The Impact of Human Gene Knockouts in Type 2 Diabetes and Related Traits

人类基因敲除对 2 型糖尿病及相关特征的影响

基本信息

批准号：
8460348
负责人：
David Altshuler
金额：
$ 61.78万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-09-15 至 2016-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8460348
关键词：
Algorithms Alleles CCR5 gene Cataloging Catalogs Characteristics Clinical Clinical Data Code Collaborations Collection Computer Simulation DNA DNA Sequence Data Data Analyses Data Set Defect Detection Development Disease Drug Delivery Systems Europe European Evaluation Frequencies Funding Genes Genetic Genetic Research Genome Genotype Glucose Goals HIV Infections Human Human Genetics Hypertension Individual Inherited Insulin KCNJ1 gene Laboratories Lipids Low-Density Lipoproteins Metabolic Methods Morbidity - disease rate Mutation Myocardial Infarction National Institute of Diabetes and Digestive and Kidney Diseases Non-Insulin-Dependent Diabetes Mellitus Nucleotides Pain Pharmaceutical Preparations Play Population Predisposition Prevalence Prevention Prevention approach Prevention therapy Proteins Public Health Research Personnel Risk Role Sampling Statistical Methods Technology Testing Therapeutic Validation Variant base case control design diabetes control diabetes risk drug discovery effective therapy exome follow-up gene discovery gene function genetic analysis genome sequencing genome wide association study improved in vivo insertion/deletion mutation insight knockout gene loss of function mortality next generation novel research study therapeutic target trait

项目摘要

DESCRIPTION (provided by applicant): The development of new and effective therapies for type 2 diabetes (T2D) requires the identification of novel drug targets, ideally ones that are validated by strong evidence of clinical benefit from studies in human populations. Inherited loss of function (LoF) variants offer one approach to assess the impact of reducing gene activity in humans in vivo. Particularly strong evidence for target validation can be obtained by observing LoF variants that provide protection against disease without undesirable consequences (as in CCR5 and PCSK9). The applicants have collected high coverage exome sequencing data in DNA samples from each of 2,800 individuals (T2D cases and controls), and will have genotyped a comprehensive collection of non-synonymous protein altering variants in >45,000 individuals (T2D cases and controls) using the "exome" array. To perform a systematic and well powered analysis of these data for LoF variants, several challenges must be overcome: (a) development and application of algorithms for robust detection of insertion and deletion variants (a major mechanism for LoF variants which is poorly characterized with today's algorithms), and for the accurate annotation of all classes of LoF variants; (b) characterization of statistical tests that re sensitive for the frequency spectrum and characteristics of LoF variants, and their application to the catalogue of LoF variants detected in cases and controls; and (c) follow-up of putative LoF associations in large, independent samples. To test systematically the role of rare protein-altering LoF variants in risk of T2D, the applicants propose: (a) to develop algorithms to detect indels in sequence data, and larger deletions using data from the exome array; to apply these algorithms to sequence and genotype data totalling >47,000 DNA samples; and to annotate LoF variants across the genome; (b) to evaluate the power of rare variant tests for LoF analysis, and to perform association analyses using chosen methods for LoF variants, both singly and for sets of LoF variants within a gene, with T2D, as well as with the related metabolic traits of glucose, insulin, lipids, and BMI; and (c) to validate putative associations of LoF variants with altered rik of T2D (in particular, protection from T2D) by performing in silico follow-up in data on up to 10,000 individuals (T2D cases and controls) from the T2D-GENES Project, and by targeted sequencing in 20,000 additional individuals (T2D cases and controls). A central goal of human genetics research is to provide insights that can guide breakthrough approaches to prevention and therapy. The applicants have been leaders in the development of datasets, laboratory methods, and algorithms for genetic analysis, and have collaborated for over a decade to apply these methods to discover genes for T2D. Now, the convergence of large clinical samples from T2D cases and controls, of next-generation sequencing technology, and of algorithmic improvements make it possible to evaluate systematically LoF variants for effects on T2D, nominating and validating potential therapeutic targets. PUBLIC HEALTH RELEVANCE: The rising prevalence of type 2 diabetes in the US and worldwide represents one of the major challenges to public health, and improved options for treatment and prevention are required. The present proposal builds on a longstanding and productive collaboration between researchers in the US and Europe to understand the genetic basis of type 2 diabetes, and to use this information to reveal disease mechanisms. In this proposal, we will focus on the subset of DNA sequence variants that have the most dramatic effects on gene function (loss of function coding variants), and seek to define the role that these play in type 2 diabetes predisposition.

描述（由申请人提供）：开发 2 型糖尿病 (T2D) 的新型有效疗法需要确定新的药物靶点，最好是通过人群研究的临床益处的有力证据进行验证的药物靶点。遗传性功能丧失 (LoF) 变异提供了一种评估人类体内基因活性降低的影响的方法。通过观察 LoF 变体可以获得特别有力的目标验证证据，这些变体可提供针对疾病的保护而不会产生不良后果（如 CCR5 和 PCSK9）。申请人已收集了 2,800 名个体（T2D 病例和对照）DNA 样本中的高覆盖率外显子组测序数据，并将使用“外显子组”数组。为了对 LoF 变体的这些数据进行系统且有力的分析，必须克服几个挑战：（a）开发和应用用于稳健检测插入和删除变体的算法（LoF 变体的主要机制，但当今的特征分析很少）算法），以及所有类别 LoF 变体的准确注释； (b) 对 LoF 变体的频谱和特征敏感的统计测试的表征，及其在病例和对照中检测到的 LoF 变体目录中的应用； (c) 对大型独立样本中假定的 LoF 关联进行跟踪。为了系统地测试罕见的蛋白质改变 LoF 变体在 T2D 风险中的作用，申请人建议：(a) 开发算法来检测序列数据中的插入缺失，以及使用来自外显子组阵列的数据检测更大的缺失；将这些算法应用于总计超过 47,000 个 DNA 样本的测序和基因型数据；并注释整个基因组中的 LoF 变体； (b) 评估用于 LoF 分析的罕见变异测试的功效，并使用选定的 LoF 变异方法（无论是单个 LoF 变异还是基因内的 LoF 变异组）与 T2D 以及相关代谢性状进行关联分析葡萄糖、胰岛素、血脂和体重指数； (c) 通过对来自 T2D-GENES 项目的多达 10,000 名个体（T2D 病例和对照）的数据进行计算机跟踪，验证 LoF 变异与 T2D 风险改变（特别是预防 T2D）之间的假定关联，并通过对另外 20,000 名个体（T2D 病例和对照）进行靶向测序。人类遗传学研究的一个中心目标是提供可以指导突破性预防和治疗方法的见解。申请人一直是基因分析数据集、实验室方法和算法开发领域的领导者，并已合作十多年，应用这些方法来发现 T2D 基因。现在，来自 T2D 病例和对照的大量临床样本、下一代测序技术以及算法改进的融合使得系统地评估 LoF 变异对 T2D 的影响、提名和验证潜在的治疗靶点成为可能。公共卫生相关性：美国和全球 2 型糖尿病患病率的上升是公共卫生面临的主要挑战之一，需要改进治疗和预防方案。目前的提案建立在美国和欧洲研究人员之间长期且富有成效的合作基础上，以了解 2 型糖尿病的遗传基础，并利用这些信息揭示疾病机制。在本提案中，我们将重点关注对基因功能影响最显着的 DNA 序列变体子集（功能缺失编码变体），并寻求定义这些变体的作用。在 2 型糖尿病易感性中发挥作用。