Sequence Variations in Low Copy Repeats on 22q11.2

22q11.2 上低拷贝重复序列的序列变异

• 批准号: 7816809
• 负责人: BERNICE E MORROW
• 金额: $ 20.75万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7816809
• 关键词: 22q11.2; Alleles; Area; Chromosomes; Chromosomes, Human, Pair 22; Complex; Congenital Abnormality; Contig Mapping; Copy Number Polymorphism; DNA; DNA Sequence Analysis; DNA Sequence Rearrangement; DNA copy number; Data; DiGeorge Syndrome; Diagnostic; Disease; Event; Evolution; Exploratory/Developmental Grant; Face; Family; Foundations; Future; Gene Conversion; Genetic Polymorphism; Genetic Recombination; Genome; Genomic Instability; Genomics; Genotype; Goals; Human; Human Genome; Lead; Length; Libraries; Light; Live Birth; Location; Maps; Mediating; Meiosis; Mental Retardation; Methods; Mission; Modeling; Molecular; Nucleotides; Parents; Patients; Physical Map of the Human Genome; Primates; Reading; Repetitive Sequence; Risk; Role; Screening procedure; Sequence Analysis; Shprintzen syndrome; Structure; Technology; Testing; Variant; Work; base; cohort; comparative genomic hybridization; developmental disease; homologous recombination; insertion/deletion mutation; insight; instrument; next generation; programs; public health relevance

DESCRIPTION (provided by applicant): Low copy repeats (LCRs; also known as segmental duplications) constitute roughly 5% of the human genome and are known to mediate chromosome rearrangements associated with mental retardation disorders. The long-term goal of our program is to assess the roles in which LCRs confer genome instability using the 22q11.2 region as a model. Non-allelic homologous recombination (NAHR) events between two, 240 kb low copy repeats, termed LCR22-2 and LCR22-4, mapping 3 Mb apart, lead to several genomic disorders including velo-cardio-facial/DiGeorge syndrome (VCFS/DGS), occurring in 1/4,000 live births. Our hypothesis, based upon preliminary data, is that there are clusters of shared polymorphic sequences (SPSs) between the two LCR22s, representing intervals of enhanced historic gene conversion events. Such regions might serve as recombination hotspots responsible for NAHR events. Sequences flanking these clusters would be unique to one LCR or the other and would be marked by paralogous sequence variants (PSVs). PSV based markers could be used to then type VCFS/DGS families to narrow deletion endpoints in the LCR22s to identify hotspots for rearrangements in the future. Although the complete sequence of the two LCR22s is available for two alleles of chromosomes 22 and it allowed us to generate this hypothesis, it is insufficient to test it. To test our hypothesis, we propose to generate the finished sequence of LCR22-2 and -4 from additional normal alleles of chromosome 22 from existing BAC libraries, roughly 4.4 Mb of sequence. In Specific Aim 1, we will characterize the modular domain organization of LCR22-2 and LCR22-4, by generating BAC based physical maps by screening filters containing BAC clones from different libraries, obtaining end sequence and typing with PCR markers. Structural and sequence variation within the two LCR22s has not been defined. In Specific Aim 2, the minimal tiling path of BAC clones encompassing five alleles will be sequenced and a variation map containing all the insertions, deletions or inversions as well as nucleotide polymorphisms, will be generated. In Specific Aim 3, we will test the hypothesis that there are varied regions of historic gene conversion within the LCR22s and will define a set of PSV markers flanking these regions. The PSV markers will be used in the future to type our cohort of 250 VCFS/DGS patients with the typical 3 Mb deletion and their normal parents to identify signatures of genomic instability. Understanding the basis for 22q11.2 rearrangements on the sequence level can serve as a model for other newly discovered genomic disorders, such as the reciprocal duplication disorder on 22q11.2 and elsewhere in the genome. In addition, the detailed maps of the LCR22s will serve as an ideal template for future programs utilizing next generation approaches. PUBLIC HEALTH RELEVANCE: The chromosome 22q11.2 region is associated with multiple developmental disorders. We propose to define unstable regions on 22q11.2 by DNA sequence analysis. This will enable us to understand why chromosomes can rearrange during meiosis resulting in loss or gains in DNA copy number causing birth defects.

描述（由申请人提供）：低复制重复序列（LCR；也称为节段性重复）约占人类基因组的5％，众所周知可以介导与智力低下的染色体重排。我们计划的长期目标是评估LCR使用22q11.2区域作为模型赋予基因组不稳定性的作用。两个，240 Kb低复制重复序列之间的非平行性同源重组（NAHR）事件，称为LCR222-2和LCR22-4，分开映射3 MB，导致几种基因组疾病发生在1/4,000 Live Births中。我们的假设基于初步数据，是两个LCR22之间存在共享多态性序列（SPS）的簇，代表增强历史基因转化事件的间隔。这些地区可能是负责NAHR事件的重组热点。这些簇侧面的序列将是一个LCR或另一个LCR唯一的，并以寄生态序列变体（PSV）为标志。基于PSV的标记可用于键入VCFS/DGS家族，以缩小LCR22中的删除终点，以识别将来重排的热点。尽管两个LCR22的完整序列可用于两个染色体22等位基因，并且它使我们能够生成此假设，但它不足以测试它。为了检验我们的假设，我们建议从现有BAC库的22染色体的其他正常等位基因中生成LCR222-2和-4的完成序列，约为4.4 MB的序列。在特定的目标1中，我们将通过筛选包含来自不同文库的BAC克隆的过滤器来生成基于BAC的物理图，从而表征LCR22-2和LCR22-4的模块化结构域组织，从而获得了来自不同库的BAC克隆，从而获得了最终序列并使用PCR标记键入。尚未定义两个LCR22S内的结构和序列变化。在特定的目标2中，将测序包含五个等位基因的BAC克隆的最小平铺路径，并将生成包含所有插入，缺失或反转以及核苷酸多态性的变体图。在特定的目标3中，我们将检验以下假设：LCR22S中存在各种历史基因转化区域，并将定义这些区域内两侧的一组PSV标记。将来将使用PSV标记来键入典型3 MB缺失及其正常父母的250名VCFS/DGS患者的队列，以鉴定基因组不稳定性的特征。了解序列水平上22q11.2重排的基础可以作为其他新发现的基因组疾病的模型，例如22q11.2和基因组中其他地方的相互重复障碍。此外，LCR22S的详细地图将作为使用下一代方法的未来程序的理想模板。 公共卫生相关性：22q11.2染色体区域与多种发育障碍有关。我们建议通过DNA序列分析在22Q11.2上定义不稳定区域。这将使我们能够理解为什么在减数分裂过程中染色体可以重新排列，从而导致DNA拷贝数的损失或增加导致出生缺陷。