Novel approaches to identify tandem repeat expansions in neurodegenerative disease

阿尔茨海默病（Alzheimer's disease，AD）是最常见的神经退行性疾病之一， 健康负担。虽然已经确定了几个AD遗传风险位点，但这些基因组中的致病变异- 广泛关联研究（GWAS）位点仍然是未知的，尽管密集的测序努力。重要的是， 然而，大多数全基因组测序方法不能准确地解析串联重复序列， 这是神经系统疾病的关键驱动因素。我们假设，一个相当大的部分遗传 可变数目串联重复序列（VNTR）是AD的重要组成部分， 单位20个核苷酸或更多，直到现在还没有系统地评估全基因组。我们 通过建立最先进的长读段测序技术， 技术来扩增和表征跨串联重复的确切核苷酸序列。我们最近 报道了在WDR 7中鉴定出一个串联重复序列，该序列与肌萎缩侧索硬化相关， 硬化症（ALS）。使用我们建立的串联重复序列长度估计和验证管道， 我们建议在AD中表征人类特异性串联重复扩增。我们激动人心的初赛 分析揭示了AD中具有增加或减少的长度的重复的许多实例。几个这样 在先前与AD有关的GWAS基因座中存在显著差异扩增的重复序列。值得注意的是， 这些基因座上前导SNP与杂合子个体中重复序列长度的逐步变化有关 或纯合子的风险等位基因，这表明VNTR甚至可能在这些基因座上发挥因果作用。我们 还可以识别罕见的大规模扩张和/或内部序列差异，这些差异取决于 疾病状态。我们的目标是评估易于扩增的串联重复序列，以估计VNTR长度基因组- 在AD中广泛使用，以确定疾病中新的重复扩增的贡献。我们利用大量的 阿尔茨海默病测序项目的全基因组序列数据。成千上万的 可用的基因组意味着我们可以检测到西班牙裔，非洲裔美国人和非裔美国人的VNTR扩增。 西班牙裔白色个体以及VNTR扩增的性别特异性效应。然后我们将表演 AD DNA样本的靶向长读段测序，以解析串联重复序列的完整序列 并明确了内部序列变异对AD的影响。最后，我们将努力建立 AD中新型串联重复序列扩增的发病机制。我们建议的研究将 建立一个新的范式来询问重复扩展的机制，并将揭示洞察 导致或调节AD风险的新遗传因素。

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.