背景:片段重复(SD)之间的高序列同一性可以通过非等位基因同源重组(NAHR)促进拷贝数变体(CNV)。这些CNV是基因组疾病如3q29缺失综合征(del3q29S)的根本原因之一。由于这种反复的1.6Mbp缺失或重复,有21个蛋白质编码基因丢失或获得。分别,在3q29位点。虽然NAHR在CNV发生中起作用,在该特定位点增加NAHR风险的因素尚不清楚.
方法:我们采用光学基因组作图技术来表征161个未受影响个体的3q29基因座,16个先证者与del3q29S及其父母,和2位3q29重复综合征的先证者(dup3q29S)。基于长读数测序的单倍型从44个未受影响的个体重新组装,1个三重奏用于单倍型和缺失断点的正交验证。
结果:总计,我们发现了34个单倍型,其中19种为新型单倍型。在这19种新型单倍型中,在未受影响的个体中检测到18个,而del3q29S在先证者的亲本起源染色体上检测到1种新的单倍型。来自44个未受影响的个体的分阶段组装使得能够对20个单倍型进行正交验证。在89%(16/18)的先证者中,断点仅限于3q29SD中20kbp片段的旁系同源拷贝。在一个del3q29S先证中,使用长读数测序,断点被限制在374bp区域.此外,我们根据断点将del3q29S病例分为三类,将dup3q29S病例分为两类。最后,我们在原染色体中没有发现倒置的证据.
结论:我们使用未受影响的个体为3q29基因座生成了最全面的单倍型图谱,带del3q29S或dup3q29S的先证者,和可用的父母,并确定缺失断点在一个具有del3q29S的先证中的374bp区域内。这些结果应该提供对潜在遗传结构的更好理解,这些遗传结构有助于del3q29S和dup3q29S的病因。
High sequence identity between segmental duplications (SDs) can facilitate copy number variants (CNVs) via non-allelic homologous recombination (NAHR). These CNVs are one of the fundamental causes of genomic disorders such as the
3q29 deletion syndrome (del3q29S). There are 21 protein-coding genes lost or gained as a result of such recurrent 1.6-Mbp deletions or duplications, respectively, in the
3q29 locus. While NAHR plays a role in CNV occurrence, the factors that increase the risk of NAHR at this particular locus are not well understood.
We employed an optical genome mapping technique to characterize the
3q29 locus in 161 unaffected individuals, 16 probands with del3q29S and their parents, and 2 probands with the
3q29 duplication syndrome (dup3q29S). Long-read sequencing-based haplotype resolved de novo assemblies from 44 unaffected individuals, and 1 trio was used for orthogonal validation of haplotypes and deletion breakpoints.
In total, we discovered 34 haplotypes, of which 19 were novel haplotypes. Among these 19 novel haplotypes, 18 were detected in unaffected individuals, while 1 novel haplotype was detected on the parent-of-origin chromosome of a proband with the del3q29S. Phased assemblies from 44 unaffected individuals enabled the orthogonal validation of 20 haplotypes. In 89% (16/18) of the probands, breakpoints were confined to paralogous copies of a 20-kbp segment within the
3q29 SDs. In one del3q29S proband, the breakpoint was confined to a 374-bp region using long-read sequencing. Furthermore, we categorized del3q29S cases into three classes and dup3q29S cases into two classes based on breakpoints. Finally, we found no evidence of inversions in parent-of-origin chromosomes.
We have generated the most comprehensive haplotype map for the 3q29 locus using unaffected individuals, probands with del3q29S or dup3q29S, and available parents, and also determined the deletion breakpoint to be within a 374-bp region in one proband with del3q29S. These results should provide a better understanding of the underlying genetic architecture that contributes to the etiology of del3q29S and dup3q29S.