive expansions, and/or internal sequence differences that depend on disease state. Our goal is to assess tandem repeats prone to expansion to estimate VNTR length genome- wide in AD to identify the contribution of novel repeat expansions in disease. We leverage large cohorts of whole genome sequence data from the Alzheimer’s Disease Sequencing Project. The thousands of genomes available means we can detect VNTR expansions in Hispanic, African American and Non- Hispanic White individuals as well as sex-specific effects of VNTR expansions. We will then perform targeted long-read sequencing of AD DNA samples to resolve the complete sequence of tandem repeats and define the consequence of internal sequence variation to AD. Finally, we will work to establish mechanisms of pathogenesis of novel tandem repeat expansions in AD. Our proposed studies will establish a novel paradigm to interrogate the mechanism of repeat expansion and will reveal insight into novel genetic factors that cause or modulate risk for AD.