McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
J Transl Med. 2019 Apr 29;17(1):138. doi: 10.1186/s12967-019-1887-2.
Genomic disorders present a wide spectrum of unrelated clinical entities that result from genomic rearrangements. Interstitial insertions requiring three points of breakage are rare genomic rearrangement events. The pseudoautosomal region PAR1, homologous between the Xp22 and Yp11 loci, has a high crossover and recombination rate. A 180 bp human-specific palindrome at Xq27.1 appears to be a hotspot for genomic rearrangement, and several genetic diseases/phenotypes associated with Xq27.1 palindrome-driven genomic rearrangement have been reported. Here we investigate a Chinese family with an extremely rare X-linked compound phenotype that remains undiagnosed. We attempt to identify underlying genetic causes by an integrated genome analysis.
A five-generation Chinese family with a distinct X-linked compound phenotype was recruited. Peripheral blood samples were collected and genomic DNA was extracted. Systemic physical and lab examinations were performed to evaluate the phenotype. An integrated genomic analysis was performed. Genotyping and linkage analysis were conducted to map the disease locus. Whole exome sequencing was performed to detect mutations in coding region. Whole genome sequencing was used to detect single nucleotide variations, small insertions, small deletions, or large structural variations. Copy number variation scanning was also performed on the genome scale. Interstitial insertion was confirmed by gap-PCR and quantitative-PCR, and breakpoint junctions were identified by genome walking and direct sequencing. Expression of products of genes nearby to the Xq27.1 palindrome was measured in peripheral blood from patients and unrelated controls via quantitative-PCR.
The identified compound phenotype of genu varum, cubitus valgus, and everted lipsdoes not match any reported clinical entities. Fine mapping and linkage analysis identified a candidate interval of 4 Mb on the X chromosome. No potential coding region mutations were detected. A 105 kb genomic fragment of PAR1 containing no coding genes was duplicated and inserted into the center of a human-specific palindrome at Xq27.1. The interstitial insertion fully cosegregated with the family phenotype. No expression of FGF13 or SOX3 was detected in peripheral blood from the proband or unrelated controls.
We report an extremely rare phenotype associated with an infrequently-seen genomic rearrangement. The novel compound phenotype is X-linked and characterized by genu varum, cubitus valgus, and everted lips. A 105 kb interstitial insertion of a PAR1 fragment into the Xq27.1 palindrome is associated with the phenotype in the family. The present study identified the underlying genetic cause of the phenotype, expanding the spectrum of known human-specific Xq27.1 palindrome insertion events and associated phenotypes.
基因组疾病呈现出广泛的无关联临床实体，这些临床实体是由基因组重排引起的。需要三个断裂点的插入性重排是罕见的基因组重排事件。假常染色体区域 PAR1 在 Xp22 和 Yp11 基因座之间是同源的，其具有较高的交叉和重组率。Xq27.1 处的 180bp 人类特异性回文似乎是基因组重排的热点，并且已经报道了几种与 Xq27.1 回文驱动的基因组重排相关的遗传疾病/表型。在这里，我们研究了一个具有非常罕见的 X 连锁复合表型的中国家庭，该表型仍未得到诊断。我们试图通过综合基因组分析来确定潜在的遗传原因。
我们招募了一个具有明显 X 连锁复合表型的五代中国家庭。采集外周血样本并提取基因组 DNA。进行系统的体格和实验室检查以评估表型。进行综合基因组分析。进行基因分型和连锁分析以定位疾病基因座。进行外显子组测序以检测编码区的突变。使用全基因组测序检测单核苷酸变异、小插入、小缺失或大片段结构变异。还对基因组规模进行拷贝数变异扫描。通过缺口-PCR 和定量-PCR 确认插入性重排，通过基因组步移和直接测序鉴定断点连接。通过定量-PCR 测量患者和无关对照外周血中附近基因的产物表达。
鉴定出的复合表型包括膝内翻、肘外翻和外翻唇，与任何已报道的临床实体都不匹配。精细定位和连锁分析确定了 X 染色体上的一个 4Mb 候选区间。未发现潜在的编码区突变。PAR1 的一个包含非编码基因的 105kb 基因组片段重复并插入 Xq27.1 的人类特异性回文结构的中心。该插入性重排与家系表型完全共分离。在患者和无关对照的外周血中均未检测到 FGF13 或 SOX3 的表达。
我们报告了一种与罕见基因组重排相关的极为罕见的表型。新型复合表型是 X 连锁的，其特征是膝内翻、肘外翻和外翻唇。PAR1 片段的 105kb 插入性重排插入 Xq27.1 回文结构与家系表型相关。本研究确定了该表型的潜在遗传原因，扩大了已知人类特异性 Xq27.1 回文插入事件和相关表型的范围。
