背景:基于Trio的全外显子组测序(trio-WES)能够鉴定致病变异,包括拷贝数变体(CNVs),在患有无法解释的神经发育迟缓(NDD)和神经发育合并症(NDC)的儿童中,包括自闭症谱系障碍(ASD),癫痫,注意力缺陷多动障碍.对trio-WES测试的NDD-NDC病例的进一步表型和遗传分析可能有助于确定与使用trio-WES和与临床环境中NDC相关的新风险基因的更高诊断产量相关的关键表型因素。
方法:在本研究中,我们对163名经三重WES测试的NDD-NDC儿童进行了表型分析,以确定基因诊断组和非基因诊断组之间的表型差异.此外,我们在西蒙斯自闭症研究所基金会(SFARI)基因数据库的帮助下,对ASD基因进行了遗传分析,以确定遗传NDD疾病潜在的新的可能的ASD风险基因.
结果:在这163名患者中,82例(82/163,50.3%),包括20例CNVs。通过多元二元logistic回归分析比较基因诊断组(82例)和非基因诊断组(81例)的表型变量,我们发现NDD-NDC病例表现为严重深度NDD[53/82vs17/81,调整OR(95CI):4.865(2.213-10.694),调整P<0.001]或具有多个NDC[26/82vs8/81,调整OR(95CI):3.731(1.399-9.950),调整后的P=0.009]或伴随的ASD[64/82vs35/81,调整后的OR(95CI):3.256(1.479-7.168),调整P=0.003]和头围异常[33/82vs11/81,调整OR(95CI):2.788(1.148-6.774),调整后的P=0.024]更有可能使用trio-WES进行遗传诊断。此外,在48例遗传诊断为NDD-ASD的患者中鉴定出37种具有单基因变异的基因,在16例携带CNVs的NDD-ASD个体中鉴定出15个剂量敏感基因。这些基因中的大多数已被证明是ASD相关基因。然而,其中一些(9个基因)没有被证明与ASD充分相关。通过文献回顾和构建这9个候选ASD风险基因和从SFARI基因数据库获得的102个已建立的ASD基因之间的蛋白质-蛋白质相互作用网络,我们确定了CUL4B,KCNH1和PLA2G6是遗传NDD疾病潜在的新的可能的ASD风险基因。
结论:Trio-WES测试推荐用于患有原因不明的NDD-NDC的患者,这些患者具有严重的深度NDD或多个NDC,特别是那些伴随ASD和头围异常的人,因为这些独立因素可能会增加使用trio-WES进行基因诊断的可能性。此外,在CUL4B中具有致病变异的NDD患者,KCNH1和PLA2G6应该意识到在其疾病过程中发生ASD的潜在风险。
BACKGROUND: Trio-based whole-exome sequencing (trio-WES) enables identification of pathogenic variants, including copy-number variants (CNVs), in children with unexplained neurodevelopmental delay (NDD) and neurodevelopmental comorbidities (NDCs), including autism spectrum disorder (ASD), epilepsy, and attention deficit hyperactivity disorder. Further phenotypic and genetic analysis on trio-WES-tested NDD-NDCs cases may help to identify key phenotypic factors related to higher diagnostic yield of using trio-WES and novel risk genes associated with NDCs in clinical settings.
METHODS: In this study, we retrospectively performed phenotypic analysis on 163 trio-WES-tested NDD-NDCs children to determine the phenotypic differences between genetically diagnosed and non-genetically diagnosed groups. Additionally, we conducted genetic analysis of ASD genes with the help of Simons Foundation for Autism Research Institute (SFARI) Gene database to identify novel possible ASD-risk genes underlying genetic NDD conditions.
RESULTS: Among these 163 patients, pathogenic variants were identified in 82 cases (82/163, 50.3%), including 20 cases with CNVs. By comparing phenotypic variables between genetically diagnosed group (82 cases) and non-genetically diagnosed group (81 cases) with multivariate binary logistic regression analysis, we revealed that NDD-NDCs cases presenting with severe-profound NDD [53/82 vs 17/81, adjusted-OR (95%CI): 4.865 (2.213 - 10.694), adjusted-P < 0.001] or having multiple NDCs [26/82 vs 8/81, adjusted-OR (95%CI): 3.731 (1.399 - 9.950), adjusted-P = 0.009] or accompanying ASD [64/82 vs 35/81, adjusted-OR (95%CI): 3.256 (1.479 - 7.168), adjusted-P = 0.003] and head circumference abnormality [33/82 vs 11/81, adjusted-OR (95%CI): 2.788 (1.148 - 6.774), adjusted-P = 0.024] were more likely to have a genetic diagnosis using trio-WES. Moreover, 37 genes with monogenetic variants were identified in 48 patients genetically diagnosed with NDD-ASD, and 15 dosage-sensitive genes were identified in 16 individuals with NDD-ASD carrying CNVs. Most of those genes had been proven to be ASD-related genes. However, some of them (9 genes) were not proven sufficiently to correlate with ASD. By literature review and constructing protein-protein interaction networks among these 9 candidate ASD-risk genes and 102 established ASD genes obtained from the SFARI Gene database, we identified CUL4B, KCNH1, and PLA2G6 as novel possible ASD-risk genes underlying genetic NDD conditions.
CONCLUSIONS: Trio-WES testing is recommended for patients with unexplained NDD-NDCs that have severe-profound NDD or multiple NDCs, particularly those with accompanying ASD and head circumference abnormality, as these independent factors may increase the likelihood of genetic diagnosis using trio-WES. Moreover, NDD patients with pathogenic variants in CUL4B, KCNH1 and PLA2G6 should be aware of potential risks of developing ASD during their disease courses.