Molecular Dissection of the 22q11.2 Deletion Syndrome

22q11.2 缺失综合征的分子解剖

• 批准号: 9763601
• 负责人: BEVERLY S EMANUEL
• 金额: $ 40.97万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2021-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9763601
• 关键词: 22q11; 22q11.2; Address; Affect; African; African American; Biological Assay; Characteristics; Child; Childhood; Chromosomes; Chromosomes, Human, Pair 22; Comb animal structure; Complex; Computer software; Copy Number Polymorphism; Coupled; DNA; Data; Diagnosis; Disease; Dissection; Elements; Fiber FISH; Frequencies; General Population; Genes; Genetic Polymorphism; Genetic Recombination; Genome; Genomic DNA; Genomic Segment; Genomics; High-Throughput Nucleotide Sequencing; Hospitals; Human Genome; Individual; Live Birth; Maps; Mediating; Methodology; Molecular; Optics; Outcome; Parents; Pathology; Patients; Phenotype; Play; Population; Prevalence; Risk; Risk Factors; Role; Structure; Technology; Testing; Variant; base; cohort; conotruncal anomaly face syndrome; design; homologous recombination; innovation; innovative technologies; insight; microdeletion; nanochannel; neuropsychiatry; next generation; novel strategies; offspring; proband; recruit; screening; single molecule; whole genome

The 22q11.2 deletion syndrome (22q11DS) is the most common microdeletion disorder. It is associated with significant phenotypic and neuropsychiatric pathology, both of which are widely variable. In the majority of affected individuals, the deletion occurs de novo as a result of aberrant recombination mediated by four large chromosome 22-specific low copy repeats (LCRA, -B, -C and -D) in 22q11. Their size and the presence of numerous segments with near-identical sequence render chromosome specific LCRs as substrates for non- allelic homologous recombination (NAHR). The results of NAHR are numerous genomic disorders, including the 22q11DS. LCR22s are extremely difficult to reliably map and sequence because of their structural characteristics. Currently, an accurate reference sequence for the region does not exist. Also, LCR22s are recalcitrant to short read sequencing such that the level of their polymorphism and variability in the general population is unknown. However, optical mapping of the region with BioNano Genomics’ Irys technology overcomes this difficulty. In fact, our preliminary BioNano optical mapping data suggests a complex organization of a duplicated 160kb module within LCRA and LCRD that includes copy number and orientation differences. Further, a common inversion polymorphism in the LCRC to LCRD region has been identified with the aid of fiber- FISH. The inversion appears to dramatically increase the risk for deletion. Remarkably, our preliminary data suggests this polymorphic inversion is absent in African Americans (AAs), which would finally explain the relative deficit of AAs in our CHOP- based 22q11DS cohort. In this proposed study, we will use the innovative BioNano optical mapping technology to determine the frequency of these 22q11.2 polymorphisms in the general population and determine the role they play in facilitating NAHR leading to the deletion. In order to investigate the basis of these observations we propose to determine the prevalence of the LCRC-D inversion in several different populations (CEU, African, and African American subjects from the 1000 Genomes Project; local African Americans and 22q11DS trios). We will also analyze in detail the LCR22-containing regions associated with 22q11DS in these same populations to determine their structure and variation. The breakpoints for the inversion polymorphism will be defined and a PCR assay to screen for it as a risk factor for NAHR will be developed. Finally, we propose to analyze and PCR amplify the breakpoint of the typical 3Mb 22q11.2 deletion guided by BioNano optical maps derived from probands in the 22q11DS trios. By leveraging the increased sensitivity afforded by long single molecule optical mapping on nanochannel arrays coupled with 10X Genomics whole- genome sequence and molecular combing, this proposal will elucidate the previously unmapped structure and variation of the LCR22s and surrounding regions. The data and maps generated herein will provide access to many other difficult to map and sequence genomic regions.

22Q11.2缺失综合征（22q11ds）是最常见的微骨骼障碍。它与 显着的表型和神经精神病病理学，这两种病理都是广泛的。在大多数 受影响的个体，删除是由于四个大介导的异常重组而从头开始的 22q11中的染色体22特异性低复制重复序列（LCRA，-B，-C和-D）。他们的大小和许多 具有近相同序列的片段呈现染色体特异性LCR作为非等位基因的底物 同源重组（NAHR）。 NAHR的结果是许多基因组疾病，包括 22q11ds。 LCR22由于其结构而难以可靠地映射和顺序 特征。当前，该区域的准确参考顺序不存在。另外，LCR22是 顽固的简短读取测序，使其多态性和一般多态性水平 人口未知。但是，使用Bionano Genomics的IRYS技术对该地区的光学映射克服了 这个困难。实际上，我们的初步Bionano光学映射数据表明，复制的复杂组织 LCRA和LCRD中的160KB模块，其中包括拷贝数和方向差异。此外，一个常见 在LCRC到LCRD区域的反转多态性借助纤维鱼被鉴定出来。反转 似乎大大增加了删除的风险。值得注意的是，我们的初步数据表明这种多态性 非洲裔美国人（AAS）不存在倒置，这最终将解释我们在我们的章中的相对赤字 - 基于22q11ds队列。在这项拟议的研究中，我们将使用创新的Bionano光学映射技术 确定这些22q11.2多态性在一般人群中的频率，并确定 他们在促进NAHR导致删除的角色中所扮演的角色。为了研究这些观察的基础 我们建议确定几个不同人群中LCRC-D反转的流行率（CEU，非洲，非洲， 和1000个基因组项目的非裔美国人受试者；当地的非裔美国人和22q11ds三重奏）。我们 还将详细分析这些人群中与22q11ds相关的含LCR22的区域 确定它们的结构和变化。将定义反转多态性的断点，并 PCR主张将开发为NAHR的危险因素进行筛选。最后，我们建议分析和 PCR放大了由Bionano光学图引导的典型3MB 22Q11.2删除的断点 22q11ds三重奏中的概率。通过利用长单分子光学提供的提高灵敏度 在纳米渠道阵列上的映射以及10倍基因组学全基因组序列和分子组合的映射， 该提案将阐明LCR22和周围的先前未覆盖的结构和变化 地区。本文生成的数据和地图将提供许多其他难以映射和顺序的访问 基因组区域。