Search of Diabetes Nephropathy Genes in Type 1 Diabetes

1 型糖尿病中糖尿病肾病基因的搜索

• 批准号: 8299606
• 负责人: Marcus Guy Pezzolesi
• 金额: $ 11.84万
• 依托单位: JOSLIN DIABETES CENTER
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2016-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8299606
• 关键词: 13q; Accounting; Address; Aging; Albuminuria; Architecture; Area; Award; Bioinformatics; Biological; Biopsy; Cataloging; Catalogs; Chromosomes; Code; Collection; Complex; Consent; DNA; DNA Resequencing; DNA Sequence; Data; Development; Development Plans; Diabetes Mellitus; Diabetic Nephropathy; Disease; Distal; Exons; Foundations; Frequencies; Future; Gene Expression Regulation; Gene Targeting; Genes; Genetic; Genetic Variation; Genome; Genomics; Genotype; Goals; Haplotypes; Hereditary Disease; Heritability; In Vitro; Insulin-Dependent Diabetes Mellitus; Intercistronic Region; Investigation; Kidney; Kidney Diseases; Laboratories; Maps; Mentored Research Scientist Development Award; Mentors; Methodology; Mind; Molecular Conformation; Mus; Myosin Heavy Chains; Non-Insulin-Dependent Diabetes Mellitus; Pathogenesis; Patients; Population Genetics; Predisposition; Proteins; RNA; Research; Research Activity; Research Methodology; Research Training; Risk; Sampling; Source; Structure; Susceptibility Gene; Technology; Training; Training Activity; Transcript; Variant; base; career; career development; diabetes mellitus genetics; experience; follow-up; genetic association; genetic variant; genome wide association study; human IRS2 protein; human disease; interest; knowledge base; neuronal growth; next generation; novel; post-doctoral training; skills; skills training; success

DESCRIPTION (provided by applicant): This Mentored Research Scientist Development Award (K01) application aims to expand upon the base knowledge I have acquired during my post-doctoral training in the genetics of diabetic nephropathy (DN) and develop expertise in both analytical and laboratory skills that will prepare me for a long and impactful career in research on the genetics of diabetes and its complications. Through carefully structured career development and training activities, an exceptional network of mentored support, and a research plan aimed at addressing specific challenges in investigations on the genetics of DN, I fully expect to accomplish this goal. Recent advances in population genetics and genomics have expanded our understanding of genetic variation across our genome and facilitated cutting-edge technologies that have transformed our ability to identify genes that underlie human disease. Genome-wide association (GWA) studies have spearheaded this revolution, successfully identifying hundreds of common genetic variants associated with complex disease. Despite these successes, a number of important challenges lie ahead to fully appreciate the genetic basis of these complex diseases. At the forefront of these challenges is pinpointing the causal functional variants that underlie the identified associations, a task that is particularly formidable when the associated SNP is localized to a region devoid of evidence of protein-coding genes. Additionally, somewhat surprisingly, the first wave of GWA studies has shown that the effect size of common variants is more modest than previously suspected, leading to speculation that other sources, including rare, low frequency variants, account for a portion of this 'missing heritability'. Each of these challenges was manifest in our recent GWA scan of DN in the Genetics of Kidneys in Diabetes (GoKinD) type 1 diabetes (T1D) Nephropathy Collection. With these challenges in mind, my proposed training seeks to build on my previous experience while moving this area of research forward. This will be accomplished through extensive didactic and hands-on training in both analytical and laboratory aspects of population genetics and genomics that includes the development of statistical and analytical skills, training in new methodologies of next-generation sequencing and gene regulation to investigate the relationship between genetic variations and disease predisposition, and training in analytical methodologies and research strategies for investigating complex disease. My proposed research aims to further investigate genetic associations identified in our GWA scan of the GoKinD collection on chromosomes 1p and 13q and identify both i) the causative genetics variants and ii) the disease genes underlying the associations at each of these loci. This goal will be accomplished through two Specific Aims. 1) To identify DNA sequence differences that are causally related to DN in the associated regions on chromosomes 1p and 13q. To accomplish this, I will a) establish a comprehensive catalog of all DNA sequence differences located in the intervals containing the associated SNPs using next-generation sequencing technology. This will be accomplished by targeted resequencing of these regions, including the haplotype blocks/LD intervals containing the associated variants and the exons of all known genes in the 1p and 13q regions, in pooled DNA samples from the GoKinD T1D Nephropathy Collection using filter-based hybridization capture followed by massively parallel DNA resequencing. I will then b) prioritize these candidate causal variants based on their bioinformatic, biological, and statistical significance. This will be accomplished using a variety of criteria to identify the most promising functional candidates followed by follow-up genotyping in the entire GoKinD T1D Nephropathy Collection. 2) To identify the DN susceptibility genes at the chromosome 1p and 13q regions by mapping the candidate causal variants to their target DN disease gene. To accomplish this I will a) establish a comprehensive renal transcript map for the associated regions on chromosome 1p and 13q using RNA-Seq technology and kidney biopsies obtained from T1D patients with early DN, b) map the long-range interaction between the candidate DN risk variants on 13q and its distal target gene using Chromosome Conformation Capture technology, and c) perform in vitro studies to examine the impact of each candidate causal variant on the expression of their target DN susceptibility gene within the 1p and 13q chromosomal regions. These targeted studies will be the foundation for future, more detailed functional studies. Together, this goal and these Specific Aims offer a tractable course of investigation that builds on convincing preliminary data. They will have a profound impact on our understanding of the allelic architecture of DN and its underlying mechanism. Importantly, they also faithfully integrate highly-focused research activities with my overall training and career development goals.

描述（由申请人提供）：这项受过指导的研究科学家发展奖（K01）的申请旨在扩展我在糖尿病性肾病（DN）遗传学后培训期间获得的基本知识，并在分析和实验室方面发展了专业知识，并为我提供了长期和有影响力的遗传学生涯，以使我对遗传学和糖尿病的研究做好了准备。通过精心结构的职业发展和培训活动，一个卓越的指导支持网络以及旨在解决DN遗传学调查中的具体挑战的研究计划，我完全希望实现这一目标。 人口遗传学和基因组学的最新进展扩大了我们对基因组遗传变异的理解，并促进了尖端技术，这些技术改变了我们鉴定人类疾病基因的能力。全基因组关联（GWA）的研究率先率先进行了这场革命，成功地识别了数百种与复杂疾病相关的常见遗传变异。 尽管取得了这些成功，但仍有许多重要的挑战以充分理解这些复杂疾病的遗传基础。这些挑战的最前沿是指出了基于确定关联的因果功能变体，当关联的SNP定位到没有蛋白质编码基因证据的区域时，这项任务尤其强大。此外，令人惊讶的是，第一波的GWA研究表明，公共变体的效果大小比以前怀疑的效果更适中，导致人们猜测其他来源（包括罕见的，低频变体）占了这种“缺失的遗传力”的一部分。这些挑战中的每一个都在我们最近的GWA DN扫描中表现出了糖尿病（Gokind）1型糖尿病（T1D）肾病的肾脏遗传学的扫描。 考虑到这些挑战，我提出的培训旨在基于我以前的经验，同时推动这一研究领域的发展。这将通过在人群遗传学和基因组学方面进行广泛的教学和实践培训来实现，包括开发统计和分析技能，在下一代测序的新方法中培训以及研究遗传变异和疾病抗病疗法的关系以及研究复杂性疾病的遗传变异和培训之间的关系。 我提出的研究旨在进一步研究GOKIND染色体1p和13q的GOKIND收集的GWA扫描中鉴定出的遗传关联，并确定i）i）遗传学变体和II）疾病基因在每个基因座的疾病基因。 这个目标将通过两个具体目标来实现。 1）确定与染色体1p和13q的相关区域中与DN有因果关系的DNA序列差异。为此，我将a）建立使用下一代测序技术的间隔中所有DNA序列差异的全面目录。这将通过针对这些区域进行针对性重新方程，包括包含1P和13Q区域中所有已知基因的外显子的单倍型块/LD间隔，在Gokind T1D T1D Nephropathy收集的汇总DNA样品中，使用基于滤光片的杂交捕获捕获量捕获了大量的DNA Resquallalecect resequalceenceccect resequalceenceccect squally Bareacor captarect castect castect castects capparect caption。然后，我将b）基于其生物信息，生物学和统计意义的这些候选因果变异的优先级。这将使用各种标准来确定最有希望的功能候选者，然后在整个Gokind T1D T1D肾病收集中进行后续基因分型。 2）通过将候选因果变体映射到其靶标DN疾病基因上，以确定1P染色体和13Q区域的DN敏感性基因。 To accomplish this I will a) establish a comprehensive renal transcript map for the associated regions on chromosome 1p and 13q using RNA-Seq technology and kidney biopsies obtained from T1D patients with early DN, b) map the long-range interaction between the candidate DN risk variants on 13q and its distal target gene using Chromosome Conformation Capture technology, and c) perform in vitro studies to examine the impact of each candidate causal variant关于其目标DN易感基因在1p和13q染色体区域内的表达。这些有针对性的研究将是未来，更详细的功能研究的基础。 共同，这些目标和这些特定目标提供了可访问的调查过程，以令人信服的初步数据为基础。他们将对我们对DN等位基因建筑及其潜在机制的理解产生深远的影响。重要的是，他们还忠实地将高度关注的研究活动与我的整体培训和职业发展目标相结合。