Computational Methods for Identification of Genetic Factors Affecting the Response to Drug Abuse

识别影响药物滥用反应的遗传因素的计算方法

• 批准号: 10406825
• 负责人: GARY A PELTZ
• 金额: $ 1.39万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2022-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10406825
• 关键词: Affect; Alleles; Biochemical Pathway; Brain; Chromosome Mapping; Cocaine; Communities; Computing Methodologies; Consumption; Custom; Data; Data Analyses; Data Set; Development; Drug Addiction; Drug abuse; Engineering; Fentanyl; Gene Expression; Genes; Genetic; Genetic Transcription; Genetic Variation; Genome; Genomic Segment; Haplotypes; Inbred Strain; Inbred Strains Mice; Individual; Measures; Methamphetamine; Methods; Morbidity - disease rate; Morphine; Mus; Nicotine; Pathway interactions; Pattern; Phenotype; Play; Population; Populations at Risk; Predisposition; Prevention; Property; Public Health; Research Personnel; Role; Science; Testing; Time; Tissues; Validation; Work; addiction; base; computerized tools; cost; drug of abuse; experimental study; genetic analysis; genetic variant; interest; large datasets; metabolomics; multiple omics; new therapeutic target; novel; response; societal costs; therapeutic development; trait

Project Summary/Abstract Due to the increased morbidity and societal cost of drug abuse, identification of genetic factors affecting the response to drugs of abuse (DOA) are of particular interest because this will aid in identifying at risk populations and could provide potential novel targets for therapeutic development. However, a major challenge in biomedical science is determining how genetic differences within a population affect the properties (i.e. phenotypes, traits) of an individual. Using conventional methods, it often requires years of painstaking work to discover and characterize a genetic variant that affects a given phenotypic response. Several years ago, we developed a more efficient method for mapping genes to traits, called haplotype-based computational genetic mapping (HBCGM). In an HBCGM experiment, a property of interest is measured in inbred mouse strains; and genetic factors are computationally predicted by identifying the genomic regions where the pattern of genetic variation correlates with the distribution of trait values among the strains. HBCGM analyses are completed much more quickly than conventional genetic analysis methods. However, the methods used for experimental validation of genetic factors have limitations and are time consuming. This project will further develop computational methods that will enable genetic factors affecting many important biomedical traits to be discovered and experimentally characterized. A high-throughput version of HBCGM (HT- HBCGM) will be used to analyze 8,225 publicly available datasets, which measure 213,000 responses in panels of inbred mouse strains. We deploy a novel method that increases genetic discovery power by exploiting the redundancy present in the many datasets that examine similar responses. Novel computational tools that facilitate the integrated analysis of genetic, transcriptional and metabolomic data will also be developed. This includes specialized metabolic networks (for brain and 3 other tissues) for computationally identifying metabolomic changes that correlate with gene expression or genetic differences. To stimulate other investigators to make genetic discoveries, all results and methods from this project will be made fully available to the scientific community. These computational tools will be used to analyze customized ‘multi-omic’ (genetic, transcriptional, and metabolomic) datasets that measure: (i) fifteen responses of inbred strain panels to four DOA (cocaine, methamphetamine, fentanyl, and nicotine); and (ii) corresponding DOA induced transcriptional and metabolomic changes in brain. Integrated analysis of this data will identify genes/pathways affecting the response to DOA. We then apply a high efficiency method for engineering specific allelic changes into the genome of inbred strains, and the engineered lines are used to experimentally test the effect of an identified genetic factor on the response to a DOA.

项目总结/摘要 由于药物滥用的发病率和社会成本增加， 药物滥用（DOA）的反应，因为这将有助于识别风险人群 并可能为治疗开发提供潜在的新靶点。然而，生物医学领域的一个重大挑战是， 科学正在确定群体内的遗传差异如何影响特性（即表型，性状） 一个人。使用传统的方法，它往往需要多年的艰苦工作来发现， 表征影响给定表型反应的遗传变体。几年前，我们开发了一种 一种将基因定位到性状的有效方法，称为基于单体型的计算遗传作图（HBCGM）。 在HBCGM实验中，在近交系小鼠品系中测量感兴趣的性质;并且在近交系小鼠品系中测量遗传因子。 通过识别遗传变异模式相关的基因组区域来计算预测 与品系间性状值的分布有关。HBCGM分析的完成速度比 传统的遗传分析方法。然而，用于遗传因素实验验证的方法 具有局限性并且耗时。 该项目将进一步发展计算方法，使遗传因素影响许多重要的 生物医学特性有待发现和实验表征。高通量版本的HBCGM（HT- HBCGM）将用于分析8，225个公开可用的数据集，这些数据集在面板中测量213，000个响应 近交系小鼠品系。我们部署了一种新的方法，通过利用 冗余存在于检查类似响应的许多数据集中。新颖的计算工具， 还将开发促进遗传、转录和代谢组学数据综合分析的技术。这 包括专门的代谢网络（用于大脑和其他3种组织），用于计算识别 与基因表达或遗传差异相关的代谢组学变化。为了刺激其他研究者 为了进行基因发现，该项目的所有结果和方法都将完全提供给科学界。 社区这些计算工具将用于分析定制的“多组学”（遗传，转录， 和代谢组学）数据集，其测量：（i）近交系组对四种DOA（可卡因， 甲基苯丙胺、芬太尼和尼古丁）;和（ii）相应的DOA诱导的转录和 大脑的代谢变化。这些数据的综合分析将确定影响基因/途径， 对DOA的回应然后，我们应用一种高效的方法将特定的等位基因改变工程化到 使用近交系的基因组和工程化品系来实验性地测试鉴定的 遗传因素对死者的反应