Institute of Human Genetics, University of Ulm, Ulm, Germany.
Department of Neurology, University Hospital Hamburg Eppendorf, Hamburg, Germany.
Hum Mutat. 2017 Dec;38(12):1711-1722. doi: 10.1002/humu.23319. Epub 2017 Sep 22.
Precise characterization of nonallelic homologous recombination (NAHR) breakpoints is key to identifying those features that influence NAHR frequency. Until now, analysis of NAHR-mediated rearrangements has generally been performed by comparison of the breakpoint-spanning sequences with the human genome reference sequence. We show here that the haplotype diversity of NAHR hotspots may interfere with breakpoint-mapping. We studied the transmitting parents of individuals with germline type-1 NF1 deletions mediated by NAHR within the paralogous recombination site 1 (PRS1) or paralogous recombination site 2 (PRS2) hotspots. Several parental wild-type PRS1 and PRS2 haplotypes were identified that exhibited considerable sequence differences with respect to the reference sequence, which also affected the number of predicted PRDM9-binding sites. Sequence comparisons between the parental wild-type PRS1 or PRS2 haplotypes and the deletion breakpoint-spanning sequences from the patients (method #2) turned out to be an accurate means to assign NF1 deletion breakpoints and proved superior to crude reference sequence comparisons that neglect to consider haplotype diversity (method #1). The mean length of the deletion breakpoint regions assigned by method #2 was 269-bp in contrast to 502-bp by method #1. Our findings imply that paralog-specific haplotype diversity of NAHR hotspots (such as PRS2) and population-specific haplotype diversity must be taken into account in order to accurately ascertain NAHR-mediated rearrangement breakpoints.
精确描述非等位基因同源重组（NAHR）的断裂点是识别影响 NAHR 频率的特征的关键。到目前为止，NAHR 介导的重排分析通常通过比较断点跨越序列与人类基因组参考序列来进行。我们在这里表明，NAHR 热点的单倍型多样性可能会干扰断点映射。我们研究了由 NAHR 介导的生殖系 1 型 NF1 缺失的传递父母，这些缺失发生在旁系同源重组位点 1（PRS1）或旁系同源重组位点 2（PRS2）热点内。鉴定出了几个野生型 PRS1 和 PRS2 旁系同源重组热点的亲本野生型单倍型，它们与参考序列存在相当大的序列差异，这也影响了 PRDM9 结合位点的数量。将亲本野生型 PRS1 或 PRS2 单倍型与患者的缺失断点跨越序列（方法#2）进行序列比较，结果表明这是一种准确的方法，可以分配 NF1 缺失断点，并优于忽略考虑单倍型多样性的粗参考序列比较（方法#1）。方法#2 分配的缺失断点区域的平均长度为 269-bp，而方法#1 为 502-bp。我们的发现意味着，为了准确确定 NAHR 介导的重排断裂点，必须考虑 NAHR 热点（如 PRS2）的等位基因特异性单倍型多样性和群体特异性单倍型多样性。
