背景:全球发育迟缓或智力障碍通常伴随着各种遗传性疾病作为综合征的一部分,其中可能包括癫痫发作,自闭症谱系障碍和多种先天性异常。下一代测序(NGS)技术改善了致病变体和与发育延迟相关的基因的识别。这项研究旨在评估乌克兰儿科队列中全外显子组测序(WES)和神经发育障碍基因组测序的产量。此外,该研究基于最近公布的来自该国健康人群的遗传数据,计算预测了不确定显著性变异(VUS)的影响。
方法:该研究回顾性分析了417名全球发育迟缓儿童的WES或基因组测序结果,智力残疾,和/或其他症状。使用CADD-Phred和SIFT预测评分对不确定意义的变体进行了注释,并估计其在乌克兰健康人口中的频率。
结果:在66(15.8%)的个体中建立了明确的分子诊断。WES诊断出37例中的22例(59.4%),而神经发育基因小组在380名受试患者中确定了44例明确诊断(12.1%)。350例(83.2%)个体报告了非诊断结果(VUS和携带者)。最常诊断的疾病是与严重癫痫和GDD/ID相关的发育性和癫痫性脑病(相关基因ARX,CDKL5,STXBP1,KCNQ2,SCN2A,KCNT1、KCNA2)。此外,我们注释了221个被归类为潜在破坏性的VUS,AD或X-linked,有可能将诊断率提高30%,但其中18种变异存在于乌克兰的健康人群中.
结论:这是在乌克兰进行的关于GDD/ID遗传原因的首次综合研究。这项研究首次全面调查了乌克兰GDD/ID的遗传原因。它提供了与GDD/ID相关的已诊断遗传状况的大量数据集。结果支持利用NGS基因面板和WES作为GDD/ID病例的一线诊断工具,特别是在资源有限的环境中。解决VUS的全面方法,包括计算效果预测,人口频率分析,和表型评估,可以帮助对有害的VUS进行进一步的重新分类,并指导家庭中的进一步测试。
BACKGROUND: Global developmental delay or intellectual disability usually accompanies various genetic disorders as a part of the syndrome, which may include seizures, autism spectrum disorder and multiple congenital abnormalities. Next-generation sequencing (NGS) techniques have improved the identification of pathogenic variants and genes related to developmental delay. This study aimed to evaluate the yield of whole exome sequencing (WES) and neurodevelopmental disorder gene panel sequencing in a pediatric cohort from Ukraine. Additionally, the study computationally predicted the effect of variants of uncertain significance (VUS) based on recently published genetic data from the country\'s healthy population.
METHODS: The study retrospectively analyzed WES or gene panel sequencing findings of 417 children with global developmental delay, intellectual disability, and/or other symptoms. Variants of uncertain significance were annotated using CADD-Phred and SIFT prediction scores, and their frequency in the healthy population of Ukraine was estimated.
RESULTS: A definitive molecular diagnosis was established in 66 (15.8%) of the individuals. WES diagnosed 22 out of 37 cases (59.4%), while the neurodevelopmental gene panel identified 44 definitive diagnoses among the 380 tested patients (12.1%). Non-diagnostic findings (VUS and carrier) were reported in 350 (83.2%) individuals. The most frequently diagnosed conditions were developmental and epileptic encephalopathies associated with severe epilepsy and GDD/ID (associated genes ARX, CDKL5, STXBP1, KCNQ2, SCN2A, KCNT1, KCNA2). Additionally, we annotated 221 VUS classified as potentially damaging, AD or X-linked, potentially increasing the diagnostic yield by 30%, but 18 of these variants were present in the healthy population of Ukraine.
CONCLUSIONS: This is the first comprehensive study on genetic causes of GDD/ID conducted in Ukraine. This study provides the first comprehensive investigation of the genetic causes of GDD/ID in Ukraine. It presents a substantial dataset of diagnosed genetic conditions associated with GDD/ID. The results support the utilization of NGS gene panels and WES as first-line diagnostic tools for GDD/ID cases, particularly in resource-limited settings. A comprehensive approach to resolving VUS, including computational effect prediction, population frequency analysis, and phenotype assessment, can aid in further reclassification of deleterious VUS and guide further testing in families.