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）：我们将结合使用第二代和第三代深度测序对选定的候选区域、整个外显子组和 mRNA 进行鉴定，以鉴定易导致 PBC 易感性的常见和不常见变异。对 150 例病例和 150 例对照中选定的染色体区域进行测序，将目标是鉴定在我们的 PBC GWAS 中鉴定出的 IL12A、SPIB 和 17 号染色体基因座 (IKZF3/ORMDL3) 关联基础上的变异。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。对 400 个病例和 400 个对照的外显子组测序将筛选出不适合 GWAS 检测的罕见遗传变异，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，对 PBC 发病机制涉及的两个细胞群（CD8+ 和 CD4+ T 细胞）进行 mRNA 测序将补充染色体区域和外显子组结果。为此，将对 75 例病例和 75 例对照进行 mRNA 测序。这种 mRNA 测序连同目标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 的优先顺序，以便使用 Golden Gate 1536 SNPlex 对大量 1100 个 PBC 病例和 2200 个对照（不包括发现主题集）进行验证和测试。测序和复制研究都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识别不常见以及更常见变异的能力，这些变异在这种自身免疫性疾病的发病机制中很重要。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背后的致病基因变异。原发性胆汁性肝硬化被认为是一种典型的自身免疫性疾病，定义免疫病理学的遗传基础不仅可以帮助患有这种疾病的患者，而且对于自身免疫也很重要。该研究将利用最新的技术进步来提供 DNA 序列差异，并有机会将遗传变异与功能变化联系起来，从而提高这种高发病率和死亡率的疾病的易感性。这些研究将为 PBC 的发病机制提供有价值的见解，从而可能导致治疗方法的开发。