Epilepsy Multiplatform Variant Prediction (EpiMVP)

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。在过去的十年中，数百个基因与癫痫有关，揭示了这种疾病中可能出错的生物机制的多样性。然而，我们发现与癫痫有关的新基因的速度现在超过了我们研究疾病机制的能力。此外，临床基因面板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做法。基因检测在临床护理中的快速同化导致了不确定意义遗传变异（VUS）数量的激增，特别是错义VUS的发生。这些VUS在致病性和良性之间被划分为一个不确定的范围，这使得遗传咨询师、临床医生、患者和家庭的解释复杂化，以及评估进一步检测的必要性。在此，我们提议建立一个“没有围墙的中心”，名为“癫痫多平台变异预测”（EpiMVP），跨越5个机构，整合来自遗传学家、临床医生、计算生物学家、神经科学家、干细胞生物学家、药理学家和电生理学家的专业知识，他们在合作出版物和资助方面有着良好的记录，并且是国家和国际癫痫组织的领导者。EpiMVP将开发一种模块化、高度集成的平台方法，以加速确定与一系列临床癫痫类型相关的遗传变异的功能、药理学、神经网络和全动物后果。我们将研究非离子通道，非受体基因通常涉及癫痫，并参与多种生物过程。我们的最终目标是设计一个有效的实验平台来测试VUS在癫痫相关基因中的致病性，并生成一个计算模型（EpiPred）来预测变异是致病的还是良性的可能性。这项工作对于寻求新的治疗方法和个性化医疗的前景至关重要。中心的总体里程碑是：1。评估与癫痫相关的基因并选择候选基因进行分析，为EpiPred的开发建模数据，并分析所有项目数据，EpiPred是一种迭代机器学习模型，用于对癫痫相关基因的变异进行分类。2. 使用中等通量的体外方法测试选定的VUS。3. 使用诱导多能干细胞方法在人类皮质神经元或人脑类器官中测试选定的VUS。4. 在临床前和体内模型中测试选定的VUS。预期结果是：1。为临床医生提供一个免费的预测工具，以区分与癫痫有关的基因的致病和良性变异；2. 提供实验模型来研究特定变异的功能后果；3. 提供ClinVar/ClinGen中VUS的重新分类，并制定将功能读数纳入ACMG标准的新指南；4. 告知治疗癫痫的新疗法的未来发展。

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.