Functional Assessment of Variants in Organisms of Research (FAVOR) - Profiling Canonical Human Genes and their Variants through Disease Model Phenotyping.

研究有机体变异的功能评估 (FAVOR) - 通过疾病模型表型分析典型人类基因及其变异。

• 批准号: 10011229
• 负责人: Trisha Brock
• 金额: $ 35万
• 依托单位: NEMAMETRIX, INC.
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2023-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10011229
• 关键词: Address; Adopted; Algorithms; Alleles; Animal Experimentation; Animal Model; Animal Testing Alternatives; Animals; Behavior; Benchmarking; Benign; Bioinformatics; Biological Models; Biology; Caenorhabditis elegans; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Complementary DNA; DNA sequencing; Data Set; Defect; Development; Diagnosis; Diagnostic; Disease; Disease model; Distant; Epilepsy; Genes; Genetic Diseases; Genetic Transcription; Genetic Variation; Genome; Genomics; Goals; Health; Human; Human Genetics; Locomotion; Measures; Metabolic Pathway; Methodology; Methods; Modeling; Molecular; Nematoda; Nerve Degeneration; Organism; Orthologous Gene; Pathogenicity; Pathologic; Pathway interactions; Patient-Focused Outcomes; Patients; Phase; Phenotype; Presynaptic Terminals; Probability; Production; Proteins; Research; Resolution; Signal Pathway; Small Business Innovation Research Grant; Structure; System; Technology; Testing; TimeLine; Transgenic Animals; Transgenic Organisms; Variant; Work; biological systems; clinical practice; dark matter; gene function; genetic variant; genome-wide; genomic locus; human disease; improved; in vivo; innovation; insight; knockout animal; molecular phenotype; mouse model; new technology; novel; patient population; precision medicine; prevent; screening; success; transcriptome; variant of unknown significance

Project Summary / Abstract Genome wide DNA sequencing is now being adopted in clinical practice and an increasing number of variants are identified in epilepsy-associated genes, yet the clinical interpretation of the new variants is challenging. Some of the variants are known to be either pathological or benign, yet a majority of the gene variations remain unknown for their functional consequence. A large number of Variant of Uncertain Significance (VUS) are becoming commonplace in genes for human diseases, providing a significant barrier in making diagnoses and implementing therapies. Bioinformatic approaches can provide some insight into pathogenic probability of VUS alleles, but functional studies in animal model systems are often needed to make definitive of pathogenicity assignments. The expense and long timelines of mouse model production make the use of alternative small animal models attractive. In this proposal, the ​C. elegans​nematode is used as an alternative model capable of fast high-throughput production and screening. Human genes are installed as gene-swap replacements of the native disease-gene homologs. In preliminary work, gene-swap humanization of STXBP1 in the ​unc-18​locus rescued severe locomotion and behavior defects present in the gene knock-out animals. Pathogenic variants into the STXBP1​​gene-swap loci leads to significant disruption of activity. In this proposal, significant and novel improvements are made to our existing pipeline for the functional analysis of variants in vivo. In Aim 1, the relevance and extensibility of the C. elegans model system for studying human disease is improved through simultaneous humanization of multiple related loci. In Aim 2, new methods are developed for molecular phenotyping, improving the resolution of inputs pathogenicity determination algorithms, and yielding mechanism-of-action level readouts to variant manipulations. In Aim 3, the improvements to the pipeline are tested to quantify gains in pathogenicity determination on a test set of variants.

项目总结/摘要 全基因组DNA测序现在正被应用于临床实践，并且越来越多的变体 在癫痫相关基因中发现了新的突变，但对新突变的临床解释是具有挑战性的。 已知一些变异是病理性的或良性的，但大多数基因变异仍然存在 其功能后果未知。大量的不确定意义的变体（VUS）是 在人类疾病的基因中变得司空见惯，为诊断提供了重大障碍， 实施治疗。生物信息学方法可以为VUS的致病概率提供一些见解 等位基因，但通常需要在动物模型系统中进行功能研究以确定致病性 分配任务。小鼠模型生产的费用和较长的时间表使得替代方法的使用变得很小。 动物模型很有吸引力。在这个建议中，C.秀丽线虫被用作能够 快速高通量生产和筛选。人类基因是作为基因交换替代物安装的， 天然疾病基因同源物。在初步工作中，在unc-18基因座中STXBP 1的基因交换人源化 挽救了基因敲除动物中存在的严重运动和行为缺陷。致病性变异 进入STXBP 1基因交换位点导致活性的显著破坏。在这个提议中，意义重大， 我们对现有的体内变体功能分析管道进行了改进。在目标1中， 的相关性和扩展性。改进了用于研究人类疾病的elegans模型系统， 多个相关基因座的同时人源化。在目标2中，开发了分子生物学的新方法， 表型，提高输入致病性确定算法的分辨率，并产生 作用机制水平读数到变量操作。在目标3中，对管道的改进是 测试以量化在变体的测试集上的致病性确定中的增益。