Expanding the accessible genetic architecture of autism by single molecule sequencing

通过单分子测序扩展自闭症的可访问遗传结构

• 批准号: 9980506
• 负责人: Jonathan Sebat
• 金额: $ 87.66万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-06 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9980506
• 关键词: Biological Sciences; Brain; Clinical; Collection; Complex; Custom; DNA; Data; Data Set; Detection; Development; Family; Frequencies; Gene Expression; Genes; Genetic; Genetic Diseases; Genetic Predisposition to Disease; Genetic Risk; Genetic Variation; Genome; Genomic Segment; Genotype; Glean; Goals; Haplotypes; Heritability; High-Throughput Nucleotide Sequencing; Human; Human Genome; Hybrids; Impairment; Inherited; Investigation; Knowledge; Length; Measures; Mosaicism; Mutation; Neurobiology; Parents; Pattern; Point Mutation; Production; Regulatory Element; Repetitive Sequence; Risk; Sampling; Severities; Shapes; Siblings; Structure; Tandem Repeat Sequences; Technology; Testing; Validation; Variant; analysis pipeline; autism spectrum disorder; base; clinical phenotype; cohort; de novo mutation; disorder risk; exome sequencing; gene function; genetic architecture; genetic association; genetic information; genetic variant; genome sequencing; genome wide association study; genome-wide; improved; novel; novel sequencing technology; prediction algorithm; risk variant; sequencing platform; single molecule; social; technological innovation; trait; whole genome

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.

项目摘要 在过去的十年中，在理解自闭症谱系的遗传基础方面取得了重大进展 自闭症（ASD）。基于外显子组测序研究和基于微阵列的基因分型，认识到 ASD的遗传结构由具有大影响的罕见突变组成，包括结构变体（SV）， 和影响基因的从头点突变，以及常见的多基因突变的重要贡献， 变化量然而，ASD的大多数遗传风险仍然无法解释。一部分失踪者 ASD的遗传可能归因于遗传变异， 包括大部分结构变体（SV）和序列变异的通量测序平台， 发生在基因组的重复序列中。对这些新的遗传类别的系统分析 变异可以填补我们对ASD遗传学知识的重大空白。新单的开发- 分子测序平台现在能够直接测序长DNA片段（平均读取长度 > 5，000bp）。这些技术使得能够在复杂和复杂的系统中进行序列组装和变异识别。 基因组的重复区域，并大大增加了结构和串联的比例， 重复（TR）变异，其可以通过全基因组测序（WGS）捕获。长读的应用 WGS到ASD家庭样本可以大大扩展自闭症遗传原因的知识。本研究将 研究复杂的遗传变异对ASD风险的贡献，使用长读码和 短读技术。(1)我们将在一个原始样本中描述遗传变异的全球模式， ASD家族（N=373例，127例同胞对照及其父母），使用Pacific Biosciences进行WGS （SEQUEL）平台，并且这些数据将与Illumina短读段的现有WGS数据集组合， 同样的样品。(2)我们将研究基因中新类型的SV和TR的遗传关联 以及控制基因表达的调控元件，新的发现将在Illumina WGS中复制 Simons Simplex Collection（SSC）的2600个ASD家庭的数据（3）然后我们将调查 新的风险等位基因对家族临床表型的影响，并通过实验证实突变对 基因功能我们提出的研究将扩大我们对ASD遗传结构的了解， 新的风险等位基因和潜在疾病风险的遗传机制。