Nonrecurrent rearrangements, genome architecture and neurodegenerative disease.

描述(申请人提供)：在过去的二十年中，许多神经疾病的特征已经变得明显，不是由于基因内的编码区突变，而是由于基因组的改变而表现出来的。基因组疾病是一类由基因组重排引起的疾病，而不是DNA序列的碱基对改变。一般来说，观察到两种主要类型的重排：复发性和非复发性基因组改变。反复重排在不同的患者中有一个共同的大小；在这些患者中，断点发生在固定的基因组位置，或断点聚集区。这些断点聚集在人类基因组的平行片段(也称为低拷贝重复序列，LCR或片段复制，SD)中，通过刺激和调节重排来促进非等位基因同源重组(Nahr)。非复发性重排在不同的患者中可能有不同的大小，但通常共享一个关键基因组内容和/或基因(S)所在的最小重叠区域(SRO)。由非复发性重排引起的基因组疾病为研究基因/表型相关性提供了独特的挑战。不同的大小和基因组含量，以及复杂的改变(如三联体和倒置)的频繁共存，可能与非复发性重排一起发生，这进一步增加了根据每个患者的临床表现来解释基因组和基因变异的复杂性。我们假设非经常性重排可能通过与同源重组机制不同的机制发生；我们的初步研究和最近发布的这项刺激拨款第一年的出版物强烈支持这一假设。此外，我们认为一些非重复性重排可能是由于特定的基因组结构特征导致对此类重排的易感性造成的。我们计划研究这些假说，试图了解导致非重复性重排的机制的“规则”。我们将通过以下方式对这些假设进行实验研究：1)映射复制重排、三重重排和复杂重排的断点。2)对重排的基因组区域进行生物信息学分析，3)通过重组接头的直接DNA序列确定重组产物，即断点测序。4)用全基因组芯片研究由疾病相关从头基因重排患者及其未受影响的双亲组成的三组中的标记基因，以通过标记单倍型的分离来推测链交换或潜在的模板开关。最后，我们将试图通过对具有多个从头CNV事件的受试者或这些受试者的父母的个人基因组进行全基因组测序，来阐明可能对这些重排过程重要的基因。通过这种方式，我们将确定重组的底物，深入了解相关区域的基因组结构，并潜在地推断重组的机制。 公共卫生相关性：该项目与公共卫生的相关性在于，该项目将为非经常性重排导致的基因组变化机制提供新的见解，从而实现更好的诊断和通过纠正基因剂量来潜在的新的治疗途径。这种基因组重排会导致基因拷贝数变异(CNV)，从而导致神经发育障碍(如智力低下)、行为障碍(如自闭症)、精神疾病(如精神分裂症)以及神经退行性疾病(如阿尔茨海默病、帕金森病和Charcot-Marie-Tooth疾病)。

DESCRIPTION (provided by applicant): It has become apparent during the previous twenty years that many neurological disease traits do not result from coding region mutations within genes, but instead manifest because of alterations of the genome. Genomic disorders are a class of conditions that result from genomic rearrangements rather than base pair changes of DNA sequence. In general, two major types of rearrangements are observed: recurrent and nonrecurrent genomic changes. Recurrent rearrangements have a common size in different patients; in which the breakpoints occur at 'fixed' genomic positions, or breakpoint cluster regions. The breakpoints cluster in paralogous segments of the human genome (also referred to as low-copy repeats, LCRs, or segmental duplications, SDs) that facilitate a non-allelic homologous recombination (NAHR) by both stimulating and mediating the rearrangement. Nonrecurrent rearrangements can be of different sizes in different patients, but usually share a "smallest region of overlap" (SRO) in which the critical genomic contents and/or gene(s) reside. Genomic disorders produced by non-recurrent rearrangements provide a unique challenge for studies of genotype/phenotype correlations. The variable size and genomic content as well as the frequent co- occurrence of complex alterations (e.g. triplications and inversions) that can occur with nonrecurrent rearrangements add further complexity to interpreting the genome and gene variation in the context of each patient's clinical manifestations. We hypothesize that nonrecurrent rearrangements may occur by mechanisms that are distinct from homologous recombination mechanisms; our preliminary studies and recent publications from the first year of this stimulus grant strongly support this hypothesis. Furthermore, we suggested some nonrecurrent rearrangements may result because of specific genome architectural features causing susceptibility to such rearrangements. We plan to investigate these hypotheses in an attempt to learn "the rules" for mechanisms leading to nonrecurrent rearrangements. We will investigate these hypotheses experimentally by; 1) mapping breakpoints of duplication rearrangements, triplication rearrangements, and complex rearrangements. 2) performing bioinformatic analyses of the genomic region undergoing rearrangement, and 3) determining the products of recombination through direct DNA sequences of the recombinant junction; i.e. breakpoint sequencing. 4) studying marker genotypes by whole-genome arrays in trios that consist of patients with disease associated de novo complex rearrangements and their unaffected parents to surmise strand exchanges or potential template switches by the segregation of marker haplotypes. Finally, we will attempt to elucidate genes that may be important to these rearrangement processes by whole genome sequencing of personal genomes in subjects, or parents of these subjects, with multiple de novo CNV events. In this manner we will identify the substrates for recombination, gain insights into genome architecture in regions involved, and potentially infer mechanisms for the rearrangements. PUBLIC HEALTH RELEVANCE: The relevance to public health is that the project will provide new insights into mechanisms for genomic changes that result from nonrecurrent rearrangements enabling better diagnostics and potential new avenues for therapy by correcting gene dosage. Such genome rearrangements cause gene copy number variations (CNV) that result in neurodevelopmental disorders such as mental retardation, behavioral disorders such as autism, psychiatric conditions such as schizophrenia, and neurodegenerative disease such as Alzheimer dementia, Parkinson disease and Charcot-Marie-Tooth disorders.