Functional Genomics of Cardiac Sodium Channel Variants
心脏钠通道变异的功能基因组学
基本信息
- 批准号:10538620
- 负责人:
- 金额:$ 73.54万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2020
- 资助国家:美国
- 起止时间:2020-01-01 至 2024-11-30
- 项目状态:已结题
- 来源:
- 关键词:Action PotentialsAmericanAmino AcidsAtrial FibrillationBRCA1 geneBenignBrugada syndromeCALM1 geneCardiacCategoriesCellsClassificationClinVarCodeCommunitiesComputerized Medical RecordCoupledDNADataData SetDatabasesDiseaseElectronic Health RecordElectronic Medical Records and Genomics NetworkElectrophysiology (science)FamilyGene FrequencyGeneral PopulationGenesGenetic DiseasesGenomic medicineGenomicsHealthHeartHeart failureIn VitroIndividualIon ChannelLeadLearningLifeLong QT SyndromeMainstreamingMapsMedical GeneticsMedicineMendelian disorderMethodsModelingMutagensMutationNucleotidesPTEN geneParticipantPathogenicityPatient CarePatientsPersonsPharmaceutical PreparationsPhenotypePlayPopulationProteinsProviderRecommendationRecording of previous eventsReportingRiskRoleScanningSodiumSodium ChannelStatistical ModelsStructural ModelsStructureSurfaceSyncopeSystemTPMT geneTachyarrhythmiasTestingTransfectionTransmembrane DomainUnited States National Institutes of HealthValidationVariantVentricularWorkbody systemcandidate identificationclinical decision-makingdisorder riskexperimental studyfallsfunctional genomicsgain of functiongenetic testinggenetic variantgenome sequencingheart functionheart rhythmhuman diseaseimprovedindium arsenideloss of functionmedical schoolsmutantmutation screeningnext generation sequencingnovelnovel strategiespatch clampprotein functionprotein structurepublic health relevancerare variantresponsescale upsudden cardiac deathvariant detectionvariant of unknown significance
项目摘要
As clinical genetic testing is becoming widely deployed for patients with suspected Mendelian diseases as well
as in the broad population, a major emerging challenge is the accurate prediction of pathogenicity of DNA
variants. Multiple features, including allele frequencies across populations, family history, and functional
studies, are currently being used to assign known or new variants to three broad categories: benign,
pathogenic, or (most commonly) variant of uncertain significance (VUS). We propose here to test the
hypothesis that deploying novel phenotyping methods will improve variant classification, and we will focus here
on SCN5A, encoding the cardiac sodium channel. Despite the fact that this channel plays a critical role in
normal heart function, SCN5A variants are surprisingly common and have been associated with serious and
occasionally life-threatening phenotypes including type 1 Brugada Syndrome (BrS1), type 3 Long QT
Syndrome (LQT3), conduction system disease, heart failure, and atrial fibrillation. In aim 1, we will determine
the utility of phenotyping in the electronic health record (EHR) coupled to functional studies to assess
SCN5A VUS pathogenicity. The Electronic Medical Records and Genomics (eMERGE) network in which we
are participants is completing sequencing of 109 Mendelian disease genes, including SCN5A, in 25,000
subjects with EHRs. We will assess VUS pathogenicity by analyzing SCN5A-related EHR phenotypes in
subjects with and without SCN5A rare variants and establishing in vitro function for newly-detected variants
using multiplexed semi-automated electrophysiologic methods. In aim 2, we will build on preliminary data using
deep mutational scanning (DMS) – a high-throughput method to mutagenize each nucleotide in a target
genomic sequence and establish its functional consequences – to identify SCN5A coding variants with
BrS1 or LQT3 features. In a pilot experiment, we developed a drug challenge that biases survival toward cells
that do not express sodium current at their surface (the BrS phenotype) and against cells that display
enhanced sustained sodium current (LQT3). We then generated all 252 possible non-synonymous or
nonsense single amino acid (aa) variants across a 12aa regon of SCN5A, exposed a pool of cells transfected
with one mutant/cell to the drug challenge, used next-generation sequencing pre- and post-drug challenge to
identify variants with BrS1 and LQT3 features, and validated predictions with conventional patch clamp
methods. We will now scale up to scan larger regions, starting with the 253 aa encoding transmembrane
domain IV, known to harbor dozens of pathogenic variants. Further, we will map DMS results onto a model of
the channel to probe the structural basis of loss and gain of function variants. We will incorporate DMS data
into available and new statistical models to build an improved model of SCN5A variant disease risk. The result
of this work will be new approaches to establish functional consequences of rare variants in SCN5A (and
ultimately other genes), and thus enable genomic medicine.
随着临床基因检测也广泛应用于疑似孟德尔疾病的患者
与广大人群一样,新出现的一个主要挑战是准确预测 DNA 的致病性
变种。多种特征,包括人群中的等位基因频率、家族史和功能
研究目前正用于将已知或新的变异分为三大类:良性、
致病性或(最常见)意义不确定的变异(VUS)。我们建议在这里测试
假设部署新的表型分析方法将改善变异分类,我们将在这里重点关注
位于 SCN5A 上,编码心脏钠通道。尽管这个渠道在
正常心脏功能中,SCN5A 变异非常常见,并且与严重和严重的心脏功能相关。
偶尔危及生命的表型,包括 1 型布鲁格达综合征 (BrS1)、3 型长 QT
综合征 (LQT3)、传导系统疾病、心力衰竭和心房颤动。在目标 1 中,我们将确定
电子健康记录 (EHR) 中表型分析的效用与功能研究相结合以评估
SCN5A VUS 致病性。我们在其中的电子病历和基因组学 (eMERGE) 网络
参与者正在 25,000 人中完成 109 个孟德尔疾病基因的测序,其中包括 SCN5A
具有 EHR 的受试者。我们将通过分析 SCN5A 相关 EHR 表型来评估 VUS 致病性
具有和不具有 SCN5A 罕见变异的受试者,并建立新检测到的变异的体外功能
使用多重半自动电生理学方法。在目标 2 中,我们将利用初步数据
深度突变扫描 (DMS) – 一种诱变靶标中每个核苷酸的高通量方法
基因组序列并确定其功能结果 – 识别 SCN5A 编码变体
BrS1 或 LQT3 功能。在一项试点实验中,我们开发了一种药物挑战,使细胞的存活率偏向
其表面不表达钠电流(BrS 表型),并且针对显示钠电流的细胞
增强的持续钠电流(LQT3)。然后我们生成了所有 252 个可能的非同义或
SCN5A 12aa 区域的无义单氨基酸 (aa) 变体,暴露了一组转染的细胞
使用一种突变体/细胞进行药物挑战,在药物挑战前和后使用下一代测序来
识别具有 BrS1 和 LQT3 特征的变异,并使用传统膜片钳验证预测
方法。我们现在将扩大扫描更大的区域,从 253 个氨基酸编码跨膜开始
IV 域,已知含有数十种致病变异。此外,我们将把 DMS 结果映射到一个模型上
探索功能变体的损失和增益的结构基础的通道。我们将合并 DMS 数据
入可用的新统计模型,以建立 SCN5A 变异疾病风险的改进模型。结果
这项工作的重点将是建立 SCN5A 中罕见变异的功能后果的新方法(以及
最终是其他基因),从而使基因组医学成为可能。
项目成果
期刊论文数量(1)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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{{ truncateString('DAN M RODEN', 18)}}的其他基金
Vanderbilt Genome-Electronic Records (VGER) Project
范德比尔特基因组电子记录 (VGER) 项目
- 批准号:
10771648 - 财政年份:2023
- 资助金额:
$ 73.54万 - 项目类别:
Vanderbilt Genome-Electronic Records (VGER) Project
范德比尔特基因组电子记录 (VGER) 项目
- 批准号:
10207727 - 财政年份:2020
- 资助金额:
$ 73.54万 - 项目类别:
Vanderbilt Genome-Electronic Records (VGER) Project
范德比尔特基因组电子记录 (VGER) 项目
- 批准号:
10659136 - 财政年份:2020
- 资助金额:
$ 73.54万 - 项目类别:
Vanderbilt Genome-Electronic Records (VGER) Project
范德比尔特基因组电子记录 (VGER) 项目
- 批准号:
10450009 - 财政年份:2020
- 资助金额:
$ 73.54万 - 项目类别:
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