Nonrecurrent rearrangements, genome architecture and neurodegenerative disease.

描述（由申请人提供）：在过去的二十年中，很明显，许多神经系统疾病的特征不是由基因内编码区突变引起的，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而非DNA序列碱基对变化引起的疾病。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变化。不同患者复发性重排大小相同；其中断点发生在“固定”的基因组位置，或断点簇区域。断点聚集在人类基因组的同源片段上（也称为低拷贝重复，lcr，或片段重复，SDs），通过刺激和介导重排促进非等位基因同源重组（NAHR）。在不同的患者中，非复发性重排的大小可能不同，但通常共享一个“最小重叠区”（SRO），其中存在关键的基因组内容和/或基因。由非复发性重排产生的基因组疾病为基因型/表型相关性的研究提供了独特的挑战。可变的大小和基因组内容，以及非复发性重排可能发生的复杂改变（如三倍和倒置）的频繁共存，进一步增加了在每个患者临床表现背景下解释基因组和基因变异的复杂性。我们假设非复发性重排可能通过不同于同源重组机制的机制发生；我们的初步研究和这项刺激计划第一年的最新出版物有力地支持了这一假设。此外，我们认为一些非经常性的重排可能是由于特定的基因组结构特征导致了这些重排的易感性。我们计划研究这些假设，试图了解导致非周期性重排的机制的“规则”。我们将通过实验研究这些假设；1)重复重排、三次重排和复杂重排的映射断点。2)对重排的基因组区域进行生物信息学分析，3)通过重组接点的直接DNA序列确定重组产物；即断点排序。4)利用全基因组阵列研究由与疾病相关的新生复杂重排患者及其未受影响的父母组成的三联体的标记基因型，通过标记单倍型的分离推测链交换或潜在的模板开关。最后，我们将尝试通过对具有多个新生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，并可能推断重排的机制。

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.