Genome Variation Underlying Alcohol Action

描述（由申请人提供）：本申请的主要目标是鉴定酒精作用的基因和其他基因组特征。 虽然我们通过使用小鼠数量性状基因座（QTL）定位、基因表达谱和比较DNA测序在这一目标上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化：1）哺乳动物基因组变异，包括拷贝数变异（CNV），比以前预期的要普遍得多，和2）小鼠基因组序列含有许多缺口和复杂的、重复丰富的区域，这些区域可能被错误组装。 我们计划应用两个最近开发的基因组策略，规避许多这些限制。 第一个策略是对已知酒精相关表型不同的几种小鼠品系（ILS、ISS、LXS RI和HS 4）进行基于极高密度阵列的比较基因组杂交（aCGH），并鉴定导致这些品系之间酒精作用差异的CNV。 将独立确认CNV，使用定制aCGH阵列精细绘制CNV边界，并鉴定和表征CNV内的基因。 据我们所知，这项研究将是第一个全基因组研究CNV在酒精作用中的作用。 第二个策略将是获得和比较四个QTL区域（Lores 1，2，4和5）的完整DNA序列之间的菌株已被选择为不同的敏感性酒精（ILS和ISS）。 这将通过阵列捕获来自每个菌株的QTL特异性DNA，然后使用下一代DNA测序技术对完整QTL区间进行超高通量DNA测序来进行。 本研究将确定每个Lore QTL内的所有DNA序列变异，因此，将代表对这些酒精相关QTL的基因组变异的最完整评估。 公共卫生相关性：拟议的实验有可能确定重要的新基因和途径，这些基因和途径是酒精在哺乳动物系统中作用的基础。 这些新的见解可能会导致改善治疗和预防酗酒和酗酒的战略。

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.