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Genomic and Functional Architecture of Congenital Heart Disease

先天性心脏病的基因组和功能结构

基本信息

批准号：
8986651
负责人：
SAMIR ZAIDI
金额：
$ 2.85万
依托单位：
YALE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-12-01 至 2016-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8986651
关键词：
Accounting Affect Algorithms Alleles Animal Model Antisense RNA Architecture Autistic Disorder Bioinformatics CHARGE syndrome CHD7 gene Cardiac Cardiac development Cells Cessation of life Chromatin Cilia Collection Congenital Abnormality Copy Number Polymorphism Defect Development Developmental Gene Dideoxy Chain Termination DNA Sequencing Disease Disease Clusterings Embryo Ensure Environment Etiology European Excision Family Functional disorder GATA4 gene Gene Dosage Gene Expression Profile Gene Frequency Gene-Modified Genes Genetic Genetic Counseling Genetic Predisposition to Disease Genomic DNA Genomics Genotype Goals Health Heart Heterogeneity Histones Image Individual Inherited Injection of therapeutic agent KDM5B gene Kabuki Make-Up Syndrome Left Link Live Birth MLL2 gene Massive Parallel Sequencing Mediating Mentors Methylation Modeling Molecular Morphogenesis Morphology Mus Mutation NOTCH1 gene Nature Newborn Infant Parents Pathway interactions Patient Care Patients Pattern Pediatric Cardiac Genomics Consortium Phase Phenotype Play Population Prenatal Diagnosis Prevalence Production Reading Reporting Risk Role Sampling Siblings Side Situs Inversus Staging Staining method Stains Structure Tadpoles Translating Tubulin Ubiquitination Validation Variant Writing Xenopus burden of illness cardiogenesis case control clinical care cohort congenital heart disorder demethylation disease-causing mutation exome exome sequencing functional genomics gene discovery genome analysis human data improved insight knock-down next generation next generation sequencing novel offspring proband rare variant reproductive fitness xenopus development

项目摘要

DESCRIPTION (provided by applicant): Congenital heart disease (CHD) is the most common cause of non-infectious death in newborns. Although there is evidence to support a genetic etiology, only a small fraction of the disease burden is explained by known inherited mutations and copy number variations. Clinically, however, severe CHD often occurs sporadically and impairs reproductive fitness, suggesting that de novo mutations play a crucial role in its etiology Using next generation exome sequencing, we recently reported a high burden of de novo mutations in severely affected CHD patients in genes expressed at high levels in the developing murine heart (Zaidi et al., Nature, 2013; PMCID# 3706629). We found a marked excess of such mutations in nine chromatin- modifying genes involved in H3K4 or H3K27 methylation or H2BK120 ubiquitination. As defects in the genetic control of cardiac morphogenesis underlie a majority of CHD, it is essential that once new causative genes are discovered we study their effect in an animal model. The Xenopus heart allows the rapid study of effects of gene dosage on specific stages of cardiac morphogenesis. The overall goal of this proposal is to more fully characterize the genomic and functional architecture of severe CHD. Towards this end, we hypothesize that hitherto yet uncharacterized de novo and inherited mutations will be identifiable by next generation sequencing, and that the newly identified genes will act at specific stages of morphogenesis to disrupt normal heart development. In Specific Aim 1, using our self-written, validated Bayesian algorithm, we will identify novel de novo mutations that are present in probands, but are absent in parents. We have obtained samples from a further 445 case (NHLBI's Pediatric Cardiac Genomics Consortium) and 645 control trios (unaffected siblings of autism cases from Simon Simplex Autism Collection). These new trios will be used to expand and independently validate our original cohort. Per our power calculations, an additional 445 trios should identify 44 new (95% CI, 22-66) risk-associated genes. In Specific Aim 2, we will investigate the contribution of rare transmitted variants to CHD by clustering our cohort with CEU HapMap3 (European) individuals, and studying both dominantly and recessively inherited rare variants using population allele frequencies of <0.1% and/or d1%, with or without stratifying for mutation type or heart expression. In Specific Aim 3, we will study the effect of knocking down three of the nine histone-modifying genes, namely Wdr5 (H3K4 methylation), Kdm5b (H3K4 demethylation), and Rnf20 (H2BK120 ubiquitination), on development of the Xenopus heart. We will examine for heart looping, left-right patterning, number, structure, and function of cilia, and heart morphology and function. The Department of Genetics, HHMI, and my mentor, Dr. Richard Lifton, have provided a far- reaching intellectual environment, including enrichment activities, and biostatistical, bioinformatic, and technical support, which together should ensure successful completion. We envisage that the studies should not only improve our understanding of heart development, but may also translate into improved patient care.

描述（由申请人提供）：先天性心脏病（CHD）是新生儿非感染性死亡的最常见原因。虽然有证据支持遗传病因，但只有一小部分疾病负担是由已知的遗传突变和拷贝数变异解释的。然而，在临床上，严重的CHD经常零星地发生并且损害生殖健康，这表明新生突变在其病因学中起关键作用。使用下一代外显子组测序，我们最近报道了在发育中的鼠心脏中以高水平表达的基因中，在严重受影响的CHD患者中新生突变的高负担（Zaidi等人，Nature，2013; PMCID#3706629）。我们发现在9个参与H3 K4或H3 K27甲基化或H2 BK 120泛素化的染色质修饰基因中有明显过量的此类突变。由于心脏形态发生的遗传控制缺陷是大多数CHD的基础，因此一旦发现新的致病基因，我们就必须在动物模型中研究它们的作用。非洲爪蟾心脏可以快速研究基因剂量对心脏形态发生特定阶段的影响。该提案的总体目标是更全面地描述严重CHD的基因组和功能结构。为此，我们假设，迄今尚未表征的从头和遗传突变将通过下一代测序来识别，并且新识别的基因将在形态发生的特定阶段起作用，以破坏正常的心脏发育。在具体目标1中，使用我们自己编写的，经过验证的贝叶斯算法，我们将识别存在于先证者中但不存在于父母中的新的从头突变。我们从另外445例（NHLBI的儿科心脏基因组学联盟）和645例对照三人组（来自Simon Simplex自闭症收集的自闭症病例的未受影响的兄弟姐妹）中获得了样本。这些新的三人组将用于扩展和独立验证我们的原始队列。根据我们的功效计算，额外的445个trios应该识别出44个新的（95%CI，22-66）风险相关基因。在具体目标2中，我们将通过将我们的队列与CEU HapMap 3（欧洲）个体进行聚类，并使用<0.1%和/或d1%的群体等位基因频率研究显性和隐性遗传的罕见变异，研究罕见传播变异对CHD的贡献，有或没有突变类型或心脏表达的分层。在具体目标3中，我们将研究敲除9个组蛋白修饰基因中的3个，即Wdr 5（H3 K4甲基化），Kdm 5 b（H3 K4去甲基化）和Rnf 20（H2 BK 120泛素化）对非洲爪蟾心脏发育的影响。我们将检查心脏循环，左右模式，数量，结构和功能，纤毛和心脏的形态和功能。HHMI遗传学系和我的导师理查德利夫顿博士提供了一个影响深远的智力环境，包括富集活动，生物统计学，生物信息学和技术支持，这些加在一起应该确保成功完成。我们设想，这些研究不仅应该提高我们对心脏发育的理解，而且还可能转化为改善患者护理。