Integrated clinical, genetic and functional analysis of the ABCA4 locus

ABCA4 基因座的综合临床、遗传和功能分析

• 批准号: 10155493
• 负责人: RANDO L ALLIKMETS
• 金额: $ 42.08万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10155493
• 关键词: 220kDa rod outer segment rim protein; Address; Affect; Age; Alleles; Atrophic; Biological Assay; CRISPR/Cas technology; Cell Culture Techniques; Cell Line; Clinical; Clinical Data; Clinical Treatment; Clinical Trials; Code; Collection; Consensus Sequence; Counseling; Coupled; Data; Defect; Diagnosis; Diagnostic; Disease; Enhancers; Family; Flecks; Frequencies; Future; Gene Expression; Genes; Genetic; Genetic Databases; Genetic Screening; Genetic Variation; Genomics; Genotype; Goals; Image; Introns; Knowledge; Link; Lipofuscin; Medical Genetics; Messenger RNA; Methodology; Methods; Modality; Mus; Mutate; Mutation; Onset of illness; Outcome Study; Pathogenicity; Patient Care; Patients; Pattern; Penetrance; Phenotype; Population; Prognosis; RNA; RNA Splicing; Rare Diseases; Reporter; Research; Rest; Retina; Retinal Degeneration; Retinal Diseases; Retinitis Pigmentosa; Severities; Site; Spliced Genes; Stargardt' s disease; Statistical Data Interpretation; Structure; Subgroup; Testing; United States; Untranslated RNA; Variant; base; cell type; clinical care; clinical database; clinical heterogeneity; clinical phenotype; cohort; combinatorial; cone-rod dystrophy; design; diagnostic accuracy; disease diagnosis; disease heterogeneity; disorder subtype; genetic analysis; genetic approach; genetic testing; genotyped patients; improved; in silico; induced pluripotent stem cell; insight; molecular modeling; mutant; novel; patient screening; predictive modeling; prognostic; programs; promoter; segregation; therapy design; translational study

Mutations in the ABCA4 gene are responsible for a wide variety of retinal degeneration phenotypes, including Stargardt disease (STGD), cone-rod dystrophy (CRD) and retinitis pigmentosa (RP). Different combinations of >900 ABCA4 mutant alleles result in distinct phenotypes in a continuum of disease manifestations. Variation in the ABCA4 locus has emerged as the most prevalent cause of Mendelian retinal disease, with an estimated 1/20 people across all populations carrying a potential disease-associated variant in this gene. Genetic analyses of ABCA4-associated retinal disease have been substantially advanced in recent years. New methods, such as direct sequencing of the entire genomic ABCA4 locus, have allowed detecting up to 80% of the disease-associated ABCA4 alleles, including 2 (both) mutations in ~65-75% of patients. Of these 75% are in the coding region and 25% in introns, more than half of which are outside of splice consensus sequences. Of the rest, 1 mutation is detected in ~20% of patients while no disease-associated alleles are found in another 10% of screened patients with phenotypes compatible with the ABCA4 disease. These data suggest that many (rare) disease-associated ABCA4 alleles are yet to be identified and, most importantly, unequivocally confirmed by adequate functional analyses. We will test the hypothesis that a combination of advanced genetic screening coupled with advanced functional analyses of ABCA4 alleles from non-coding sequences is necessary to unequivocally determine the ABCA4-associated disease load. The proposed research program, based on large, comprehensively characterized familial cohort of ABCA4 disease, is using integrated approaches of genetic analyses, quantified clinical data and functional analyses to generate a predictive model for ABCA4 disease. The ultimate goal of the proposed project is to complete the analysis of the ABCA4 locus. The research program is organized into two Specific Aims. In the first Aim, we propose a novel combinatorial pipeline utilizing our existing clinical and genetic databases, accumulated knowledge, and advanced in silico methodology to predict most disease-associated variants in the coding and non-coding sequences of the entire ABCA4 locus. In the second Aim we will confirm or reject the variants in non-coding sequences for disease association by functional testing ABCA4 RNA from mutated iPSC lines for splicing and expression defects. The outcome of these studies will substantially aid in disease diagnosis, prognosis and will serve as a platform for selecting patients for emerging clinical trials geared to delay the onset, or arrest the progression, of ABCA4-associated diseases.

ABCA 4基因的突变导致多种视网膜变性表型， 包括Stargardt病（STGD）、视锥-视杆营养不良（CRD）和色素性视网膜炎（RP）。不同 >900个ABCA 4突变等位基因的组合导致疾病连续体中不同的表型 表现。ABCA 4基因座的变异已成为孟德尔视网膜病变最常见的原因。 疾病，估计所有人群中有1/20的人携带潜在的疾病相关变异， 这个基因。近年来，ABCA 4相关视网膜疾病的遗传分析已经取得了实质性进展。 年新的方法，如整个基因组ABCA 4基因座的直接测序，已经允许检测 高达80%的疾病相关ABCA 4等位基因，包括约65-75%患者的2种（两种）突变。的 这75%位于编码区，25%位于内含子，其中一半以上位于剪接区之外 共有序列在其余的患者中，在约20%的患者中检测到1种突变，而没有疾病相关的突变。 在另外10%的筛选患者中发现了与ABCA 4疾病相容的表型的等位基因。 这些数据表明，许多（罕见）疾病相关的ABCA 4等位基因尚未确定，大多数 重要的是，通过充分的功能分析明确证实。我们将检验一个假设， 结合先进的遗传筛选与ABCA 4等位基因的先进功能分析， 非编码序列是明确确定ABCA 4相关疾病负荷所必需的。的 提出的研究计划，基于ABCA 4疾病的大型，全面表征的家族性队列， 正在使用遗传分析、量化临床数据和功能分析的综合方法， ABCA 4疾病的预测模型。该项目的最终目标是完成对以下问题的分析： ABCA 4基因座 研究计划分为两个具体目标。在第一个目标中，我们提出了一个新的 利用我们现有的临床和遗传数据库，积累的知识， 先进的计算机模拟方法可预测编码和非编码中大多数疾病相关变异 完整ABCA 4基因座的序列。在第二个目标中，我们将确认或拒绝非编码中的变体 通过功能性测试来自突变iPSC系的ABCA 4 RNA的剪接， 表达缺陷这些研究的结果将大大有助于疾病诊断、预后，并将 作为一个平台，为新兴的临床试验选择患者，以延迟发病或阻止疾病的发生。 ABCA 4相关疾病的进展。