Analysis of the NAHR-associated de novo mutation rate using type-1 NF1 deletions as a model

使用 1 型 NF1 缺失作为模型分析 NAHR 相关的从头突变率

• 批准号: 251427287
• 负责人: Professorin Dr. Hildegard Kehrer-Sawatzki
• 金额: --
• 依托单位: Institut für Humangenetik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2014
• 资助国家: 德国
• 起止时间: 2013-12-31 至 2017-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/251427287?language=en
• 关键词: Analysis; NAHR; associated; de; novo

Non-allelic homologous recombination (NAHR) is an important mutational mechanism causing disease-associated deletions and duplications in the human genome. Despite its key role as one of the major mutational mechanism underlying recurrent genomic rearrangements, the molecular basis and characteristic features of NAHR are poorly understood. This project aims to study the NAHR-associated de novo mutation rate in the breakpoint-flanking regions of 30 type-1 NF1 deletions, the most frequently recurring mutations in neurofibromatosis type-1. The breakpoints of these deletions are located in the NAHR hotspots PRS1 and PRS2 within the low copy repeats NF1-REPa and NF1-REPc. To distinguish de novo mutations from inherited variants, we plan to compare the deletion breakpoint-flanking sequences with the non-recombinant haplotypes in PRS1 and PRS2 of the transmitting parents who are not themselves affected by NF1 and who do not harbour the NF1 deletion in their blood. In such cases, the NF1 deletion had occurred de novo during meiosis in the germlines of the transmitting parents before being passed on to the affected children. NF1 deletions are rare, occurring with an estimated frequency of 1:60000. Thus, our cohort of 30 type-1 NF1 deletion patients and their clinically unaffected transmitting parents is uniquely valuable for the analysis of the NAHR-associated de novo mutation rate in breakpoint-flanking regions. The NAHR-associated de novo mutation rate measured in breakpoint-flanking regions will be directly compared with the mutation rate detected in regions of the NF1-REPs that are not involved in NAHR-associated crossovers. The assessment of the NAHR-associated de novo mutation rate will be complemented by a high-resolution gene conversion analysis within breakpoint-flanking regions of type-1 NF1 deletions including not only paralog-specific variants (PSVs), as performed in our previous project, but also single nucleotide variants (SNVs). To this end, it will be necessary to investigate the parental haplotypes within the non-recombinant PRS1 and PRS2 regions of the transmitting parents and to determine the phase of these haplotypes. These analyses should indicate the relative extent to which NAHR-associated de novo mutations and gene conversion influence the sequence composition of NAHR hotspots and hence their activity which is sequence-dependent. NF1 deletions therefore serve as an excellent model for the investigation of the molecular basis of NAHR; findings from this analysis should also be applicable to other NAHR-mediated rearrangements. Indeed, we aim to identify an NAHR-associated molecular signature that would help to predict NAHR hotspots in other regions of the genome. The finding of an increased de novo mutation rate in crossover-flanking regions would indicate a hitherto unknown similarity between allelic homologous recombination (AHR) and NAHR during meiosis which would help us to understand the molecular basis of both key mechanisms.

非等位基因同源重组（NAHR）是人类基因组中引起疾病相关缺失和重复的重要突变机制。尽管NAHR是复发性基因组重排的主要突变机制之一，但其分子基础和特征尚不清楚。本项目旨在研究30个1型NF1缺失的断点侧翼区域nahr相关的新生突变率，NF1缺失是1型神经纤维瘤病中最常见的复发突变。这些缺失的断点位于低拷贝重复序列NF1-REPa和NF1-REPc内的NAHR热点PRS1和PRS2。为了区分新生突变和遗传变异，我们计划将缺失断点侧翼序列与自身不受NF1影响且血液中不含NF1缺失的传递父母的PRS1和PRS2中的非重组单倍型进行比较。在这种情况下，NF1缺失在传给受影响的孩子之前，在传递父母的种系减数分裂期间从头发生。NF1缺失是罕见的，发生的频率估计为1:6万。因此，我们的30例1型NF1缺失患者及其临床未受影响的遗传父母队列对于分析断点侧翼区域nahr相关的新生突变率具有独特的价值。在断点侧翼区域测量的nahr相关的新生突变率将直接与在nf1 - rep中未参与nahr相关交叉的区域检测到的突变率进行比较。对nahr相关的新发突变率的评估将通过对1型NF1缺失的断点侧翼区域的高分辨率基因转换分析来补充，该分析不仅包括我们之前项目中执行的旁系特异性变异（psv），还包括单核苷酸变异（snv）。为此，有必要研究传代亲本的非重组PRS1和PRS2区域内的亲本单倍型，并确定这些单倍型的阶段。这些分析应该表明与NAHR相关的新生突变和基因转换对NAHR热点序列组成的影响程度，因此它们的活性依赖于序列。因此，NF1缺失是研究NAHR分子基础的一个很好的模型；该分析的结果也应适用于其他nahr介导的重排。事实上，我们的目标是确定一个与NAHR相关的分子特征，这将有助于预测基因组其他区域的NAHR热点。交叉侧翼区新生突变率增加的发现表明，在减数分裂过程中，等位基因同源重组（AHR）和NAHR之间存在迄今未知的相似性，这将有助于我们了解这两种关键机制的分子基础。

项目成果

Consideration of the haplotype diversity at nonallelic homologous recombination hotspots improves the precision of rearrangement breakpoint identification

• DOI: 10.1002/humu.23319
• 发表时间: 2017-12-01
• 期刊: HUMAN MUTATION
• 影响因子: 3.9
• 作者: Hillmer, Morten;Summerer, Anna;Kehrer-Sawatzki, Hildegard
• 通讯作者: Kehrer-Sawatzki, Hildegard

Pronounced maternal parent-of-origin bias for type-1 NF1 microdeletions

1 型 NF1 微缺失存在明显的母系亲本偏差

• DOI: 10.1007/s00439-018-1888-x
• 发表时间: 2018
• 期刊: Human Genetics
• 影响因子: 5.3
• 作者: Neuhäusler L;Summerer A;Cooper DN;Mautner VF;Kehrer-Sawatzki H
• 通讯作者: Kehrer-Sawatzki H

Ultra-deep amplicon sequencing indicates absence of low-grade mosaicism with normal cells in patients with type-1 NF1 deletions

• DOI: 10.1007/s00439-018-1961-5
• 发表时间: 2019-01-01
• 期刊: HUMAN GENETICS
• 影响因子: 5.3
• 作者: Summerer, Anna;Schaefer, Eleonora;Kehrer-Sawatzki, Hildegard
• 通讯作者: Kehrer-Sawatzki, Hildegard

Extreme clustering of type-1 NF1 deletion breakpoints co-locating with G-quadruplex forming sequences

• DOI: 10.1007/s00439-018-1904-1
• 发表时间: 2018-07
• 期刊: Human Genetics
• 影响因子: 5.3
• 作者: Anna Summerer;V. Mautner;M. Upadhyaya;K. Claes;J. Högel;D. Cooper;L. Messiaen;H. Kehrer-Sawatzki