The Oculome Panel Test Next-Generation Sequencing to Diagnose a Diverse Range of Genetic Developmental Eye Disorders
The Oculome Panel Test Next-Generation Sequencing to Diagnose a Diverse Range of Genetic Developmental Eye Disorders
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DOI：
10.1016/j.ophtha.2018.12.050
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发表时间：
2019-06-01
期刊：
影响因子：
13.7
通讯作者：
Sowden, Jane C.
中科院分区：
文献类型：
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作者：
Patel, Aara;Hayward, Jane D.;Sowden, Jane C.
目的：开发一种全面的下一代测序板检测，用于筛查已知导致发育性眼病和遗传性眼病的基因，并评估其在患有地球仪畸形、眼前节异常、儿童青光眼或其组合的儿科队列中的诊断率。设计：诊断测试的评估。参与者：277名0至16岁的儿童，在没有基因诊断的情况下被诊断为非综合征性或综合征性眼发育缺陷。我们使用定制设计的Agilent SureSelect QXT目标捕获方法开发了一种新的目镜面板（Agilent Technologies，Santa Clara，CA）来捕获和进行与眼部病症相关的429个基因的平行高通量测序分析。双向桑格测序证实了可疑的致病变异。主要结果测量：整理临床细节和oculome分子遗传学结果。结果：oculome设计涵盖了429个已知的眼病基因;这些基因被细分为5个重叠的虚拟子面板，用于眼前段发育异常，包括青光眼（ASDA; 59个基因），小眼-无眼-缺损（MAC; 86个基因）、先天性白内障和晶状体相关疾病（70个基因）、视网膜营养不良（RET; 235个基因）和白化病（15个基因），以及涉及视神经萎缩和复杂性斜视的其他基因（10个基因）。样本组开发和测试包括使用Illumine测序平台分析277份临床样本和3份阳性对照样本; 99.5%的目标1.77-Mb区域实现了超过30 x读取深度。使用基于Freebayes和ExomeDepth的流水线进行生物信息学分析，分别识别编码序列和拷贝数变体，在277个样本中的68个中得到明确诊断，表型亚组之间的诊断率存在差异：MAC，8.2%（98例中8例解决）; ASDA，24.8%（113例中28例解决）;其他或综合征，37.5%（8例病例中3例已解决）; RET，42.8%（49例中有21例得到解决）;先天性白内障和晶状体相关疾病，88.9%（9例中有8例已解决）。结论：眼科检查诊断了影响眼睛发育的一系列遗传疾病，有可能取代长期和昂贵的多学科评估，并允许更快地进行有针对性的管理。在我们的各种眼部出生缺陷的样本队列中，oculome使大量病例的分子诊断成为可能。(C)2019年美国眼科学会
Purpose: To develop a comprehensive next-generation sequencing panel assay that screens genes known to cause developmental eye disorders and inherited eye disease and to evaluate its diagnostic yield in a pediatric cohort with malformations of the globe, anterior segment anomalies, childhood glaucoma, or a combination thereof.Design: Evaluation of diagnostic test.Participants: Two hundred seventy-seven children, 0 to 16 years of age, diagnosed with nonsyndromic or syndromic developmental eye defects without a genetic diagnosis.Methods: We developed a new oculome panel using a custom-designed Agilent SureSelect QXT target capture method (Agilent Technologies, Santa Clara, CA) to capture and perform parallel high-throughput sequencing analysis of 429 genes associated with eye disorders. Bidirectional Sanger sequencing confirmed suspected pathogenic variants.Main Outcome Measures: Collated clinical details and oculome molecular genetic results.Results: The oculome design covers 429 known eye disease genes; these are subdivided into 5 overlapping virtual subpanels for anterior segment developmental anomalies including glaucoma (ASDA; 59 genes), microphthalmia-anophthalmia-coloboma (MAC; 86 genes), congenital cataracts and lens-associated conditions (70 genes), retinal dystrophies (RET; 235 genes), and albinism (15 genes), as well as additional genes implicated in optic atrophy and complex strabismus (10 genes). Panel development and testing included analyzing 277 clinical samples and 3 positive control samples using Illumine sequencing platforms; more than 30 x read depth was achieved for 99.5% of the targeted 1.77-Mb region. Bioinformatics analysis performed using a pipeline based on Freebayes and ExomeDepth to identify coding sequence and copy number variants, respectively, resulted in a definitive diagnosis in 68 of 277 samples, with variability in diagnostic yield between phenotypic subgroups: MAC, 8.2% (8 of 98 cases solved); ASDA, 24.8% (28 of 113 cases solved); other or syndromic, 37.5% (3 of 8 cases solved); RET, 42.8% (21 of 49 cases solved); and congenital cataracts and lens-associated conditions, 88.9% (8 of 9 cases solved).Conclusions: The oculome test diagnoses a comprehensive range of genetic conditions affecting the development of the eye, potentially replacing protracted and costly multidisciplinary assessments and allowing for faster targeted management. The oculome enabled molecular diagnosis of a significant number of cases in our sample cohort of varied ocular birth defects. (C) 2019 by the American Academy of Ophthalmology