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 Illumina sequencing platforms; more than 30× 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.

中文翻译：

---

Oculome 面板测试：用于诊断各种遗传发育性眼病的下一代测序。

目的 开发一种全面的下一代测序 panel 检测方法，用于筛查已知会导致发育性眼病和遗传性眼病的基因，并评估其在眼球畸形、眼前节异常、儿童青光眼或两者兼有的儿科队列中的诊断率其中。设计诊断测试的评估。参与者 277 名 0 至 16 岁的儿童，在没有进行基因诊断的情况下被诊断出患有非综合征性或综合征性发育性眼部缺陷。方法 我们使用定制设计的 Agilent SureSelect QXT 目标捕获方法（安捷伦科技，加利福尼亚州圣克拉拉）开发了一个新的 oculome panel，以捕获和执行与眼部疾病相关的 429 个基因的平行高通量测序分析。双向 Sanger 测序证实了疑似致病变异。主要结果测量 整理的临床细节和 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；这些被细分为 5 个重叠的虚拟子面板，用于眼前节发育异常，包括青光眼（ASDA；59 个基因）、小眼球畸形-无眼症-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），以及与视神经萎缩和复杂斜视有关的其他基因（10 个基因）。面板开发和测试包括使用 Illumina 测序平台分析 277 个临床样本和 3 个阳性对照样本；对于 99.5% 的目标 1.77-Mb 区域，实现了超过 30 倍的读取深度。使用基于 Freebayes 和 ExomeDepth 的管道分别识别编码序列和拷贝数变异的生物信息学分析导致​​ 277 个样本中的 68 个得到明确诊断，表型亚组之间的诊断率存在差异：MAC，8.2%（98 个中的 8 个）已解决的案件）；ASDA，24.8%（解决了 113 个案例中的 28 个）；其他或综合症，37.5%（8 例中的 3 例已解决）；RET，42.8%（解决了 49 个案例中的 21 个）；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 oculome 测试可诊断影响眼睛发育的一系列遗传病症，有可能取代耗时且成本高昂的多学科评估，并允许更快地进行有针对性的管理。