University of Maryland School of Medicine, Baltimore, MD (T.J., K.A.R., B.J.G., P.F.M., O.C.S., T.D.O., H.L., S.J.K., B.D.M., H.X., J.W.C.).
Boston University School of Medicine, MA (H.J.A., Q.Y., S.S.).
Stroke. 2020 Nov;51(11):3356-3360. doi: 10.1161/STROKEAHA.120.031357. Epub 2020 Sep 11.
The genetic contribution to ischemic stroke may include rare- or low-frequency variants of high-penetrance and large-effect sizes. Analyses focusing on early-onset disease, an extreme-phenotype, and on the exome, the protein-coding portion of genes, may increase the likelihood of identifying such rare functional variants. To evaluate this hypothesis, we implemented a 2-stage discovery and replication design, and then addressed whether the identified variants also associated with older-onset disease.
Discovery was performed in UMD-GEOS Study (University of Maryland-Genetics of Early-Onset Stroke), a biracial population-based study of first-ever ischemic stroke cases 15 to 49 years of age (n=723) and nonstroke controls (n=726). All participants had prior GWAS (Genome Wide Association Study) and underwent Illumina exome-chip genotyping. Logistic-regression was performed to test single-variant associations with all-ischemic stroke and TOAST (Trial of ORG 10172 in Acute Stroke Treatment) subtypes in Whites and Blacks. Population level results were combined using meta-analysis. Gene-based aggregation testing and meta-analysis were performed using seqMeta. Covariates included age and gender, and principal-components for population structure. Pathway analyses were performed across all nominally associated genes for each stroke outcome. Replication was attempted through lookups in a previously reported meta-analysis of early-onset stroke and a large-scale stroke genetics study consisting of primarily older-onset cases.
Gene burden tests identified a significant association with in small-vessel stroke (=3.79×10). Pathway analysis of the top 517 genes (<0.05) from the gene-based analysis of small-vessel stroke identified several signaling and metabolism-related pathways related to neurotransmitter, neurodevelopmental notch-signaling, and lipid/glucose metabolism. While no individual SNPs reached chip-wide significance (<2.05×10), several were near, including an intronic variant in (rs7549251; =4.08×10) and an exonic variant in (rs67383011; =5.19×10).
Exome-based analysis in the setting of early-onset stroke is a promising strategy for identifying novel genetic risk variants, loci, and pathways.
遗传性缺血性脑卒中的发生可能与低频率或罕见的高外显率、大效应量的变异相关。针对早发性疾病（一种极端表型）和外显子（基因的蛋白编码部分）的分析可能会增加识别此类罕见功能变异的可能性。为了评估这一假设，我们实施了两阶段的发现和复制设计，然后研究了鉴定出的变异是否也与发病年龄较大的疾病相关。
发现阶段在 UMD-GEOS 研究（马里兰大学早发性脑卒中遗传学研究）中进行，该研究为一项基于人群的首次 15 至 49 岁缺血性脑卒中病例（n=723）和非脑卒中对照（n=726）的研究。所有参与者均进行了全基因组关联研究（GWAS）和 Illumina 外显子组芯片基因分型。采用 logistic 回归检验在白人和黑人中所有缺血性脑卒中及 TOAST（急性脑卒中治疗 ORG 10172 试验）亚型的单变异与疾病的相关性。使用 Meta 分析合并人群水平的结果。使用 seqMeta 进行基于基因的聚集性检验和 Meta 分析。协变量包括年龄、性别、人群结构的主成分。对每个脑卒中结局的所有名义相关基因进行通路分析。通过在先前报道的早发性脑卒中荟萃分析和主要为发病年龄较大的脑卒中遗传学研究中进行查询，尝试进行复制。
基因负担检验鉴定出与小血管卒中显著相关的基因（=3.79×10）。对小血管卒中基因的基于基因分析的前 517 个基因（<0.05）进行通路分析，鉴定出与神经递质、神经发育 Notch 信号和脂质/葡萄糖代谢相关的几个信号和代谢途径。虽然没有单个 SNP 达到芯片全基因组显著性水平（<2.05×10），但有几个 SNP 接近显著性水平，包括基因内的一个内含子变异（rs7549251；=4.08×10）和基因外显子的一个变异（rs67383011；=5.19×10）。
在早发性脑卒中的背景下，基于外显子组的分析是一种很有前途的识别新的遗传风险变异、基因座和通路的策略。
