Discovery and Functional Impact of Common and Rare Variants in RA

RA 常见和罕见变异的发现及其功能影响

• 批准号: 8712363
• 负责人: Soumya Raychaudhuri
• 金额: $ 37.59万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-02 至 2018-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8712363
• 关键词: Accounting; Alleles; Asians; Base Sequence; Bioinformatics; Biological Assay; Biological Process; Biology; Cell Line; Cells; Code; DNA; Data; Data Set; Development; Diagnosis; Dideoxy Chain Termination DNA Sequencing; Disease; Disease Pathway; Drug Targeting; Ethnic group; European; Exons; Family; Gene Expression Profile; General Population; Genes; Genetic; Goals; Heritability; Human; Human Genetics; Individual; Japanese Population; Korea; Manuscripts; Maps; Methods; Molecular; Mutation; Pathogenesis; Pathway interactions; Patient Care; Preclinical Drug Evaluation; Proteins; Publishing; RNA Interference; Resources; Rheumatoid Arthritis; Risk; Role; Sampling; Series; Symptoms; TNFRSF5 gene; Techniques; Technology; Testing; Translating; Variant; analytical method; base; bone; case control; cellular engineering; deep sequencing; disorder risk; drug development; drug discovery; experience; gain of function; genetic variant; genome wide association study; high throughput screening; improved; innovation; insight; loss of function; novel; protein protein interaction; public health relevance; rare variant; research study; risk variant; small molecule; theories; tool

DESCRIPTION (provided by applicant): Genome-wide association studies (GWAS) and related approaches have identified >60 rheumatoid arthritis (RA) risk loci. Despite this, many alleles remain to be discovered to account for heritability estimates observed in families. We have published data that most common RA risk alleles are shared across diverse ethnic groups. In Aim 1, we will exploit this observation to discover new RA risk alleles - we will conduct a multi- ethnic GWAS of ~20,000 RA cases and 60,000 matched controls (Asian and European ancestry). We will also compare and contrast genetic findings across two ethnic groups, and develop new analytical methods. We have data (manuscript in press) that RA risk genes identified from GWAS harbor rare alleles that contribute to risk of RA. Together with data from other diseases, this leads to the hypothesis that causal genes at RA risk loci discovered by GWAS will contain independent, protein-coding mutations (most of which will be rare in the general population). In Aim 2, we will test this hypothesis by sequencing all genes (~650 in total) identified by GWAS in 1,300 RA case and 1,300 non-RA controls of European ancestry. We will also sequence ~2,000 RA case-control samples of Asian ancestry in order to compare and contrast genetic findings across two ethnic groups. We will perform genetic burden tests to determine which genes harbor more rare risk alleles in cases compared to controls than would be expected by chance. However, finding causal variants and genes is only the first step in translating genetic discoveries to improved patient care, and drug discovery in particular. We hypothesize that genes with an allelic series (i.e., multiple alleles that influence disease risk) re excellent drug targets, especially genes that carry loss-of-function (LOF) alleles that protect from disease. We have unpublished data on one RA risk locus that demonstrates our ability to progress from a GWAS to a high-throughput screen (HTS) of ~2,000 small molecules. In Aim 3 we will extend this approach to new RA risk genes: for at least one gene, we will understand the functional consequences of new RA risk alleles using cutting-edge molecular techniques (e.g., TALENs, RNAi), and use this information to conduct an HTS. Together, these three Aims will (1) discover new RA risk loci using GWAS in Europeans and Asians, (2) discover rare RA risk alleles at causal genes from GWAS loci (also in Europeans and Asians), and (3) translate genetic discoveries into new biology and an HTS of small molecule compounds. IMPACT: We will build upon our past accomplishments to perform the most comprehensive genetic study of RA to date (from common to rare alleles). We will develop innovative methods for integrating GWAS and sequence data, as well as innovative methods to use human genetics to guide drug discovery. Our team has all of the experience and resources to accomplish these Aims.

描述（由申请人提供）：全基因组关联研究（GWAS）和相关方法已经确定了60个类风湿关节炎（RA）风险位点。尽管如此，许多等位基因仍有待发现，以解释在家庭中观察到的遗传力估计。我们发表的数据表明，不同种族的人群中存在最常见的类风湿性关节炎风险等位基因。在Aim 1中，我们将利用这一观察结果来发现新的RA风险等位基因——我们将进行一项多种族GWAS，包括约20,000例RA病例和60,000例匹配对照（亚洲和欧洲血统）。我们还将比较和对比两个族群的基因发现，并开发新的分析方法。我们有数据显示，从GWAS中鉴定出的类风湿性关节炎风险基因含有导致类风湿性关节炎风险的罕见等位基因。结合来自其他疾病的数据，这导致了一种假设，即GWAS发现的类风湿关节炎风险位点上的致病基因将包含独立的蛋白质编码突变（其中大部分在一般人群中罕见）。在目标2中，我们将通过对所有基因（总共约650个）进行测序来验证这一假设。