IDENTIFICATION OF COMMON AND UNCOMMON GENE VARIANTS IN PBC

PBC 中常见和不常见基因变异的鉴定

• 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
• 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

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）：我们将使用选定候选区域、整个外显子组和mRNA的第二代和第三代深度测序的组合来鉴定易患PBC易感性的常见和不常见变体。对150例病例和150例对照中选定的染色体区域进行测序，将靶向鉴定在我们的PBC GWAS中鉴定的IL 12 A、SPIB和17号染色体基因座（IKZF 3/ORMDL 3）相关性的基础变异。这些区域的配对测序将提供确定编码和非编码变异（包括拷贝数变异）的机会。400例病例和400例对照的外显子组测序将筛选不适合GWAS检测的不常见遗传变异，并提供测试不依赖于常见变异假设的替代范式的机会。重要的是，PBC发病机制中涉及的两个细胞群体（CD 8+和CD 4 + T细胞）的mRNA测序将补充染色体区域和外显子组结果。为此，将在75例病例和75例对照中对mRNA进行测序。该mRNA测序连同靶向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、2）eQTN数据、3）替代外显子使用、4）RNA编辑和5）优先等位基因表达相关联的能力。使用组合数据的各种信息学方法将建立SNP的优先级，以使用Golden Gate 1536 SNP在大量1100个PBC病例和2200个对照（不包括发现受试者集）中进行验证和测试。测序和复制研究均将使用同质的意大利人群进行。总之，这种设计应该最大限度地提高我们的能力，以确定罕见的，以及更常见的变异，这是重要的病因，这种自身免疫性疾病。 公共卫生相关性：该提案的目标是确定原发性胆汁性肝硬化风险的致病遗传变异。原发性胆汁性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有助于这种疾病的患者，而且对自身免疫也具有普遍重要性。该研究将利用最新的技术进展来提供DNA序列差异，并提供将遗传变异与功能变化联系起来的机会，从而提高这种发病率和死亡率高的疾病的易感性。这些研究将为PBC的发病机制提供有价值的见解，可能导致治疗的发展。