Genome Variation Underlying Alcohol Action

酒精作用下的基因组变异

• 批准号: 8115480
• 负责人: JAMES M SIKELA
• 金额: $ 15.3万
• 依托单位: UNIVERSITY OF COLORADO DENVER
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-10 至 2012-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8115480
• 关键词: Address; Alcohol abuse; Alcohols; Complex; Computer software; Copy Number Polymorphism; Custom; DNA; DNA Microarray Chip; DNA Sequence; Detection; Elements; Foundations; Gene Expression Profiling; Genes; Genetic Variation; Genome; Genomics; Goals; Human; Hybridization Array; Inbred Strain; Individual; Investigation; Knowledge; Lead; Maps; Methods; Mouse Strains; Mus; Oligonucleotides; Pathway interactions; Phenotype; Quantitative Trait Loci; Resolution; Role; Sequence Analysis; Slide; Solid; Surveys; System; Technology; Variant; Work; alcohol sensitivity; alcoholism prevention; base; comparative; comparative genomic hybridization; density; design; genome sequencing; genome-wide; improved; insight; instrument; mammalian genome; mouse genome; next generation; public health relevance; research study; structural genomics; trait; treatment strategy

DESCRIPTION (provided by applicant): The primary goal of this application is to identify genes and other genomic features that underlie the action of alcohol. While we have made considerable progress toward this objective through the use mouse quantitative trait loci (QTL) mapping, gene expression profiling and comparative DNA sequencing, these studies were limited and complicated by two newly discovered factors related to the analysis of complex traits 1) mammalian genomic variation, including copy number variation (CNV), is much more prevalent than previously expected , and 2) mouse genome sequence contains many gaps and complex, duplication-rich regions that are likely to be misassembled. We plan to apply two recently developed genomic strategies that circumvent many of these limitations. The first strategy will be to carry out very high density array-based comparative genomic hybridization (aCGH) of several mouse strains (ILS, ISS, LXS RIs and HS4) known to differ in alcohol-related phenotypes, and identify CNVs that are contributing to differences in alcohol action between these strains. CNVs will be independently confirmed, CNV boundaries fine-mapped using custom aCGH arrays, and genes within the CNV identified and characterized. To our knowledge this study will be the first genome-wide investigation of the role of CNVs in alcohol action. The second strategy will be to obtain and compare the complete DNA sequences of four QTL regions (Lores1, 2, 4, and 5) between strains that have been selected for differential sensitivity to alcohol (ILS and ISS). This will be carried out by array-capture of QTL- specific DNAs from each strain, followed by ultra-high throughput DNA sequencing of the complete QTL interval using next generation DNA sequencing technology. This study will identify all DNA sequence variations within each Lore QTL and, as such, will represent the most complete assessment of genomic variation with these alcohol-related QTLs. PUBLIC HEALTH RELEVANCE:The proposed experiments have the potential to identify important new genes and pathways that underlie the action of alcohol in mammalian systems. Such new insights could lead to improved strategies for the treatment and prevention of alcoholism and alcohol abuse.

描述(由申请人提供)：本申请的主要目标是识别酒精作用的基因和其他基因组特征。虽然我们通过利用小鼠数量性状基因座(QTL)定位、基因表达谱分析和比较DNA测序朝着这一目标取得了相当大的进展，但这些研究受到两个新发现的与复杂性状分析相关的因素的限制和复杂：1)哺乳动物基因组变异，包括拷贝数变异(CNV)，比之前预期的要普遍得多；2)小鼠基因组序列包含许多缺口和复杂的、重复丰富的区域，很可能被错误组装。我们计划应用两种最近开发的基因组策略来绕过这些限制。第一个策略是对几个已知与酒精相关的表型不同的小鼠品系(ILS、ISS、LXS RIS和HS4)进行基于非常高密度阵列的比较基因组杂交(ACGH)，并识别导致这些品系之间酒精作用差异的CNV。CNV将被独立确认，CNV边界将使用定制的aCGH阵列精细绘制，CNV内的基因将被识别和表征。据我们所知，这项研究将是第一次全基因组范围内研究CNV在酒精作用中的作用。第二种策略是获得并比较四个QTL区域(Lores1、2、4和5)的完整DNA序列，这些菌株已被选为对酒精的差异敏感性菌株(ILS和ISS)。这将通过阵列捕获每个菌株的QTL特定DNA，然后使用下一代DNA测序技术对完整的QTL间隔进行超高通量DNA测序。这项研究将识别每个Lore QTL中的所有DNA序列变异，因此，将代表对这些与酒精相关的QTL的基因组变异的最完整的评估。与公共卫生相关：拟议的实验有可能识别重要的新基因和通路，这些基因和通路是酒精在哺乳动物系统中作用的基础。这些新的见解可能导致改善治疗和预防酗酒和酗酒的战略。