Project-004

下一代 DNA 测序的出现彻底改变了人类疾病的基因发现，包括 癫痫。在过去的十年里，数百个基因与癫痫有关，揭示了基因的多样性 在这种疾病中可能出错的生物机制。然而，我们识别新基因的速度 与癫痫有关的疾病现在已经超出了我们研究疾病机制的能力。此外，临床基因组或 外显子组测序已成为早发性、家族性和难治性癫痫患者的标准治疗方法。 基因检测迅速融入临床护理导致基因变异数量激增 意义不确定（VUS），特别是错义VUS的发生。这些 VUS 被分配给 致病性和良性之间的不确定谱，这使遗传咨询师的解释变得复杂， 临床医生、患者和家属，以及评估进一步测试的必要性。在这里我们建议建立一个中心 without Walls，名为癫痫多平台变异预测 (EpiMVP)，涵盖 5 个机构和 融合了遗传学家、临床医生、计算生物学家、神经科学家、干细胞生物学家的专业知识， 药理学家和电生理学家拥有良好的合作出版物记录， 赠款以及作为国家和国际癫痫组织领导人的地位。 EpiMVP 将开发一个 模块化、高度集成的平台方法可加速功能、药理、 与一系列临床癫痫有关的遗传变异的神经元网络和整个动物后果 类型。我们将研究通常与癫痫有关的非离子通道、非受体基因，这些基因涉及 在不同的生物过程中。我们的最终目标是设计一个有效的实验平台进行测试 VUS 在与癫痫有关的基因中的致病性，并生成计算模型 (EpiPred) 预测变异是致病性还是良性的可能性。这项工作对于追求新颖至关重要 疗法和个性化医疗的前景。该中心的总体里程碑是： 1. 评估 与癫痫相关的基因，选择用于分析的候选基因、模型数据并分析所有项目数据 用于开发 EpiPred，这是一种迭代机器学习模型，用于对相关基因的变异进行分类 癫痫。 2. 使用中等通量的体外方法测试选定的 VUS。 3. 在人体中测试选定的 VUS 使用诱导多能干细胞方法研究皮层神经元或人脑类器官。 4. 测试选定的VUS 在临床前体内模型中。预期成果是： 1. 提供免费的预测工具 临床医生区分与癫痫有关的基因的致病性和良性变异； 2. 提供 研究特定变异的功能后果的实验模型； 3. 重新分类 ClinVar/ClinGen 中的 VUS 并制定将功能读数纳入 ACMG 的新指南 标准； 4. 为治疗癫痫的新疗法的未来发展提供信息。

The advent of next generation DNA sequencing has revolutionized gene discovery in human diseases, including epilepsy. Hundreds of genes have been implicated in epilepsy in the last decade, revealing the diversity of biological mechanisms that can go awry in this disorder. However, the rate at which we are identifying new genes involved in epilepsy is now outpacing our ability to study disease mechanisms. Moreover, clinical gene panel or exome sequencing has become standard practice for patients with early-onset, familial, and refractory epilepsies. This rapid assimilation of genetic testing into clinical care has led to a surge in the number of genetic variants of uncertain significance (VUS), particularly the occurrence of missense VUS. These VUS are assigned to an indeterminate spectrum between pathogenic and benign, which complicate interpretation for genetic counselors, clinicians, patients and families, as well as assessment of the need for further testing. Here we propose a Center without Walls, entitled Epilepsy Multiplatform Variant Prediction (EpiMVP), spanning 5 institutions and incorporating expertise from geneticists, clinicians, computational biologists, neuroscientists, stem cell biologists, pharmacologists and electrophysiologists who have a proven track record of collaborative publications and grants, as well as stature as leaders of national and international epilepsy organizations. EpiMVP will develop a modular, highly integrated platform approach to accelerate determination of the functional, pharmacological, neuronal network and whole animal consequences of genetic variants implicated in a range of clinical epilepsy types. We will study non-ion-channel, non-receptor genes commonly implicated in epilepsy, and that are involved in diverse biological processes. Our ultimate goals are to devise an effective experimental platform for testing the pathogenicity of VUS in genes implicated in epilepsy and to generate a computational model (EpiPred) that predicts the likelihood that a variant is pathogenic or benign. This work is crucial in the pursuit of novel therapeutics and the promise of personalized medicine. The overall milestones of the Center are: 1. Evaluate genes associated with epilepsy and select candidates for analysis, model data for, and analyze all project data for development of EpiPred an iterative machine learning model to classify variants in genes implicated in epilepsy. 2. Test selected VUS using medium throughput, in vitro approaches. 3. Test selected VUS in human cortical neurons or human brain organoids using induced pluripotent stem cell approaches. 4. Test selected VUS in pre-clinical, in vivo models. The expected outcomes are: 1. Provide a freely available prediction tool for clinicians to differentiate between pathogenic and benign variants for genes implicated in epilepsy; 2. Provide experimental models to study the functional consequences of specific variants; 3. Provide a reclassification of VUS in ClinVar/ClinGen and to develop new guidelines for incorporating functional readouts into the ACMG criteria; 4. Inform the future development of novel therapeutics to treat epilepsy.