Kim Namshin, Kim Kyoung Hyoun, Lim Won-Jun, Kim Jiwoong, Kim Soon Ae, Yoo Hee Jeong
Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea.
Genes (Basel). 2020 Dec 22;12(1):1. doi: 10.3390/genes12010001.
Autism spectrum disorder (ASD) is a highly heritable condition caused by a combination of environmental and genetic factors such as de novo and inherited variants, as well as rare or common variants among hundreds of related genes. Previous genome-wide association studies have identified susceptibility genes; however, most ASD-associated genes remain undiscovered. This study aimed to examine rare de novo variants to identify genetic risk factors of ASD using whole exome sequencing (WES), functional characterization, and genetic network analyses of identified variants using Korean familial dataset. We recruited children with ASD and their biological parents. The clinical best estimate diagnosis of ASD was made according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), using comprehensive diagnostic instruments. The final analyses included a total of 151 individuals from 51 families. Variants were identified and filtered using the GATK Best Practices for bioinformatics analysis, followed by genome alignments and annotation to the reference genome assembly GRCh37 (liftover to GRCh38), and further annotated using dbSNP 154 build databases. To evaluate allele frequencies of de novo variants, we used the dbSNP, gnomAD exome v2.1.1, and genome v3.0. We used Ingenuity Pathway Analysis (IPA, Qiagen) software to construct networks using all identified de novo variants with known autism-related genes to find probable relationships. We identified 36 de novo variants with potential relations to ASD; 27 missense, two silent, one nonsense, one splice region, one splice site, one 5' UTR, and one intronic SNV and two frameshift deletions. We identified six networks with functional relationships. Among the interactions between de novo variants, the IPA assay found that the NF-κB signaling pathway and its interacting genes were commonly observed at two networks. The relatively small cohort size may affect the results of novel ASD genes with de novo variants described in our findings. We did not conduct functional experiments in this study. Because of the diversity and heterogeneity of ASD, the primary purpose of this study was to investigate probable causative relationships between novel de novo variants and known autism genes. Additionally, we based functional relationships with known genes on network analysis rather than on statistical analysis. We identified new variants that may underlie genetic factors contributing to ASD in Korean families using WES and genetic network analyses. We observed novel de novo variants that might be functionally linked to ASD, of which the variants interact with six genetic networks.
自闭症谱系障碍（ASD）是一种高度可遗传的疾病，由环境和遗传因素共同引起，如新生变异和遗传变异，以及数百个相关基因中的罕见或常见变异。先前的全基因组关联研究已经确定了易感基因；然而，大多数与ASD相关的基因仍未被发现。本研究旨在通过全外显子组测序（WES）、功能表征以及对使用韩国家族数据集鉴定出的变异进行遗传网络分析，来检测罕见的新生变异，以确定ASD的遗传风险因素。我们招募了患有ASD的儿童及其亲生父母。根据《精神疾病诊断与统计手册》（DSM-5），使用综合诊断工具对ASD进行临床最佳估计诊断。最终分析共纳入了来自51个家庭的151名个体。使用GATK最佳实践进行生物信息学分析来鉴定和筛选变异，随后进行基因组比对并注释到参考基因组组装GRCh37（提升到GRCh38），并使用dbSNP 154构建数据库进行进一步注释。为了评估新生变异的等位基因频率，我们使用了dbSNP、gnomAD外显子组v2.1.1和基因组v3.0。我们使用 Ingenuity Pathway Analysis（IPA，Qiagen）软件，利用所有鉴定出的与已知自闭症相关基因的新生变异构建网络，以寻找可能的关系。我们鉴定出36个与ASD可能相关的新生变异；27个错义变异、2个沉默变异、1个无义变异、1个剪接区域变异、1个剪接位点变异、1个5' UTR变异、1个内含子单核苷酸变异和2个移码缺失。我们鉴定出六个具有功能关系的网络。在新生变异之间的相互作用中，IPA分析发现NF-κB信号通路及其相互作用基因在两个网络中普遍存在。相对较小的样本量可能会影响我们研究结果中描述的具有新生变异的新型ASD基因的结果。本研究未进行功能实验。由于ASD的多样性和异质性，本研究的主要目的是研究新型新生变异与已知自闭症基因之间可能的因果关系。此外，我们基于网络分析而非统计分析来确定与已知基因的功能关系。我们使用WES和遗传网络分析，鉴定出可能是韩国家庭中导致ASD的遗传因素基础的新变异。我们观察到可能与ASD功能相关的新型新生变异，其中这些变异与六个遗传网络相互作用。
