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）：低拷贝重复序列（LCR；也称为片段重复）约占人类基因组的 5%，已知可介导与精神发育迟滞疾病相关的染色体重排。我们计划的长期目标是使用 22q11.2 区域作为模型来评估 LCR 赋予基因组不稳定性的作用。两个 240 kb 低拷贝重复序列（称为 LCR22-2 和 LCR22-4）之间的非等位基因同源重组 (NAHR) 事件，间隔 3 Mb，导致多种基因组疾病，包括 velo-cardio-facial/DiGeorge 综合征 (VCFS/DGS)，该疾病发生在 1/4,000 活产中。基于初步数据，我们的假设是两个 LCR22 之间存在共享多态序列 (SPS) 簇，代表增强的历史基因转换事件的间隔。这些区域可能作为导致 NAHR 事件的重组热点。这些簇侧翼的序列对于一种 LCR 或另一种来说是独特的，并且由旁系同源序列变体 (PSV) 标记。基于 PSV 的标记可用于对 VCFS/DGS 家族进行分型，以缩小 LCR22 中的删除终点，从而识别未来重排的热点。尽管 22 号染色体的两个等位基因的两个 LCR22 的完整序列是可用的，并且它允许我们生成这个假设，但不足以对其进行检验。为了检验我们的假设，我们建议从现有 BAC 文库中 22 号染色体的其他正常等位基因生成 LCR22-2 和 -4 的最终序列，大约 4.4 Mb 的序列。在具体目标 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、获得末端序列并使用 PCR 标记进行分型，生成基于 BAC 的物理图谱，从而表征 LCR22-2 和 LCR22-4 的模块化结构域组织。两个 LCR22 内的结构和序列变异尚未确定。在具体目标 2 中，将对包含五个等位基因的 BAC 克隆的最小平铺路径进行测序，并将生成包含所有插入、缺失或倒位以及核苷酸多态性的变异图。在具体目标 3 中，我们将测试 LCR22 内存在历史基因转换的不同区域的假设，并将定义这些区域侧翼的一组 PSV 标记。 PSV 标记将来将用于对我们的 250 名具有典型 3 Mb 缺失的 VCFS/DGS 患者及其正常父母进行分型，以识别基因组不稳定的特征。了解 22q11.2 在序列水平上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 和基因组其他位置的相互重复疾病。此外，LCR22 的详细地图将作为未来利用下一代方法的计划的理想模板。 公共卫生相关性：染色体 22q11.2 区域与多种发育障碍相关。我们建议通过 DNA 序列分析来定义 22q11.2 上的不稳定区域。这将使我们能够理解为什么染色体在减数分裂过程中会重新排列，导致 DNA 拷贝数的损失或增加，从而导致出生缺陷。