IDENTIFICATION OF COMMON AND UNCOMMON GENE VARIANTS IN PBC

PBC 中常见和不常见基因变异的鉴定

基本信息

批准号：
8240361
负责人：
MERRILL E GERSHWIN
金额：
$ 67.04万
依托单位：
UNIVERSITY OF CALIFORNIA AT DAVIS
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-09-19 至 2015-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8240361
关键词：
Affect Alleles Antithymoglobulin Autoimmune Diseases Autoimmunity CD4 Positive T Lymphocytes CD8B1 gene Cells Chromosomes Chromosomes, Human, Pair 17 Chromosomes, Human, Pair 19 Chromosomes, Human, Pair 3 Code Complement Complex Computer Simulation Consensus Custom DNA DNA Sequence Data Data Set Detection Disease Disease susceptibility Exclusion Exons Frequencies Functional RNA Gene Combinations Gene Expression Generations Genetic Genetic Risk Genetic Variation Genome Genomics Genotype Goals Haplotypes Hereditary Disease Human Hybrids IL12A gene Immune response Individual Informatics Lead Link Messenger RNA Meta-Analysis MicroRNAs Missense Mutation Modeling Morbidity - disease rate Nucleotides Pathogenesis Pathway interactions Patients Peripheral Blood Mononuclear Cell Phenotype Population Population Group Predisposition Primary biliary cirrhosis RNA RNA Editing RNA Splicing Reading Reading Frames Risk Sampling Shotguns Signal Transduction Single Nucleotide Polymorphism in Coding Sequence Site Sorting - Cell Movement Splice-Site Mutation T-Lymphocyte Technology Terminator Codon Testing Transcript Validation Variant base candidate validation case control cohort design digital exome genetic variant genome wide association study genome-wide immunopathology insight mortality novel therapeutic development tool trait

项目摘要

DESCRIPTION (provided by applicant): We will use a combination of second and third generation deep sequencing of selected candidate regions, whole exomes and mRNAs to identify both common and uncommon variants that predispose to PBC susceptibility. The sequencing of selected chromosome regions in 150 cases and 150 controls will target identification of variants that underlie the association of IL12A, SPIB, and a chromosome 17 locus (IKZF3/ORMDL3) that are identified in our PBC GWAS. The paired sequencing of these regions will provide the opportunity to ascertain coding and non-coding variation including copy number variants. The exome sequencing of 400 cases and 400 controls will screen for uncommon genetic variants that are not amenable to GWAS detection and provide the opportunity to test an alternate paradigm that does not depend on the common variant hypothesis. Importantly, mRNA sequencing of two cell populations implicated in PBC pathogenesis (CD8+ and CD4+ T cells) will complement both the chromosome region and exome results. For this aspect, mRNA will be sequenced in 75 cases and 75 controls. This mRNA sequencing together with the targeted chromosomal region sequencing and exome sequencing will provide the ability to correlate sequence variation with 1) gene expression, 2) eQTN data, 3) alternative exon usage, 4) RNA editing and 5) preferential allelic expression. A variety of informatics approaches using the combined data will establish a prioritization of SNPs for validation and testing in large numbers 1100 PBC cases and 2200 controls (not including discovery subject set) using a Golden Gate 1536 SNPlex. Both the sequencing and replication studies will be performed using a homogeneous Italian population. Together this design should maximize our ability to identify uncommon as well as more common variants that are important in the etiopathogenesis of this autoimmune disease. PUBLIC HEALTH RELEVANCE: The goal of this proposal is to identify causal genetic variants underlying the risk for primary biliary cirrhosis. Primary biliary cirrhosis is considered a model autoimmune disease and defining the genetic basis of immunopathology will not only help patients with this disease, but will also be generically important for autoimmunity. The study will utilize the recent advances in technology to provide DNA sequence differences and an opportunity to link genetic variation to functional changes import in the susceptibility of this disease with high morbidity and mortality. These studies will provide valuable insight into the pathogenesis of PBC that may lead to therapeutic development.

描述（由申请人提供）：我们将使用对选定候选区域，整个外部和mRNA的第二代和第三代深度测序的组合来识别易于PBC敏感性的常见和罕见变体。在150例病例和150个对照中对选定的染色体区域进行测序将针对IL12A，SPIB和17个染色体基因座（IKZF3/ORMDL3）的变体的鉴定，这些变体在我们的PBC GWAS中鉴定出来。这些区域的配对测序将为确定编码和非编码变化（包括拷贝数变体）提供机会。 400例和400个对照的外显子组测序将筛选出不适用于GWAS检测的不常见遗传变异，并提供了测试不取决于常见变体假设的替代范式的机会。重要的是，与PBC发病机理（CD8+和CD4+ T细胞）有关的两个细胞群体的mRNA测序将同时补充染色体区域和外部结果。在这方面，将在75例和75个对照中测序mRNA。该mRNA测序与靶向的染色体区域测序和外显子组测序将提供将序列变异与1）基因表达相关的能力，2）EQTN数据，3）替代外显子使用，4）RNA编辑和5）优先等位基因表达。使用合并数据的多种信息学方法将建立SNP的优先级，用于验证和测试，以1100个PBC案例和2200个控制（不包括发现主题集）使用Golden Gate 1536 SNPLEX。测序和复制研究都将使用同质意大利人口进行。这种设计共同使我们识别出罕见的能力以及在这种自身免疫性疾病的病原体中很重要的更常见变体的能力。公共卫生相关性：该提案的目的是确定原发性胆汁肝硬化风险的因果遗传变异。原发性胆道肝硬化被认为是一种模型自身免疫性疾病，定义免疫病理学的遗传基础不仅会帮助患有这种疾病的患者，而且对于自身免疫性也很重要。该研究将利用技术的最新进展提供DNA序列差异，并有机会将遗传变异与该疾病易感性的功能变化联系起来，并具有高发病率和死亡率。这些研究将为可能导致治疗发育的PBC发病机理提供宝贵的见解。