The role of retrotransposons in autism spectrum disorders

描述（由申请人提供）：本申请是对 RFA 编号 RFA-OD-10-005 的回应，涉及主题领域 1：应用基因组学和其他高通量技术。逆转录转座子是哺乳动物个体间基因组变异的一个经常被忽视的来源。人类基因组中这种变异的主要驱动力是 LINE-1 (L1) 逆转录转座，它存在约 500,000 个拷贝，分布在一系列亚科中，每个亚科都在进化史上的某个时刻活跃。目前活跃的亚家族被称为 L1Hs（人类特异性）或 L1-Ta（转录组 a），每个单倍体基因组由约 1000 个成员组成，其中一小部分处于活跃状态。我们开发了一种通过高通量测序定位逆转录转座子插入的技术，具有良好的特异性和敏感性，并一直使用它来寻找来自不同个体的人类特异性 L1 和 SVA（另一种人类逆转录转座子）插入。与此同时，犹他大学 Lynn Jorde 实验室开发了一种类似的基于下一代测序的方法，以在全基因组范围内识别 Alu 插入。此外，我们正处于开发珠阵列平台的第一阶段，该平台用于高通量检测已知的反转录转座子插入多态性 (RIP)，以便使用 RIP 作为 SNP 和 CNV 的替代标记进行关联研究。在我们的资助申请中，我们将建议使用这些技术来研究 LINE-1 和 Alu 逆转录转座是否在自闭症谱系障碍 (ASD) 的遗传易感性中发挥作用。这项研究将遵循 3 个目标：1. 使用我们的测序技术，在由父母和受影响的先证者组成的有限数量的三人组中，研究所有（低频和高频）L1 和 Alu 多态性与 ASD 的关联，2. 通过研究不一致的同卵双胞胎来确定，研究 ASD 患者基因组中体细胞从头插入 L1 和 Alu 的比率，以及 3. 中高频逆转录转座子的关联使用基于阵列的方法筛选许多个体 (RIP-GWAS) 来检测自闭症谱系障碍 (ASD) 的多态性。 公共卫生相关性：自闭症谱系障碍 (ASD) 是影响美国大部分儿童（每 166 名活产儿中就有 1 名）的主要神经系统疾病。迄今为止，人们已经利用单核苷酸多态性和拷贝数变异来探索其病因学的预测主要遗传成分，并成功地找到了少数自闭症谱系障碍病例的病因。在这里，我们建议添加另一种形式的基因组变异，即逆转录转座子诱导的多态性（RIP），以寻找自闭症谱系障碍（ASD）病因。

DESCRIPTION (provided by applicant): This application is in response to RFA number RFA-OD-10-005 and addresses thematic area 1: Applying genomics and other high throughput technologies. Retrotransposons are an often-overlooked source of inter-individual genomic variation in mammals. The primary driver of this variation in the human genome is the LINE-1 (L1) retrotransposition, which exists in ~500,000 copies spread across a succession of subfamilies each of which was active at some point in evolutionary history. The currently active subfamily is known as either L1Hs (for Human-specific) or L1-Ta (for Transcribed group a) and consists of some ~1000 members per haploid genome, a small subset of which are actively mobilized. We have developed a technique to locate retrotransposon insertions with good specificity and sensitivity by high-throughput sequencing, and have been using it to find human-specific L1 and SVA (another human retrotransposon) insertions from various individuals. In parallel, the laboratory of Lynn Jorde at the University of Utah has developed a similar next-generation sequencing-based approach to identify Alu insertions on a genome-wide scale. Additionally, we are in the first stages of developing a bead-array platform for the high-throughput detection of known retrotransposon insertion polymorphisms (RIPs) in order to perform an association study using RIPs as an alternate marker to SNPs and CNVs. In our grant application, we will propose to use these technologies to study whether LINE-1 and Alu retrotransposition plays a role in the genetic susceptibility to autism-spectrum disorders (ASDs). This study will follow 3 aims: 1. The association of all (low and high frequency) L1 and Alu polymorphisms with ASDs using our sequencing technique in a limited number of trios consisting of the parents and affected proband, 2. Studying the rate of somatic de novo L1 and Alu insertion in ASD patient genomes, ascertained through the study of discordant monozygotic twins, and 3. The association of moderate- to high-frequency retrotransposon polymorphisms with ASDs using an array-based approach to screen many individuals (RIP-GWAS). PUBLIC HEALTH RELEVANCE: Autism spectrum disorders (ASD) are major neurological conditions affecting a large proportion of the US population of children (1 in 166 live births). To date, the predicted major genetic component of their etiology has been explored using single nucleotide polymorphisms and copy number variations with success in finding the cause of a small minority of ASD cases. Here we propose to add another form of genome variation, retrotransposon-induced polymorphisms (RIPs), to the search for ASD etiology.