Genome-wide SNP genotyping and expression analysis in human livers

描述(申请人提供)：肝脏中的大量肝细胞具有多种功能，包括血浆蛋白质合成、碳水化合物代谢、氨基酸代谢、脂肪代谢、药物代谢和胆汁酸分泌。在之前对少量肝脏进行的一些研究中，观察到了基因表达的高度个体间变异性。导致个体间表达差异的潜在遗传因素可能是几个，例如基因的复制和缺失、单核苷酸多态(SNPs)、拷贝数变异(CNV)等。研究这些因素中的每一个对组织表达谱的相对贡献被视为一项艰巨的挑战。最近可获得的高吞吐量SNP平台允许对一个人的数十万个SNP进行讯问。此外，它们还提供对基因组中CNV模式的评估。因此，在这个项目中，我们将评估来自高加索捐赠者的220个正常人类肝脏的全基因组mRNA表达模式和遗传变异。这项提案的总体目标是首次获得人类肝脏中基因表达调控的基因组签名。DNA和RNA样本已经提取，并有足够的数量用于全基因组SNP和表达分析。DNA的全基因组SNP扫描将使用Affymetrix Human SNP阵列6.0进行。将使用基因芯片(注册商标)人类基因1.0 ST阵列来测量信使核糖核酸的表达。使用标准和新的统计技术，我们将识别和表征顺式和反式作用的eQTL以及人类肝脏中基因表达的调控网络。由于这些基因调控因子可能在肝功能、肝病、糖尿病和药物反应的变异性中发挥关键作用，因此对这些基因表达调控因子的鉴定具有重要意义。它们可能是治疗干预的新靶点。公共卫生相关性：这项研究的目的是发现基因组DNA变异模式和肝脏基因表达的个体间变异之间存在的关系。确定人类肝脏中mRNA表达的基因调控因子具有重要意义，因为这些基因调控因子可能在肝功能、肝脏疾病和糖尿病中发挥关键作用，并可能成为治疗干预的新靶点。

DESCRIPTION (provided by applicant): The large number of hepatocytes in the liver fulfills multiple functions, including plasma protein synthesis, carbohydrate metabolism, amino acid metabolism, lipid metabolism, drug metabolism, and bile acid secretion. In a few studies conducted previously in a small number of livers, high inter-individual variability in gene expression has been observed. The underlying genetic factors responsible for such differences in expression among individuals are likely to be several, for example, duplications and deletions of genes, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. The investigation of the relative contributions of each of these factors to the expression profile of a tissue was seen as a daunting challenge. The recent availability of high-throughput SNP platforms allows the interrogation of hundreds of thousands of SNPs in an individual. In addition, they also provide the assessment of the CNV pattern in the genome. Hence, in this project, we will assess the pattern of genome wide mRNA expression and genetic variation in 220 normal human livers from Caucasian donors. The overall goal of this proposal is to obtain, for the first time, the genomic signature of the regulation of gene expression in the human liver. DNA and RNA samples are already extracted and are in a sufficient amount for genome wide SNP and expression analysis. The genome wide SNP scan of DNA will be performed by using the Affymetrix Human SNP Array 6.0. mRNA expression will be measured by using the GeneChip(R) Human Gene 1.0 ST Array. Using standard and novel statistical techniques, we will identify and characterize cis- and trans-acting eQTLs and the regulatory networks of gene expression in the human liver. The identification of these genetic regulators of mRNA expression is of high interest, as they are likely to play critical roles in liver function, liver disease, diabetes, and variability in drug response. They may represent novel targets for therapeutic intervention. PUBLIC HEALTH RELEVANCE: The aim of this study is to discover the relationships existing between patterns of genomic DNA variation and inter-individual variability in gene expression in the liver. The identification of the genetic regulators of mRNA expression in the human liver has important implications, as these genetic regulators are likely to play critical roles in liver function, liver disease and diabetes, and may represent novel targets for therapeutic intervention.