Investigating tandem repeat variation as a cause of Alzheimer's disease from exome sequencing data

已知串联重复序列扩增（Tendem Repeat Expansions，TREs），最常见的是三重重复序列，如多聚（CAG）， 是超过30种人类神经系统疾病的基础。虽然迄今为止确定的大多数TREs都是 在迟发性神经退行性疾病如遗传性共济失调和亨廷顿病中发现， 已经在AD和某些类型的痴呆症患者中发现。除了短期扩张外， 串联重复序列（基序大小在1至6个碱基对之间的那些），较大重复序列的拷贝数变异 具有≥20bp的基序，也称为可变串联重复数（VNTRs），最近已与 AD的风险。然而，尽管这一证据表明串联重复序列（TR）的变异可以作为 虽然在某些AD和痴呆病例中存在致病突变，但在AD队列中没有一致的努力， 或者系统地筛选新的TREs，或者对VNTR拷贝数进行基因分型。 新开发的生物信息学方法可用于分析全外显子组测序 (WES)数据现在提供了填补这一知识空白的机会。利用专业知识和知识， 我们已经获得了其他大型数据集的工作，我们建议应用这些方法来分析> 20，0000 阿尔茨海默病测序项目产生的外显子组，可供社区使用， 将使用这些数据来研究两个假设： 1.我们假设一些AD病例是由罕见的高渗透致病性TREs引起的。使用 新的生物信息学工具，可以识别TREs，我们将寻找罕见的TREs，只观察到在AD 样品，或与对照相比，在AD病例中显示出显著富集，因此可能是 AD的原因。然后将通过PCR或长读段测序验证潜在致病性TREs， DNA样本 2.我们假设VNTR的常见多态拷贝数变异可以作为遗传风险 AD的因素。我们已经开发了一种基于读取深度的新方法来估计 来自外显子组测序数据的VNTR。我们将分析来自9，226例散发性AD的可用WES数据 样本和10，151个无关对照，产生约4，100个基因VNTR的拷贝数估计， 在WES中表示，其将用于进行VNTR拷贝数与 病例中的AD状态：对照研究。 鉴于TREs和VNTR中的多态性变异，两者都代表了已建立的突变机制， 有助于各种迟发性神经退行性疾病，我们认为，TR变异的研究， AD代表了一个逻辑步骤，它很有可能发现AD的新遗传原因。

Tandem Repeat Expansions (TREs), most commonly of triplet repeats such as poly(CAG), are known to underlie >30 different human neurological diseases. While the majority of TREs identified to date have been found in late-onset neuro-degenerative disorders such as hereditary ataxias and Huntington disease, TREs have been identified in patients with AD and certain types of dementia. In addition to expansions of short tandem repeats (those with motif sizes between 1 and 6 base pairs), copy number variation of larger repeats with motifs ≥20bp, also known as Variable Number of Tandem Repeats (VNTRs), has recently been linked to risk of AD. However, despite this evidence that variation in tandem repeat (TR) sequences can act as the causative mutations in some cases of AD and dementia, there have been no concerted efforts in AD cohorts to either systematically screen for novel TREs, or to genotype VNTR copy numbers. Newly developed bioinformatic approaches that can be applied to analyze Whole Exome Sequencing (WES) data now provide an opportunity to fill this knowledge gap. Utilizing the expertise and knowledge that we have gained working on other large datasets, we propose to apply these approaches to analyze >20,0000 exomes generated by the Alzheimer's Disease Sequencing Project that are available to the community, and will use these data to investigate two hypotheses: 1. We hypothesize that some cases of AD are caused by rare, highly penetrant pathogenic TREs. Using novel bioinformatic tools that can identify TREs, we will search for rare TREs that are observed only in AD samples, or which show significant enrichment in AD cases compared to controls, and thus are likely causative for AD. Potentially pathogenic TREs will then be validated by PCR or long-read sequencing in available DNA samples. 2. We hypothesize that common polymorphic copy number variation of VNTRs can act as genetic risk factors for AD. We have developed a novel approach based on read depth to estimate copy number of VNTRs from exome sequencing data. We will analyze available WES data from 9,226 sporadic AD samples and 10,151 unrelated controls, generating copy number estimates for ~4,100 genic VNTRs that are represented in WES, which will be used to perform association analysis of VNTR copy number with AD status in a case:control study. Given that TREs, and polymorphic variation in VNTRs, both represent established mutational mechanisms that contribute to a variety of late-onset neuro-degenerative conditions, we believe that the study of TR variation in AD represents a logical step that has a high likelihood of uncovering novel genetic causes of AD.