Expanding the accessible genetic architecture of autism by single molecule sequencing

项目摘要 在过去的十年里，在理解自闭症谱系的遗传基础方面取得了重大进展 精神障碍(ASD)。基于外显子组测序研究和基于微阵列的基因分型，人们认识到 ASD的遗传结构由罕见的大效应突变组成，包括结构变异(Svs)。 以及影响基因的从头开始点突变，以及共同的多基因 变种。然而，ASD的大部分遗传风险仍未得到解释。失踪者中的一部分 ASD的遗传性可能归因于至今仍无法达到的高水平的遗传变异 包括大多数结构变体(SVS)和序列变异的吞吐量测序平台 发生在基因组中的重复序列中。对这些新的遗传类型的系统分析 变异可能会弥合我们对ASD遗传学知识的一大空白。新单车的发展 分子测序平台现在可以对长DNA片段(平均读取长度)进行直接测序 &gt；5,000个bp)。这些技术使序列组装和变体调用能够在复杂和 基因组的重复区域，并显著增加了结构和串联的比例 可通过全基因组测序(WGS)捕获的重复(TR)变异。朗读的应用 从WGS到ASD家族样本可以极大地扩大对自闭症遗传原因的了解。这项研究将 研究复杂基因变异对ASD风险的贡献，使用长期阅读和 短文技术。(1)我们将在一个初级样本中描述全球遗传变异模式 应用太平洋生物科学的WGS对ASD家系(N=373例，127个兄弟姐妹对照及其父母)的研究 (续集)平台，这些数据将与Illumina Short Reads的现有WGS数据集合并在一起 同样的样本。(2)我们将研究新类别的SVS和TRS在基因上的遗传关联 在控制基因表达的调控元件中，新的发现将在Illumina WGS中复制 来自Simons Simplex Collection(SSC)的2600个ASD家系的数据(3)然后我们将调查其影响 研究新的危险等位基因对家系临床表型的影响，并从实验上证实突变对 基因的功能。我们建议的研究将扩大我们对ASD遗传结构的了解，并确定 新的风险等位基因和潜在疾病风险的遗传机制。

Project Summary Within the last decade, major progress has been made in understanding the genetic basis of Autism Spectrum Disorders (ASDs). Based on exome sequencing studies and microarray-based genotyping, it is recognized that the genetic architecture of ASD consists of rare mutations of large effect, including structural variants (SVs) and de novo point mutations that impact genes, as well as a significant contribution from common polygenic variation. However, a majority of the genetic risk for ASD remains unexplained. A proportion of the missing heritability of ASD could be attributable to genetic variation that remains inaccessible to today’s high throughput sequencing platforms including a majority of structural variants (SVs) and sequence variation that occurs within repetitive sequences in the genome. A systematic analysis of these novel classes of genetic variation could close a significant gap in our knowledge of ASD genetics. The development of new single- molecule sequencing platforms now enables direct sequencing of long DNA fragments (average read lengths >5,000 bp). These technologies have enable sequence assembly and variant calling within complex and repetitive regions of the genome and have dramatically increased the proportion of structural and tandem repeat (TR) variation that can be captured by whole genome sequencing (WGS). The application of long read WGS to ASD family samples could greatly expand knowledge of the genetic causes of autism. This study will investigate the contribution of complex genetic variants to risk for ASD using a combination of long-read and short-read technologies. (1) We will characterize global patterns of genetic variation in a primary sample of ASD families (N=373 cases, 127 sibling controls and their parents) by WGS using the Pacific Biosciences (SEQUEL) platform, and these data will be combined with an existing WGS dataset of Illumina short reads on the same samples. (2) We will investigate the genetic association of novel classes of SVs and TRs in genes and in regulatory elements that control gene expression, and novel findings will be replicated in Illumina WGS data on 2600 ASD families from the Simons Simplex Collection (SSC) (3) We will then investigate the influence of novel risk alleles on clinical phenotype in families and experimentally confirm the effects of mutations on gene function. Our proposed study will expand our knowledge of the genetic architecture of ASD and identify novel risk alleles and genetic mechanisms underlying disease risk.