Abstract：
There are more than 700 genes that encode proteins that function in epigenetic regulation and chromatin modification. Germline variants in these genes (typically heterozygous) are associated with rare neurodevelopmental disorders (NDDs) characterized by growth abnormalities and intellectual and developmental delay. Advancements in next-generation sequencing have dramatically increased the detection of pathogenic sequence variants in genes encoding epigenetic machinery associated with NDDs and, concurrently, the number of clinically uninterpretable variants classified as variants of uncertain significance (VUS). Recently, DNA methylation (DNAm) signatures, disorder-specific patterns of DNAm change, have emerged as a functional tool that provides insights into disorder pathophysiology and can classify pathogenicity of variants in NDDs. To date, our group and others have identified DNAm signatures for more than 60 Mendelian neurodevelopmental disorders caused by variants in genes encoding epigenetic machinery. There is broad interest in both the research and clinical communities to develop and catalog DNAm signatures in rare NDDs, but there are challenges in optimizing study design considerations and availability of platforms that integrate bioinformatics tools with the appropriate statistical framework required to analyze genome-wide DNAm data. We previously published EpigenCentral, a platform for analysis of DNAm data in rare NDDs. In this article, we utilize the published Weaver syndrome dataset to provide step-by-step protocols for using EpigenCentral for exploratory analysis to identify DNAm signatures and for classification of NDD variants. We also provide important considerations for experimental design and interpretation of DNAm results. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Exploratory analysis to identify disorder-specific DNAm signatures Basic Protocol 2: Classification of variants associated with neurodevelopmental disorders.
摘要：
有700多个基因编码在表观遗传调控和染色质修饰中起作用的蛋白质。这些基因中的种系变体（通常是杂合的）与罕见的神经发育障碍（NDD）有关，其特征是生长异常以及智力和发育延迟。下一代测序的进步极大地增加了对编码与NDD相关的表观遗传机制的基因中致病序列变体的检测，同时,分类为不确定意义变异(VUS)的临床不可解释变异的数量.最近,DNA甲基化（DNAm）签名，DNAm变化的无序特异性模式，已成为一种功能工具，可提供对疾病病理生理学的见解，并可以对NDD中变体的致病性进行分类。迄今为止,我们的研究小组和其他人已经确定了由编码表观遗传机制的基因变异引起的超过60种孟德尔神经发育障碍的DNAm特征.研究和临床社区都有广泛的兴趣来开发和分类罕见NDD中的DNAm签名，但在优化研究设计考虑因素和整合生物信息学工具和分析全基因组DNAm数据所需的适当统计框架的平台的可用性方面存在挑战。我们之前出版的EpigenCentral,用于分析罕见NDD中DNAm数据的平台。在这篇文章中,我们利用已发布的Weaver综合征数据集,提供了使用EpigenCentral进行探索性分析以鉴定DNAm特征和NDD变异分类的分步方案.我们还为DNAm结果的实验设计和解释提供了重要的考虑因素。©2022Wiley期刊有限责任公司。基本方案1:探索性分析以鉴定病症特异性DNAm特征基本方案2:与神经发育障碍相关的变体的分类。
