Project I - Human genetics of meningomyelocele and risk mitigation by folic acid

摘要-项目I：人类遗传学的脊髓脊膜膨出和风险缓解叶酸 该项目的重点是人类脑膜脊髓膨出患者的基因组变异特征 (MM)，最常见的中枢神经系统出生缺陷，遗传率估计为70-75% 1，2，累积发病率 3.72/10，000美国活产。MM是一种使人衰弱的结构性出生缺陷，是NTD最常见的形式 与生命相容，并具有显著相关的发病率和死亡率。叶酸（FA） 补充剂使发病率降低>3倍，但对其机制了解甚少。 基因-环境相互作用（GXE）。在这里，我们建议研究人类MM的分子基础， 在全球范围内招募具有严格定义的入选/排除标准的三人组，按产前FA分层 exposure.我们假设新生突变（DNM）对MM的风险有重要贡献， FA增加了表型表达所需的突变负担。MM与其他 严重的儿童疾病显示出强烈的DNM贡献，如先天性结构性疾病， 自闭症我们的初步数据表明，DNM对MM有很大的贡献，但与自闭症一样，这些DNM增加 风险，但可能与其他因素一起作用，以确定风险。我们建议小心地确定总数为2000个 表型MM三人组，全球招募，基于国家膳食FA补充状态分层 （+FA：强化vs -FA：非强化）。三人组将接受全基因组测序 (WGS)，然后分析作为风险因素的新发和遗传突变，与对照组进行比较。结果 项目I的结果将被纳入项目II和III的工作流程，以模拟突变， 项目II和III将用于完善项目I中的WGS分析。项目I将依靠核心B来确定 来自表观遗传特征变化的候选FA响应基因，以及用于生物信息学分析的核心C 分析.项目I已经：1]成立了脊柱裂测序联盟，并招募了一批 >1500例使用社交媒体的MM trios和历史队列，分层为+FA或-FA。2]提取和QC的DNA 从超过700个这样的三重奏中。3]成功竞争NICHDs Gabriella Miller-Kids First计划， 1000个WGS样本。4]对600个trios进行测序，并优化算法，以实现均匀的 变异的召唤5]确定了12个MM候选基因，包括3个复发突变基因和1个 重复拷贝数变异体（CNV）。6]发现+FA三重奏而不是-FA三重奏表现出惊人的 与对照相比，破坏性DNM的积累。我们将重新测试和继承的模型 突变与FA相互作用以确定风险。该申请建议完成招聘，确定 MM中的新发和遗传性基因突变与母体FA暴露相关，并揭示了MM的发病机制。 在临床背景下。

Abstract – Project I: Human genetics of meningomyelocele and risk mitigation by folic acid This project focuses on the characterization of genomic variation in human patients with Meningomyelocele (MM), the most common CNS birth defect, with heritability estimated at 70-75% 1,2, and a cumulative incidence of 3.72/10,000 live US births. MM is a debilitating structural birth defect, the most common form of NTD compatible with life, and with substantial associated morbidity and mortality. National folic acid (FA) supplementation has reduced incidence >3-fold, but there is little understanding of the mechanism of this Gene-Environment interaction (GXE). Here we propose to study the molecular basis of human MM through a world-wide recruitment of trios with narrowly defined inclusion/exclusion criteria, stratified by prenatal FA exposure. We hypothesize that de novo mutations (DNMs) make a critical contribution to the risk of MM, and that FA increases the mutational burden required for phenotypic expressivity. MM shares features with other severe childhood diseases that show strong DNM contributions such as congenital structural disorders and autism. Our preliminary data point to a strong DNM contribution to MM, but like autism, these DNM increase risk but likely act with other factors to determine risk. We propose to ascertain a total of 2000 carefully phenotyped MM trios, recruited worldwide, stratified based upon national dietary FA supplementation status at the time of conception (+FA:fortified vs -FA:nonfortified). Trios will undergo whole genome sequencing (WGS), then analyzed for de novo and inherited mutations as risk factors, compared with control trios. Results from Project I will be incorporated into workflow of Project II and III to model mutations, and results from Project II and III will be used to refine WGS analysis in Project I. Project I will rely on Core B to identify candidate FA-responsive genes from changes in epigenetic signatures, and on Core C for bioinformatic analysis. Project I has already: 1] Founded the Spina Bifida Sequencing Consortium and enrolled a cohort of >1500 MM trios using social media, and historic cohorts, stratified as +FA or -FA. 2] Extracted and QC’d DNA from >700 of these trios. 3] Competed successfully for NICHDs Gabriella Miller-Kids First program access for 1000 WGS samples. 4] Performed sequencing on 600 trios, as well as optimized algorithms to achieve uniform mutation calling. 5] Identified 12 MM candidate genes, including 3 recurrently mutated genes, and one recurrent copy number variant (CNV). 6] Found that +FA trios but not -FA trios demonstrate a striking accumulation of damaging DNMs compared with controls. We will test the model that de novo and inherited mutations interact with FA to determine risk. The application proposes to complete recruitment, identify de novo and inherited gene mutations in MM, correlate with maternal FA exposure, and uncover mechanisms of disease within a clinical context.