全外显子组测序和目标序列靶向捕获测序在遗传性视网膜变性基因诊断中的差异

目的:对比外显子组测序(whole exome sequencing,WES)和目标序列靶向捕获测序检测中国遗传性视网膜变性(inherited retinal dystrophies,IRDs)患者致病基因变异的差异。方法:收集182例IRDs家系,所有先证者均接受系统的眼科检查和必要的全身检查,采集患者及家属血样并提取基因组DNA。按照就诊的时间顺序将患者平均分为两组,一组91例接受WES,另一组91例应用本课题组设计并定制的“遗传性眼病基因诊断芯片” (hereditary eye disease enrichment panel,HEDEP)进行IRDs致病基因外显子区域靶向捕获测序。对候选致病基因用Sanger测序进行验证,并对家系成员进行共分离分析,使用多重连接依赖的探针扩增技术对拷贝数变异进行验证,针对二代测序捕获效率低的区域如RPGR ORF15区,应用Sanger 测序补充检测。根据美国医学遗传学与基因组学学会和分子病理学协会(American College of Medical Genetics and Genomics and the Association for Molecular Pathology,ACMG/AMP)制定的《ACMG/AMP基因变异分类标准与指南》将检测到的所有基因变异进行分类,本文只包含“致病的”、“可能致病的”的基因变异,不包含“意义不明确的”、“可能良性的”和“良性的”基因变异。结果:应用HEDEP确诊的家系共51例,阳性率为56.04%(51/91);应用WES确诊的家系共30例,阳性率为33.00%(30/91);总阳性率44.51%(81/182)。平均测序深度以及测序覆盖度方面,HEDEP优于WES,此外HEDEP具有检测拷贝数变异潜力。本研究共检测到29个IRDs基因的致病突变,最常见的致病基因为USH2A、ABCA4和RPGR,基因突变频率分别为11.54%(21/182)、6.59%(12/182)、3.85%(7/182);共发现43个新的致病突变,并检测到6例家系携带RPGR ORF15区的突变。结论:针对临床确诊的IRDs病例,HEDEP较WES能获得更高的基因诊断阳性率和更精确的诊断结果,可作为IRDs基因诊断的首选方法,WES可作为其他基因诊断方法的补充手段。同时,本研究丰富了IRDs致病基因的突变频谱,为将来IRDs基因诊断、遗传咨询和基因治疗奠定了基础。

Comparison study of whole exome sequencing and targeted panel sequencing in molecular diagnosis of inherited retinal dystrophies

Objective: To evaluate and compare whole exome sequencing (WES) and targeted panel sequencing in the clinical molecular diagnosis of the Chinese families affected with inherited retinal dystrophies (IRDs). Methods: The clinical information of 182 probands affected with IRDs was collected, including their family history and the ophthalmic examination results. Blood samples of all probands and their relatives were collected and genomic DNA was extracted by standard protocols. The first 91 cases were subjected to the WES and the other 91 cases were subjected to a specific hereditary eye disease enrichment panel (HEDEP) designed by us. All likely pathogenic and pathogenic variants in the candidate genes were determined by Sanger sequencing and co-segregation analyses were performed in available family members. Copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA). As PRGR ORF15 was difficult to capture by next generation sequencing (NGS), all the samples were subjected to Sanger sequencing for this region. All sequence changes identified by NGS were classified according to the American College of Medical Gene-tics and Genomics and the Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines. In this study, only variants identified as pathogenic or likely pathogenic were included, while those variants of uncertain significance, likely benign or benign were not included. Results: In 91 cases with WES, pathogenic or likely pathogenic variants were determined in 30 cases, obtaining a detection rate of 33.00% (30/91); While in 91 cases with HEDEP sequencing, pathogenic or likely pathogenic variants were determined in 51 cases, achieving the diagnostic rate of 56.04% (51/91), and totally, the diagnostic rate was 44.51%. HEDEP had better sequencing coverage and read depth than WES, therefore HEDEP had higher detection rate. In addition, HEDEP could detect CNVs. In this study, we detected disease-causing variants in 29 distinct IRD-associated genes, USH2A, ABCA4 and RPGR were the three most common disease-causing genes, and the frequency of these genes in Chinese IRDs population was 11.54% (21/182), 6.59% (12/182) and 3.85% (7/182), respectively. We found 43 novel variants and 6 cases carried variants in RPGR ORF15. Conclusion: NGS in conjunction with Sanger sequencing offers a reliable and effective approach for the genetic diagnosis of IRDs, and after evaluating the pros and cons of the two sequencing methods, we conclude that HEDEP should be used as a first-tier test for IRDs patients, WES can be used as a supplementary molecular diagnostic method due to its merit of detecting novel IRD-associated genes if HEDEP or other methods could not detect disease-causing va-riants in reported genes. In addition, our results enriched the mutational spectra of IRDs genes, and our methods paves the way of genetic counselling, family planning and up-coming gene-based therapies for these families.