Syndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured phenotypic ontology and next-generation sequencing (NGS)-based pipelines. A prospective and retrospective cohort study was performed on 100 probands with an a priori diagnosis of non-Usher SRDs, using available clinical data, including Human Phenotype Ontology annotation, and further classification into seven clinical categories (ciliopathies, specific syndromes and five others). Retrospective molecular diagnosis was assessed using different molecular and bioinformatic methods depending on availability. Subsequently, uncharacterized probands were prospectively screened using other NGS approaches to extend the number of analyzed genes. After phenotypic classification, ciliopathies were the most common SRD (35%). A global characterization rate of 52% was obtained, with six cases incompletely characterized for a gene that partially explained the phenotype. An improved characterization rate was achieved addressing prospective cases (83%) and well-recognizable syndrome (62%) subgroups. The 27% of the fully characterized cases were reclassified into a different clinical category after identification of the disease-causing gene. Clinical-exome sequencing is the most appropriate first-tier approach for prospective cases, whereas whole-exome sequencing and bioinformatic reanalysis increases the diagnosis of uncharacterized retrospective cases to 45%, mostly those with unspecific symptoms. Our study describes a comprehensive approach to SRDs in daily clinical practice and the importance of thorough clinical assessment and selection of the most appropriate molecular test to be used to solve these complex cases and elucidate novel associations.

综合征性视网膜疾病 (SRD) 是一组复杂的遗传性全身性疾病，具有挑战性的分子基础和临床管理。我们的主要目标是通过应用结构化表型本体和基于下一代测序 (NGS) 的管道来改善临床和分子 SRD 诊断。对 100 名先验诊断为非 Usher SRD 的先证者进行了一项前瞻性和回顾性队列研究，使用现有的临床数据，包括人类表型本体论注释，并进一步分类为七个临床类别（纤毛病、特​​定综合征和其他五个）。根据可用性，使用不同的分子和生物信息学方法评估回顾性分子诊断。随后，未鉴定的先证者使用其他 NGS 方法进行前瞻性筛选，以扩大分析基因的数量。在表型分类后，纤毛病是最常见的 SRD (35%)。获得了 52% 的全局表征率，其中 6 例未完全表征部分解释表型的基因。在处理前瞻性病例 (83%) 和易于识别的综合征 (62%) 亚组时，表征率有所提高。在确定致病基因后，27% 的完全特征病例被重新分类为不同的临床类别。临床外显子组测序是前瞻性病例最合适的一级方法，而全外显子组测序和生物信息学再分析将无特征回顾性病例的诊断率提高到 45%，主要是那些没有特定症状的人。我们的研究描述了在日常临床实践中对 SRD 的综合方法，以及彻底临床评估和选择最合适的分子测试以解决这些复杂病例和阐明新关联的重要性。