Comprehensive genomic biomarker discovery in patients with common and rare epileptic brain lesions

耐药性局灶性癫痫是一个巨大的健康负担，也是临床患者管理的主要挑战。尽管最近发现了基因，但三分之二的患者在基因检测后仍然呈阴性。对皮质发育畸形(MCD)，包括局灶性皮质发育不良(FCD)和脑肿瘤的体细胞变异研究一直是小规模的或仅针对基因的一个子集。在更常见的癫痫脑损伤中，如海马硬化(HS)的基因贡献仍未被探索。这项研究将首次对1500个致痫脑部病变进行全面的基因评估，我们的工作组处于有利地位，可以成功识别和翻译致病变异和遗传风险因素。目的1：我们将评估500例手术切除的耐药癫痫患者和经组织病理证实的脑组织样本中的躯体变异负荷：MCD=200，脑肿瘤=100，HS=200。我们将使用覆盖&gt；300x的整个外显子组测序来识别疾病基因，并应用统计模型来识别从同义变异比率到非同义变异比率偏离的基因。前50个丰富的基因将作为局灶性癫痫的新基因小组引入，在1000例独立样本队列中进行验证：MCD=400，脑肿瘤=200，HS=400)。目标2：我们将评估共同风险变量负担。与许多单基因疾病一样，尽管有相同的遗传缺陷，局灶性癫痫患者的临床表现也有很大的差异。然而，尚不清楚常见的多基因变异是否会影响总体疾病风险和/或临床表现。我们将SNP排列上述所有患者的基因(目标1)，以评估疾病的贡献，并测试先前特征的神经和神经精神障碍的多基因风险评分(n&>40分)。目的3：我们将在全基因组范围内探索外显子组阴性FCD的遗传变异。我们将检验深度(&gt；300x)全基因组测序的实用性，并分析20名“外显子阴性”FCD患者的种系和体细胞非编码和大型结构变异。目的4：我们将确定遗传上相同的病理组，并检查它们与临床生物标记物的关系，包括手术后癫痫发作自由。具有相同假定遗传病因学或风险特征的更大组患者将被重新检查，以确定特定的临床表型，目的是改善诊断、患者护理和管理。由知名原则研究人员、国际合作伙伴组成的多学科小组以及全球独特的深表型脑组织采集将确保该项目的成功实施。

Drug-resistant focal epilepsies represent a significant health burden and a major challenge for clinical patient management. Despite recent gene discoveries, two-third of patients remain negative following genetic testing. Somatic variant studies of Malformations of Cortical Development (MCD), including Focal Cortical Dysplasia (FCD) and brain tumors have been at small scale or targeted only a subset of genes. The genetic contribution in more common epileptic brain lesions such as Hippocampal Sclerosis (HS) remains unexplored. This study will be first to conduct a comprehensive genetic evaluation of 1500 epileptogenic brain lesions, and our working group is well positioned to successfully identify and translate disease-causing variants and genetic risk factors. Aim 1: We will assess somatic variant burden in surgically resected brain tissue samples from 500 patients with drug-resistant epilepsies and histopathologically confirmed lesions: MCD=200, brain tumors=100, HS=200. We will use whole exome sequencing with coverage of >300x to identify disease genes and apply statistical models to identify genes with deviations from synonymous to non-synonymous variant ratios. The top 50 enriched genes will be introduced as a new gene panel for focal epilepsies to be validated in an independent sample cohort of 1,000 cases: MCD=400, brain tumors=200, HS=400). Aim 2: We will assess common risk variant burden. As with many monogenetic diseases, despite the same genetic defects, patients with focal epilepsy have highly variable clinical presentations. Yet, it is unclear if common polygenic variation affects the overall disease risk and/or clinical manifestation. We will SNP-array the genotype of all patients included above (aim 1) to assess disease contribution and test polygenic risk scores for previously characterized neurological and neuropsychiatric disorders (n>40 scores). Aim 3: We will conduct genome-wide exploration of genetic variants in exome negative FCD. We will examine the utility of deep (>300x) whole genome sequencing and analyze germline and somatic non-coding and large structural variants in a cohort of 20 "exome negative" patients with FCD. Aim 4: We will identify genetically homogeneous pathology groups and examine their relationship with clinical biomarkers, including postsurgical seizure freedom. Larger groups of patients with the same presumptive genetic etiology or risk profile will be re-examined to identify specific clinical phenotypes, with the goal of improving diagnosis, patient care, and management. The multidisciplinary group of renown principle investigators, international collaboration partners as well the worldwide unique brain tissue collection with deep phenotypes will guarantee successful execution of the project.