Xiao Bing, Ye Xiantao, Wang Lili, Fan Yanjie, Gu Xuefan, Ji Xing, Sun Yu, Yu Yongguo
Department of Pediatric Endocrinology and Genetic Metabolism, School of Medicine, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China.
Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.
Front Genet. 2020 Jul 6;11:616. doi: 10.3389/fgene.2020.00616. eCollection 2020.
Simple copy number variations (CNVs) detected by chromosomal microarray (CMA) can result from complex structural changes. Therefore, it is necessary to characterize potential structural changes that cause pathogenic CNVs. We applied whole-genome low-coverage sequencing (WGLCS) to concurrently detect pathogenic CNVs and their associated chromosomal rearrangements in 15 patients. All the patients had an average of 2-3 pathogenic CNVs involving 1-2 chromosomes. WGLCS identified all the 34 pathogenic CNVs found by microarray. By identifying chimeric read pairs, WGLCS mapped 70 breakpoints in these patients, of which 47 were finely mapped at the nucleotide level and confirmed by subsequent PCR amplification and Sanger sequencing of the junction fragments. In 15 patients, structural rearrangements were defined at molecular level in 13 patients. In 13 patients, WGLCS reveal no additional results in two patients. In another 11 patients, WGLCS revealed new breakpoints or finely mapped the genes disrupted by breakpoints or 1-6 bp microhomology and/or short insertion (4-70 bp) in the breakpoints junctions. However, structural changes in the other two patients still remained unclear after WGLCS was performed. The structural alteration identified in the 13 patients could be divided into the following categories: (1) interstitial inverted duplication with concomitant terminal deletion (inv dup del) (P1,P4,P9,P11); (2) the product of pericentric inversion (P5); (3) ring chromosome (P8); (4) interstitial duplication and/or triplication (P6, P7); and (5) +der(22)t(11;22) (P2,P15); (6) complex structural rearrangements (P3,P12,P14). WGLCS displayed the ability to discover CNVs and define breakpoints and its disrupted genes and its surrounding sequences in one experiment at base-pair-resolution, which help us to learn more about the mechanisms of formation of observed genomic rearrangements, and in which DNA replicative/repair mechanism might contribute to the formation of complex rearrangements in 11 patients. Clear karyotype at molecular level could help provide an accurate evaluation of recurrent risk and guide prenatal diagnosis or reproductive planning.
通过染色体微阵列（CMA）检测到的简单拷贝数变异（CNV）可能源于复杂的结构变化。因此，有必要对导致致病性CNV的潜在结构变化进行特征描述。我们应用全基因组低覆盖度测序（WGLCS）来同时检测15例患者中的致病性CNV及其相关的染色体重排。所有患者平均有2 - 3个涉及1 - 2条染色体的致病性CNV。WGLCS鉴定出了微阵列检测到的所有34个致病性CNV。通过识别嵌合读对，WGLCS在这些患者中定位了70个断点，其中47个在核苷酸水平上被精细定位，并通过后续对连接片段的PCR扩增和桑格测序得到证实。在15例患者中，13例患者的结构重排在分子水平上得到了明确。在13例患者中，WGLCS在2例患者中未发现其他结果。在另外11例患者中，WGLCS揭示了新的断点，或精细定位了被断点破坏的基因，以及断点连接处1 - 6个碱基对的微同源性和/或短插入（4 - 70个碱基对）。然而，在进行WGLCS后，另外2例患者的结构变化仍不清楚。在13例患者中鉴定出的结构改变可分为以下几类：（1）间质性倒位重复伴末端缺失（inv dup del）（P1、P4、P9、P11）；（2）臂间倒位产物（P5）；（3）环状染色体（P\alpha）；（4）间质性重复和/或三倍体（P6、P7）；（5） +der(22)t(11;22)（P2、P15）；（6）复杂结构重排（P3、P12、P14）。WGLCS展示了在一次实验中以碱基对分辨率发现CNV、定义断点及其破坏的基因及其周围序列的能力，这有助于我们更多地了解观察到的基因组重排的形成机制，以及DNA复制/修复机制可能在11例患者中对复杂重排形成的作用。分子水平上清晰的核型有助于准确评估复发风险，并指导产前诊断或生殖规划。
