The role of retrotransposons in autism spectrum disorders

描述(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。反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因素是LINE-1(L1)逆转录转座，它存在于一系列亚家族中的约50万个拷贝中，每个亚家族在进化史上的某个时刻都是活跃的。目前活跃的亚家族被称为L1Hs(针对人类特异的)或L1-Ta(针对转录组a)，每个单倍体基因组由大约1000个成员组成，其中的一小部分被积极动员。我们已经开发了一种通过高通量测序以良好的特异性和敏感性来定位反转录转座子插入的技术，并一直在使用它来寻找不同个体的人类特异性L1和SVA(另一种人类反转录转座子)插入。与此同时，犹他大学的林恩·乔德的实验室也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(RIPs)，以便使用RIPs作为SNPs和CNV的替代标记进行关联研究。在我们的拨款申请中，我们将建议使用这些技术来研究LINE-1和Alu逆转位是否在自闭症谱系障碍(ASD)的遗传易感性中发挥作用。这项研究将遵循三个目标：1.利用我们的测序技术，在由父母和患病先证者组成的有限数量的三人组中，研究所有(低频率和高频)L1和Alu多态与ASD的关联；2.通过对不协调单卵双胞胎的研究，研究ASD患者基因组中体细胞从头L1和Alu插入率；以及3.使用基于阵列的方法筛选多个个体，以确定中、高频反转录转座子多态与ASD的关联(RIP-Gwas)。 公共卫生相关性：自闭症谱系障碍(ASD)是一种主要的神经系统疾病，影响着美国很大一部分儿童人口(166名活产儿中就有1名)。到目前为止，已经使用单核苷酸多态和拷贝数变异来探索其病因的预测的主要遗传成分，并成功地找到了一小部分ASD病例的原因。在这里，我们建议增加另一种形式的基因组变异，反转录转座子诱导的多态(RIPS)，以寻找ASD的病因学。

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.