Center for Genetic Studies of Drug Abuse in Outbred Rats

近交系大鼠药物滥用基因研究中心

• 批准号: 10402308
• 负责人: ABRAHAM A PALMER
• 金额: $ 48.57万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-15 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10402308
• 关键词: Behavior; Behavioral; Biological; Biology; Brain; Cocaine; Communities; DNA; DNA Sequencing Facility; Data; Development; Drug abuse; Early Intervention; Ecosystem; Female; Fishes; Funding; Gene Expression; Genetic; Genetic Techniques; Genetic study; Genotype; Grant; Heritability; Human; Individual; Intravenous; Laboratories; Lead; Libraries; Light; Maps; Measures; Mus; Nicotine; Output; Phenotype; Physiological; Procedures; Production; Publications; Quantitative Genetics; Quantitative Trait Loci; RNA; Rattus; Reaction Time; Regulation; Research; Research Project Grants; Research Support; Resources; Risk; SNP genotyping; Sampling; Self Administration; Services; Societies; Techniques; Technology; Work; comparison group; cost; discounting; expectation; genetic analysis; genetic approach; genome sequencing; genome wide association study; improved; male; novel; novel strategies; personalized medicine; phenome; public repository; reference genome; response; skills; trait; transcriptome; transcriptome sequencing; transcriptomics; whole genome

Project Summary (Core C) The purpose of this core is to obtain genotypes for ~5,000 DNA samples derived from rats that are phenotyped by Projects 1, 2, and 3. In addition, we will perform RNA Sequencing (RNASeq) in support of Research Projects 1 and 2. Finally, we use these data to perform genome wide association studies (GWAS) and a number of related analyses. In the prior funding period, Dr. Palmer was the PI of both this core and a research project that developed techniques for genetic analysis. In this renewal application, those two functions have been consolidated into this core. One of the critical technical advances that made this center possible was our development of genotyping- by-sequencing (GBS) for use in rats. Only three SNP genotyping microarrays have ever been developed for use in rats. All three are expensive (>$300 per sample) and none are currently in production. The lack of affordable genotyping platforms was a major impediment to the use of GWAS and related quantitative genetic approaches in rats. In the past funding period, our P50 center has turned the tide by further improving and widely deploying GBS for use in rats. We have continued to refine our GBS techniques, and are now able to obtain ~3.7 million SNPs for less than $50 per sample. Thus, we have increased our output by more than 30-fold while cutting the costs in half. In addition to obtaining genotypes and performing RNASeq, this core will perform genetic analyses, which include GWAS, phenome-wide association analyses (PheWAS), transcriptome wide association analyses (TWAS), heritability estimates, genetic correlations, and a new approach that we call polygenic transcriptomic risk score (PTRS) prediction. All of these analyses are routinely performed in our laboratory and have been the subjects of prior publications that used rats, mice, and humans.

项目概要（核心C） 该核心的目的是获得来自大鼠的约5，000个DNA样本的基因型， 通过项目1、2和3进行表型分型。此外，我们将进行RNA测序（RNASeq），以支持 研究项目1和2。最后，我们使用这些数据进行全基因组关联研究（GWAS）。 以及一些相关的分析。在之前的资助期间，Palmer博士是该核心和 开发基因分析技术的研究项目。在这份更新申请中，这两个 各项职能已被整合到这一核心中。 使这个中心成为可能的关键技术进步之一是我们对基因分型的发展- 通过测序（GBS）用于大鼠。只有三个SNP基因分型微阵列曾经被开发用于 在大鼠中使用。所有这三种都很昂贵（每个样品超过300美元），目前没有一种在生产中。缺乏 负担得起的基因分型平台是使用GWAS和相关定量遗传学的主要障碍。 接近老鼠。在过去的资助期间，我们的P50中心通过进一步改进和 广泛应用于大鼠。我们继续完善我们的GBS技术，现在能够 以每个样本不到50美元的价格获得约370万个SNP。因此，我们的产量增加了超过 30-同时将成本降低一半。 除了获得基因型和进行RNASeq外，该核心还将进行遗传分析， 包括GWAS、全表型关联分析（PheWAS）、全转录组关联分析 （TWAS），遗传力估计，遗传相关性，以及我们称之为多基因转录组学的新方法 风险评分（PTRS）预测。所有这些分析都是在我们的实验室进行的常规分析， 使用大鼠、小鼠和人的先前出版物的受试者。