Consideration of the haplotype diversity at nonallelic homologous recombination hotspots improves the precision of rearrangement breakpoint identification
Consideration of the haplotype diversity at nonallelic homologous recombination hotspots improves the precision of rearrangement breakpoint identification
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DOI：
10.1002/humu.23319
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发表时间：
2017-12-01
期刊：
影响因子：
3.9
通讯作者：
Kehrer-Sawatzki, Hildegard
中科院分区：
文献类型：
--
作者：
Hillmer, Morten;Summerer, Anna;Kehrer-Sawatzki, Hildegard
准确描述非等位基因同源重组(Nahr)断裂点是识别那些影响Nahr频率的特征的关键。到目前为止，Nahr介导的重排分析通常是通过将断点跨越序列与人类基因组参考序列进行比较来进行的。我们在这里表明Nahr热点的单倍型多样性可能会干扰断点定位。我们研究了在类基因重组位点1(PRS1)或类基因重组位点2(PRS2)热点内由Nahr介导的胚系1型NF1缺失个体的传递父母。鉴定了几种亲本野生型PRS1和PRS2单倍型，它们与参考序列存在相当大的序列差异，这也影响了预测的PRDM9结合位点的数量。亲本野生型PRS1或PRS2单倍型与来自患者的缺失断点跨越序列之间的序列比较(方法#2)被证明是指定NF1缺失断裂点的准确手段，并被证明优于忽略单倍型多样性的粗略参考序列比较(方法#1)。方法2指定的缺失断点区的平均长度为269个碱基，而方法1指定的缺失断点区的平均长度为502个碱基。我们的发现表明，为了准确地确定Nahr介导的重排断裂点，必须考虑Nahr热点(如PRS2)的平行对数特异性单倍型多样性和群体特异性单倍型多样性。
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.